[med-svn] [stacks] 05/07: New upstream version 1.46
Andreas Tille
tille at debian.org
Sat Jun 24 07:04:23 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository stacks.
commit 5eedfd97acab08d026c451aea3f48f56682adbd4
Author: Andreas Tille <tille at debian.org>
Date: Sat Jun 24 08:21:11 2017 +0200
New upstream version 1.46
---
ChangeLog | 34 +
Makefile.am | 47 +-
Makefile.in | 3814 ++++++++++++-----------
aclocal.m4 | 740 ++---
config.h.in | 9 +-
config/compile | 232 +-
config/depcomp | 531 ++--
config/install-sh | 385 +--
config/missing | 461 ++-
config/test-driver | 148 -
configure | 5763 +++++++++++++++++++++--------------
configure.ac | 31 +-
htslib/._INSTALL | Bin 181 -> 0 bytes
htslib/._LICENSE | Bin 181 -> 0 bytes
htslib/._Makefile | Bin 181 -> 0 bytes
htslib/._NEWS | Bin 181 -> 0 bytes
htslib/._README | Bin 181 -> 0 bytes
htslib/._bgzf.c | Bin 181 -> 0 bytes
htslib/._bgzip.c | Bin 181 -> 0 bytes
htslib/._cram | Bin 181 -> 0 bytes
htslib/._faidx.c | Bin 181 -> 0 bytes
htslib/._hfile.c | Bin 181 -> 0 bytes
htslib/._hfile_internal.h | Bin 181 -> 0 bytes
htslib/._hfile_irods.c | Bin 181 -> 0 bytes
htslib/._hfile_libcurl.c | Bin 181 -> 0 bytes
htslib/._hfile_net.c | Bin 181 -> 0 bytes
htslib/._hts.c | Bin 181 -> 0 bytes
htslib/._hts_internal.h | Bin 181 -> 0 bytes
htslib/._htsfile.c | Bin 181 -> 0 bytes
htslib/._htslib | Bin 181 -> 0 bytes
htslib/._htslib.pc.in | Bin 181 -> 0 bytes
htslib/._htslib_vars.mk | Bin 181 -> 0 bytes
htslib/._kfunc.c | Bin 181 -> 0 bytes
htslib/._knetfile.c | Bin 181 -> 0 bytes
htslib/._kstring.c | Bin 181 -> 0 bytes
htslib/._md5.c | Bin 181 -> 0 bytes
htslib/._plugin.c | Bin 181 -> 0 bytes
htslib/._regidx.c | Bin 181 -> 0 bytes
htslib/._sam.c | Bin 181 -> 0 bytes
htslib/._synced_bcf_reader.c | Bin 181 -> 0 bytes
htslib/._tabix.c | Bin 181 -> 0 bytes
htslib/._tbx.c | Bin 181 -> 0 bytes
htslib/._vcf.c | Bin 181 -> 0 bytes
htslib/._vcf_sweep.c | Bin 181 -> 0 bytes
htslib/._vcfutils.c | Bin 181 -> 0 bytes
htslib/cram/._cram.h | Bin 181 -> 0 bytes
htslib/cram/._cram_codecs.c | Bin 181 -> 0 bytes
htslib/cram/._cram_codecs.h | Bin 181 -> 0 bytes
htslib/cram/._cram_decode.c | Bin 181 -> 0 bytes
htslib/cram/._cram_decode.h | Bin 181 -> 0 bytes
htslib/cram/._cram_encode.c | Bin 181 -> 0 bytes
htslib/cram/._cram_encode.h | Bin 181 -> 0 bytes
htslib/cram/._cram_external.c | Bin 181 -> 0 bytes
htslib/cram/._cram_index.c | Bin 181 -> 0 bytes
htslib/cram/._cram_index.h | Bin 181 -> 0 bytes
htslib/cram/._cram_io.c | Bin 181 -> 0 bytes
htslib/cram/._cram_io.h | Bin 181 -> 0 bytes
htslib/cram/._cram_samtools.c | Bin 181 -> 0 bytes
htslib/cram/._cram_samtools.h | Bin 181 -> 0 bytes
htslib/cram/._cram_stats.c | Bin 181 -> 0 bytes
htslib/cram/._cram_stats.h | Bin 181 -> 0 bytes
htslib/cram/._cram_structs.h | Bin 181 -> 0 bytes
htslib/cram/._files.c | Bin 181 -> 0 bytes
htslib/cram/._mFILE.c | Bin 181 -> 0 bytes
htslib/cram/._mFILE.h | Bin 181 -> 0 bytes
htslib/cram/._misc.h | Bin 181 -> 0 bytes
htslib/cram/._open_trace_file.c | Bin 181 -> 0 bytes
htslib/cram/._open_trace_file.h | Bin 181 -> 0 bytes
htslib/cram/._os.h | Bin 181 -> 0 bytes
htslib/cram/._pooled_alloc.c | Bin 181 -> 0 bytes
htslib/cram/._pooled_alloc.h | Bin 181 -> 0 bytes
htslib/cram/._rANS_byte.h | Bin 181 -> 0 bytes
htslib/cram/._rANS_static.c | Bin 181 -> 0 bytes
htslib/cram/._rANS_static.h | Bin 181 -> 0 bytes
htslib/cram/._sam_header.c | Bin 181 -> 0 bytes
htslib/cram/._sam_header.h | Bin 181 -> 0 bytes
htslib/cram/._string_alloc.c | Bin 181 -> 0 bytes
htslib/cram/._string_alloc.h | Bin 181 -> 0 bytes
htslib/cram/._thread_pool.c | Bin 181 -> 0 bytes
htslib/cram/._thread_pool.h | Bin 181 -> 0 bytes
htslib/cram/._vlen.c | Bin 181 -> 0 bytes
htslib/cram/._vlen.h | Bin 181 -> 0 bytes
htslib/cram/._zfio.c | Bin 181 -> 0 bytes
htslib/cram/._zfio.h | Bin 181 -> 0 bytes
htslib/htslib/._bgzf.h | Bin 181 -> 0 bytes
htslib/htslib/._cram.h | Bin 181 -> 0 bytes
htslib/htslib/._faidx.h | Bin 181 -> 0 bytes
htslib/htslib/._hfile.h | Bin 181 -> 0 bytes
htslib/htslib/._hts.h | Bin 181 -> 0 bytes
htslib/htslib/._hts_defs.h | Bin 181 -> 0 bytes
htslib/htslib/._kbitset.h | Bin 181 -> 0 bytes
htslib/htslib/._kfunc.h | Bin 181 -> 0 bytes
htslib/htslib/._khash.h | Bin 181 -> 0 bytes
htslib/htslib/._khash_str2int.h | Bin 181 -> 0 bytes
htslib/htslib/._klist.h | Bin 181 -> 0 bytes
htslib/htslib/._knetfile.h | Bin 181 -> 0 bytes
htslib/htslib/._kseq.h | Bin 181 -> 0 bytes
htslib/htslib/._ksort.h | Bin 181 -> 0 bytes
htslib/htslib/._kstring.h | Bin 181 -> 0 bytes
htslib/htslib/._regidx.h | Bin 181 -> 0 bytes
htslib/htslib/._sam.h | Bin 181 -> 0 bytes
htslib/htslib/._synced_bcf_reader.h | Bin 181 -> 0 bytes
htslib/htslib/._tbx.h | Bin 181 -> 0 bytes
htslib/htslib/._vcf.h | Bin 181 -> 0 bytes
htslib/htslib/._vcf_sweep.h | Bin 181 -> 0 bytes
htslib/htslib/._vcfutils.h | Bin 181 -> 0 bytes
scripts/count_fixed_catalog_snps.py | 323 ++
scripts/denovo_map.pl | 11 +-
scripts/integrate_alignments.py | 1 +
scripts/ref_map.pl | 9 +-
src/BamI.h | 285 +-
src/MetaPopInfo.cc | 43 +-
src/MetaPopInfo.h | 6 +-
src/PopMap.h | 9 +-
src/SamI.h | 356 +--
src/Vcf.cc | 2 +
src/aln_utils.cc | 55 +-
src/aln_utils.h | 2 +-
src/bootstrap.h | 19 +-
src/catalog_utils.cc | 22 +
src/catalog_utils.h | 6 +
src/clone_filter.cc | 2 +
src/constants.cc | 88 +
src/constants.h | 85 +-
src/cstacks.cc | 160 +-
src/estacks.cc | 9 +-
src/export_formats.cc | 169 +-
src/export_formats.h | 2 -
src/file_io.cc | 24 -
src/file_io.h | 1 -
src/genotypes.cc | 13 +-
src/hstacks.cc | 2 +
src/input.cc | 38 +-
src/input.h | 9 +-
src/kmer_filter.cc | 2 +
src/locus.cc | 7 +-
src/log_utils.cc | 15 +
src/log_utils.h | 15 +-
src/mst.cc | 8 +
src/mst.h | 8 +-
src/phasedstacks.cc | 2 +
src/populations.cc | 179 +-
src/populations.h | 2 +
src/process_radtags.cc | 99 +-
src/process_shortreads.cc | 18 +-
src/pstacks.cc | 508 +--
src/pstacks.h | 13 +-
src/renz.cc | 64 +-
src/rxstacks.cc | 77 +-
src/smoothing.h | 22 +-
src/sql_utilities.cc | 6 +-
src/sstacks.cc | 143 +-
src/stacks.h | 8 +-
src/ustacks.cc | 286 +-
src/ustacks.h | 4 +-
src/utils.cc | 36 +-
src/utils.h | 30 +
157 files changed, 8489 insertions(+), 7009 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index 8b22833..b8d6061 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,37 @@
+Stacks 1.46 - Apr 17, 2017
+--------------------------
+ Feature: Added HaeIII enzyme.
+ Bugfix: Corrected memory leaks in rxstacks.
+ Bugfix: Corrected non-functioning --min_mapq parameter for pstacks.
+ Bugfix: Corrected segfault when combining a VCF input file to populations, with genomic output and masking a restriction enzyme.
+
+Stacks 1.45 - Feb 24, 2017
+--------------------------
+ Feature: Tweaked the interfaces of most programs:
+ * cstacks and sstacks now accept a population map as input.
+ * process_radtags will now reuse the input directory name in its log file name.
+ * Reworked pstacks output.
+ * Batch ID now defaults to 1 in cstacks, and sstacks and other will try to guess
+ it from the contents of the given directory/catalog path.
+ * pstacks/ustacks/process_radtags will now try to guess file formats.
+ * Default (fallback) format in process_radtags/process_shortread is now gzfastq.
+ * pstacks: Substituted --max_clipped to --min_aln_pct.
+ * ustacks -r has become the default; --keep-high-cov reverses it.
+ * cstacks now checks for sample ID unicity.
+ * Updated help messages.
+ Feature: populations now logs the 'number of SNPs per locus' distribution.
+ Feature: Added mapping quality filter in pstacks (--min_mapq).
+ Feature: Added enzyme ApaLI.
+ Bugfix: populations: Corrected a VCF-related segfault (current use of VCF's GL field was
+ improper and was removed).
+ Bugfix: rxstacks: Corrected a bug that affected locus likelihood medians.
+ Bugfix: pstacks/ustacks: Corrected a bug that affected coverage standard deviations.
+ Bugfix: populations: Fixed parsing of option --sigma.
+ Bugfix: Fixed process_radtags writing fasta (instead of fastq) discard files when input
+ files were gzfastq.
+ Bugfix: kernel smoothing was not working correctly for Fis values (values were too negative).
+ Bugfix: fixed a regression for gapped alignments in cstacks that was causing a buffer overflow.
+
Stacks 1.44 - Oct 11, 2016
--------------------------
Bugfix: corrected an error in pstacks where '=' and 'X' symbols were not recognized properly in SAM/BAM
diff --git a/Makefile.am b/Makefile.am
index 4ad1fbe..6d500f8 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,7 +1,7 @@
bin_PROGRAMS = ustacks pstacks estacks cstacks sstacks rxstacks hstacks process_radtags process_shortreads \
kmer_filter clone_filter genotypes populations phasedstacks
-ustacks_SOURCES = src/ustacks.h src/ustacks.cc src/stacks.h src/stacks.cc src/constants.h \
+ustacks_SOURCES = src/ustacks.h src/ustacks.cc src/stacks.h src/stacks.cc src/constants.h src/constants.cc \
src/mstack.h src/mstack.cc src/mst.h src/mst.cc src/cmb.h src/cmb.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
src/models.h src/models.cc src/utils.h src/utils.cc \
@@ -9,50 +9,52 @@ ustacks_SOURCES = src/ustacks.h src/ustacks.cc src/stacks.h src/stacks.cc src/co
src/input.h src/input.cc src/Tsv.h src/BowtieI.h src/FastaI.h src/FastqI.h src/SamI.h \
src/gzFasta.h src/gzFastq.h
-pstacks_SOURCES = src/pstacks.h src/pstacks.cc src/stacks.h src/stacks.cc src/constants.h \
- src/mstack.h src/mstack.cc \
+pstacks_SOURCES = src/pstacks.h src/pstacks.cc src/stacks.h src/stacks.cc src/constants.h src/constants.cc \
+ src/mstack.h src/mstack.cc src/log_utils.h src/log_utils.cc \
src/DNANSeq.h src/DNANSeq.cc src/DNASeq.h src/DNASeq.cc \
- src/models.h src/models.cc src/utils.h src/utils.cc \
+ src/models.h src/models.cc src/utils.h src/utils.cc src/aln_utils.h src/aln_utils.cc \
src/input.h src/input.cc src/Tsv.h src/BowtieI.h src/FastaI.h src/FastqI.h src/SamI.h \
src/BamI.h
-estacks_SOURCES = src/estacks.h src/estacks.cc src/stacks.h src/stacks.cc src/constants.h \
+estacks_SOURCES = src/estacks.h src/estacks.cc src/stacks.h src/stacks.cc src/constants.h src/constants.cc \
src/mstack.h src/mstack.cc \
- src/models.h src/models.cc src/utils.h src/utils.cc \
+ src/models.h src/models.cc src/utils.h src/utils.cc src/aln_utils.h src/aln_utils.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
src/input.h src/input.cc src/Tsv.h src/BowtieI.h src/FastaI.h src/FastqI.h src/SamI.h
-cstacks_SOURCES = src/cstacks.h src/cstacks.cc src/constants.h \
+cstacks_SOURCES = src/cstacks.h src/cstacks.cc src/constants.h src/constants.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
src/kmers.h src/kmers.cc src/utils.h src/utils.cc \
src/GappedAln.h src/aln_utils.h src/aln_utils.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
- src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
+ src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
+ src/MetaPopInfo.h src/MetaPopInfo.cc
-hstacks_SOURCES = src/hstacks.h src/hstacks.cc src/constants.h \
+hstacks_SOURCES = src/hstacks.h src/hstacks.cc src/constants.h src/constants.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
src/kmers.h src/kmers.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
src/utils.h src/utils.cc \
src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
-sstacks_SOURCES = src/sstacks.h src/sstacks.cc src/constants.h \
+sstacks_SOURCES = src/sstacks.h src/sstacks.cc src/constants.h src/constants.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
src/kmers.h src/kmers.cc \
src/GappedAln.h src/aln_utils.h src/aln_utils.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc src/utils.h src/utils.cc \
- src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
+ src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/catalog_utils.cc \
+ src/MetaPopInfo.h src/MetaPopInfo.cc
-rxstacks_SOURCES = src/rxstacks.h src/rxstacks.cc src/constants.h \
+rxstacks_SOURCES = src/rxstacks.h src/rxstacks.cc src/constants.h src/constants.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
src/DNANSeq.h src/DNANSeq.cc src/DNASeq.h src/DNASeq.cc \
src/mst.h src/mst.cc \
src/models.h src/models.cc \
src/aln_utils.h src/aln_utils.cc src/utils.h src/utils.cc \
- src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
+ src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/catalog_utils.cc \
src/MetaPopInfo.h src/MetaPopInfo.cc
-process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/constants.h \
+process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/constants.h src/constants.cc \
src/utils.h src/utils.cc src/log_utils.h src/log_utils.cc \
src/write.h src/write.cc \
src/clean.h src/clean.cc \
@@ -60,7 +62,7 @@ process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/const
src/input.h src/input.cc src/BustardI.h src/BamUnalignedI.h src/FastqI.h src/gzFastq.h \
src/renz.h src/renz.cc
-process_shortreads_SOURCES = src/process_shortreads.h src/process_shortreads.cc src/constants.h \
+process_shortreads_SOURCES = src/process_shortreads.h src/process_shortreads.cc src/constants.h src/constants.cc \
src/clean.h src/clean.cc \
src/file_io.h src/file_io.cc \
src/utils.h src/utils.cc src/log_utils.h src/log_utils.cc \
@@ -68,14 +70,14 @@ process_shortreads_SOURCES = src/process_shortreads.h src/process_shortreads.cc
src/kmers.h src/kmers.cc \
src/input.h src/input.cc src/BustardI.h src/BamUnalignedI.h src/FastqI.h src/gzFastq.h
-kmer_filter_SOURCES = src/kmer_filter.h src/kmer_filter.cc src/constants.h \
+kmer_filter_SOURCES = src/kmer_filter.h src/kmer_filter.cc src/constants.h src/constants.cc \
src/utils.h src/utils.cc \
src/write.h src/write.cc \
src/kmers.h src/kmers.cc \
src/input.h src/input.cc src/BustardI.h src/FastqI.h src/FastaI.h \
src/gzFastq.h src/gzFasta.h
-clone_filter_SOURCES = src/clone_filter.h src/clone_filter.cc src/constants.h \
+clone_filter_SOURCES = src/clone_filter.h src/clone_filter.cc src/constants.h src/constants.cc \
src/kmers.h src/kmers.cc \
src/utils.h src/utils.cc \
src/write.h src/write.cc \
@@ -83,7 +85,7 @@ clone_filter_SOURCES = src/clone_filter.h src/clone_filter.cc src/constants.h \
src/input.h src/input.cc src/BustardI.h src/FastqI.h src/FastaI.h \
src/gzFastq.h src/gzFasta.h
-genotypes_SOURCES = src/genotypes.h src/genotypes.cc src/constants.h \
+genotypes_SOURCES = src/genotypes.h src/genotypes.cc src/constants.h src/constants.cc \
src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc \
src/log_utils.h src/log_utils.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
@@ -93,7 +95,7 @@ genotypes_SOURCES = src/genotypes.h src/genotypes.cc src/constants.h \
src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/renz.h src/renz.cc \
src/MetaPopInfo.h src/MetaPopInfo.cc
-populations_SOURCES = src/populations.h src/populations.cc src/constants.h \
+populations_SOURCES = src/populations.h src/populations.cc src/constants.h src/constants.cc \
src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc \
src/log_utils.h src/log_utils.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
@@ -104,7 +106,7 @@ populations_SOURCES = src/populations.h src/populations.cc src/constants.h \
src/export_formats.h src/export_formats.cc \
src/MetaPopInfo.h src/MetaPopInfo.cc src/Vcf.h src/Vcf.cc
-phasedstacks_SOURCES = src/phasedstacks.h src/phasedstacks.cc src/constants.h \
+phasedstacks_SOURCES = src/phasedstacks.h src/phasedstacks.cc src/constants.h src/constants.cc \
src/locus.h src/locus.cc \
src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
src/log_utils.h src/log_utils.cc \
@@ -115,8 +117,9 @@ ustacks_LDFLAGS = $(OPENMP_CFLAGS)
pstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS) $(SPARSEHASH_CFLAGS)
pstacks_LDFLAGS = $(OPENMP_CFLAGS)
pstacks_LDADD = $(BAM_LIBS)
-estacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)
+estacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS) $(BAM_CFLAGS)
estacks_LDFLAGS = $(OPENMP_CFLAGS)
+estacks_LDADD = $(BAM_LIBS)
cstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)
cstacks_LDFLAGS = $(OPENMP_CFLAGS)
hstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)
@@ -146,7 +149,7 @@ clone_filter_LDADD = $(BAM_LIBS)
dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl scripts/export_sql.pl \
scripts/sort_read_pairs.pl scripts/exec_velvet.pl scripts/load_sequences.pl \
scripts/index_radtags.pl scripts/load_radtags.pl scripts/stacks_export_notify.pl \
- scripts/integrate_alignments.py
+ scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py
dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl
diff --git a/Makefile.in b/Makefile.in
index 7a479ef..86eae3c 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.15 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2014 Free Software Foundation, Inc.
-
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -17,61 +18,6 @@
VPATH = @srcdir@
-am__is_gnu_make = { \
- if test -z '$(MAKELEVEL)'; then \
- false; \
- elif test -n '$(MAKE_HOST)'; then \
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- true; \
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-am__make_dryrun = (target_option=n; $(am__make_running_with_option))
-am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
@@ -95,14 +41,16 @@ bin_PROGRAMS = ustacks$(EXEEXT) pstacks$(EXEEXT) estacks$(EXEEXT) \
clone_filter$(EXEEXT) genotypes$(EXEEXT) populations$(EXEEXT) \
phasedstacks$(EXEEXT)
subdir = .
+DIST_COMMON = README $(am__configure_deps) $(dist_bin_SCRIPTS) \
+ $(dist_noinst_SCRIPTS) $(srcdir)/Makefile.am \
+ $(srcdir)/Makefile.in $(srcdir)/config.h.in \
+ $(top_srcdir)/configure ChangeLog INSTALL config/compile \
+ config/depcomp config/install-sh config/missing
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
-DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \
- $(am__configure_deps) $(dist_bin_SCRIPTS) \
- $(dist_noinst_SCRIPTS) $(am__DIST_COMMON)
am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
configure.lineno config.status.lineno
mkinstalldirs = $(install_sh) -d
@@ -114,6 +62,7 @@ am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" \
PROGRAMS = $(bin_PROGRAMS)
am__dirstamp = $(am__leading_dot)dirstamp
am_clone_filter_OBJECTS = src/clone_filter-clone_filter.$(OBJEXT) \
+ src/clone_filter-constants.$(OBJEXT) \
src/clone_filter-kmers.$(OBJEXT) \
src/clone_filter-utils.$(OBJEXT) \
src/clone_filter-write.$(OBJEXT) \
@@ -126,25 +75,29 @@ clone_filter_DEPENDENCIES = $(am__DEPENDENCIES_1)
clone_filter_LINK = $(CXXLD) $(clone_filter_CXXFLAGS) $(CXXFLAGS) \
$(clone_filter_LDFLAGS) $(LDFLAGS) -o $@
am_cstacks_OBJECTS = src/cstacks-cstacks.$(OBJEXT) \
- src/cstacks-stacks.$(OBJEXT) src/cstacks-locus.$(OBJEXT) \
- src/cstacks-kmers.$(OBJEXT) src/cstacks-utils.$(OBJEXT) \
- src/cstacks-aln_utils.$(OBJEXT) src/cstacks-DNASeq.$(OBJEXT) \
- src/cstacks-DNANSeq.$(OBJEXT) src/cstacks-input.$(OBJEXT) \
- src/cstacks-sql_utilities.$(OBJEXT)
+ src/cstacks-constants.$(OBJEXT) src/cstacks-stacks.$(OBJEXT) \
+ src/cstacks-locus.$(OBJEXT) src/cstacks-kmers.$(OBJEXT) \
+ src/cstacks-utils.$(OBJEXT) src/cstacks-aln_utils.$(OBJEXT) \
+ src/cstacks-DNASeq.$(OBJEXT) src/cstacks-DNANSeq.$(OBJEXT) \
+ src/cstacks-input.$(OBJEXT) \
+ src/cstacks-sql_utilities.$(OBJEXT) \
+ src/cstacks-MetaPopInfo.$(OBJEXT)
cstacks_OBJECTS = $(am_cstacks_OBJECTS)
cstacks_LDADD = $(LDADD)
cstacks_LINK = $(CXXLD) $(cstacks_CXXFLAGS) $(CXXFLAGS) \
$(cstacks_LDFLAGS) $(LDFLAGS) -o $@
am_estacks_OBJECTS = src/estacks-estacks.$(OBJEXT) \
- src/estacks-stacks.$(OBJEXT) src/estacks-mstack.$(OBJEXT) \
- src/estacks-models.$(OBJEXT) src/estacks-utils.$(OBJEXT) \
+ src/estacks-stacks.$(OBJEXT) src/estacks-constants.$(OBJEXT) \
+ src/estacks-mstack.$(OBJEXT) src/estacks-models.$(OBJEXT) \
+ src/estacks-utils.$(OBJEXT) src/estacks-aln_utils.$(OBJEXT) \
src/estacks-DNASeq.$(OBJEXT) src/estacks-DNANSeq.$(OBJEXT) \
src/estacks-input.$(OBJEXT)
estacks_OBJECTS = $(am_estacks_OBJECTS)
-estacks_LDADD = $(LDADD)
+estacks_DEPENDENCIES = $(am__DEPENDENCIES_1)
estacks_LINK = $(CXXLD) $(estacks_CXXFLAGS) $(CXXFLAGS) \
$(estacks_LDFLAGS) $(LDFLAGS) -o $@
am_genotypes_OBJECTS = src/genotypes-genotypes.$(OBJEXT) \
+ src/genotypes-constants.$(OBJEXT) \
src/genotypes-utils.$(OBJEXT) \
src/genotypes-catalog_utils.$(OBJEXT) \
src/genotypes-log_utils.$(OBJEXT) \
@@ -161,16 +114,17 @@ genotypes_LDADD = $(LDADD)
genotypes_LINK = $(CXXLD) $(genotypes_CXXFLAGS) $(CXXFLAGS) \
$(genotypes_LDFLAGS) $(LDFLAGS) -o $@
am_hstacks_OBJECTS = src/hstacks-hstacks.$(OBJEXT) \
- src/hstacks-stacks.$(OBJEXT) src/hstacks-locus.$(OBJEXT) \
- src/hstacks-kmers.$(OBJEXT) src/hstacks-DNASeq.$(OBJEXT) \
- src/hstacks-DNANSeq.$(OBJEXT) src/hstacks-utils.$(OBJEXT) \
- src/hstacks-input.$(OBJEXT) \
+ src/hstacks-constants.$(OBJEXT) src/hstacks-stacks.$(OBJEXT) \
+ src/hstacks-locus.$(OBJEXT) src/hstacks-kmers.$(OBJEXT) \
+ src/hstacks-DNASeq.$(OBJEXT) src/hstacks-DNANSeq.$(OBJEXT) \
+ src/hstacks-utils.$(OBJEXT) src/hstacks-input.$(OBJEXT) \
src/hstacks-sql_utilities.$(OBJEXT)
hstacks_OBJECTS = $(am_hstacks_OBJECTS)
hstacks_LDADD = $(LDADD)
hstacks_LINK = $(CXXLD) $(hstacks_CXXFLAGS) $(CXXFLAGS) \
$(hstacks_LDFLAGS) $(LDFLAGS) -o $@
am_kmer_filter_OBJECTS = src/kmer_filter-kmer_filter.$(OBJEXT) \
+ src/kmer_filter-constants.$(OBJEXT) \
src/kmer_filter-utils.$(OBJEXT) \
src/kmer_filter-write.$(OBJEXT) \
src/kmer_filter-kmers.$(OBJEXT) \
@@ -180,6 +134,7 @@ kmer_filter_LDADD = $(LDADD)
kmer_filter_LINK = $(CXXLD) $(kmer_filter_CXXFLAGS) $(CXXFLAGS) \
$(kmer_filter_LDFLAGS) $(LDFLAGS) -o $@
am_phasedstacks_OBJECTS = src/phasedstacks-phasedstacks.$(OBJEXT) \
+ src/phasedstacks-constants.$(OBJEXT) \
src/phasedstacks-locus.$(OBJEXT) \
src/phasedstacks-input.$(OBJEXT) \
src/phasedstacks-sql_utilities.$(OBJEXT) \
@@ -191,6 +146,7 @@ phasedstacks_LDADD = $(LDADD)
phasedstacks_LINK = $(CXXLD) $(phasedstacks_CXXFLAGS) $(CXXFLAGS) \
$(phasedstacks_LDFLAGS) $(LDFLAGS) -o $@
am_populations_OBJECTS = src/populations-populations.$(OBJEXT) \
+ src/populations-constants.$(OBJEXT) \
src/populations-utils.$(OBJEXT) \
src/populations-catalog_utils.$(OBJEXT) \
src/populations-log_utils.$(OBJEXT) \
@@ -212,6 +168,7 @@ populations_LINK = $(CXXLD) $(populations_CXXFLAGS) $(CXXFLAGS) \
$(populations_LDFLAGS) $(LDFLAGS) -o $@
am_process_radtags_OBJECTS = \
src/process_radtags-process_radtags.$(OBJEXT) \
+ src/process_radtags-constants.$(OBJEXT) \
src/process_radtags-utils.$(OBJEXT) \
src/process_radtags-log_utils.$(OBJEXT) \
src/process_radtags-write.$(OBJEXT) \
@@ -225,6 +182,7 @@ process_radtags_LINK = $(CXXLD) $(process_radtags_CXXFLAGS) \
$(CXXFLAGS) $(process_radtags_LDFLAGS) $(LDFLAGS) -o $@
am_process_shortreads_OBJECTS = \
src/process_shortreads-process_shortreads.$(OBJEXT) \
+ src/process_shortreads-constants.$(OBJEXT) \
src/process_shortreads-clean.$(OBJEXT) \
src/process_shortreads-file_io.$(OBJEXT) \
src/process_shortreads-utils.$(OBJEXT) \
@@ -237,43 +195,48 @@ process_shortreads_DEPENDENCIES = $(am__DEPENDENCIES_1)
process_shortreads_LINK = $(CXXLD) $(process_shortreads_CXXFLAGS) \
$(CXXFLAGS) $(process_shortreads_LDFLAGS) $(LDFLAGS) -o $@
am_pstacks_OBJECTS = src/pstacks-pstacks.$(OBJEXT) \
- src/pstacks-stacks.$(OBJEXT) src/pstacks-mstack.$(OBJEXT) \
+ src/pstacks-stacks.$(OBJEXT) src/pstacks-constants.$(OBJEXT) \
+ src/pstacks-mstack.$(OBJEXT) src/pstacks-log_utils.$(OBJEXT) \
src/pstacks-DNANSeq.$(OBJEXT) src/pstacks-DNASeq.$(OBJEXT) \
src/pstacks-models.$(OBJEXT) src/pstacks-utils.$(OBJEXT) \
- src/pstacks-input.$(OBJEXT)
+ src/pstacks-aln_utils.$(OBJEXT) src/pstacks-input.$(OBJEXT)
pstacks_OBJECTS = $(am_pstacks_OBJECTS)
pstacks_DEPENDENCIES = $(am__DEPENDENCIES_1)
pstacks_LINK = $(CXXLD) $(pstacks_CXXFLAGS) $(CXXFLAGS) \
$(pstacks_LDFLAGS) $(LDFLAGS) -o $@
am_rxstacks_OBJECTS = src/rxstacks-rxstacks.$(OBJEXT) \
- src/rxstacks-stacks.$(OBJEXT) src/rxstacks-locus.$(OBJEXT) \
- src/rxstacks-DNANSeq.$(OBJEXT) src/rxstacks-DNASeq.$(OBJEXT) \
- src/rxstacks-mst.$(OBJEXT) src/rxstacks-models.$(OBJEXT) \
- src/rxstacks-aln_utils.$(OBJEXT) src/rxstacks-utils.$(OBJEXT) \
- src/rxstacks-input.$(OBJEXT) \
+ src/rxstacks-constants.$(OBJEXT) src/rxstacks-stacks.$(OBJEXT) \
+ src/rxstacks-locus.$(OBJEXT) src/rxstacks-DNANSeq.$(OBJEXT) \
+ src/rxstacks-DNASeq.$(OBJEXT) src/rxstacks-mst.$(OBJEXT) \
+ src/rxstacks-models.$(OBJEXT) src/rxstacks-aln_utils.$(OBJEXT) \
+ src/rxstacks-utils.$(OBJEXT) src/rxstacks-input.$(OBJEXT) \
src/rxstacks-sql_utilities.$(OBJEXT) \
+ src/rxstacks-catalog_utils.$(OBJEXT) \
src/rxstacks-MetaPopInfo.$(OBJEXT)
rxstacks_OBJECTS = $(am_rxstacks_OBJECTS)
rxstacks_LDADD = $(LDADD)
rxstacks_LINK = $(CXXLD) $(rxstacks_CXXFLAGS) $(CXXFLAGS) \
$(rxstacks_LDFLAGS) $(LDFLAGS) -o $@
am_sstacks_OBJECTS = src/sstacks-sstacks.$(OBJEXT) \
- src/sstacks-stacks.$(OBJEXT) src/sstacks-locus.$(OBJEXT) \
- src/sstacks-kmers.$(OBJEXT) src/sstacks-aln_utils.$(OBJEXT) \
- src/sstacks-DNASeq.$(OBJEXT) src/sstacks-DNANSeq.$(OBJEXT) \
- src/sstacks-utils.$(OBJEXT) src/sstacks-input.$(OBJEXT) \
- src/sstacks-sql_utilities.$(OBJEXT)
+ src/sstacks-constants.$(OBJEXT) src/sstacks-stacks.$(OBJEXT) \
+ src/sstacks-locus.$(OBJEXT) src/sstacks-kmers.$(OBJEXT) \
+ src/sstacks-aln_utils.$(OBJEXT) src/sstacks-DNASeq.$(OBJEXT) \
+ src/sstacks-DNANSeq.$(OBJEXT) src/sstacks-utils.$(OBJEXT) \
+ src/sstacks-input.$(OBJEXT) \
+ src/sstacks-sql_utilities.$(OBJEXT) \
+ src/sstacks-catalog_utils.$(OBJEXT) \
+ src/sstacks-MetaPopInfo.$(OBJEXT)
sstacks_OBJECTS = $(am_sstacks_OBJECTS)
sstacks_LDADD = $(LDADD)
sstacks_LINK = $(CXXLD) $(sstacks_CXXFLAGS) $(CXXFLAGS) \
$(sstacks_LDFLAGS) $(LDFLAGS) -o $@
am_ustacks_OBJECTS = src/ustacks-ustacks.$(OBJEXT) \
- src/ustacks-stacks.$(OBJEXT) src/ustacks-mstack.$(OBJEXT) \
- src/ustacks-mst.$(OBJEXT) src/ustacks-cmb.$(OBJEXT) \
- src/ustacks-DNASeq.$(OBJEXT) src/ustacks-DNANSeq.$(OBJEXT) \
- src/ustacks-models.$(OBJEXT) src/ustacks-utils.$(OBJEXT) \
- src/ustacks-kmers.$(OBJEXT) src/ustacks-aln_utils.$(OBJEXT) \
- src/ustacks-input.$(OBJEXT)
+ src/ustacks-stacks.$(OBJEXT) src/ustacks-constants.$(OBJEXT) \
+ src/ustacks-mstack.$(OBJEXT) src/ustacks-mst.$(OBJEXT) \
+ src/ustacks-cmb.$(OBJEXT) src/ustacks-DNASeq.$(OBJEXT) \
+ src/ustacks-DNANSeq.$(OBJEXT) src/ustacks-models.$(OBJEXT) \
+ src/ustacks-utils.$(OBJEXT) src/ustacks-kmers.$(OBJEXT) \
+ src/ustacks-aln_utils.$(OBJEXT) src/ustacks-input.$(OBJEXT)
ustacks_OBJECTS = $(am_ustacks_OBJECTS)
ustacks_LDADD = $(LDADD)
ustacks_LINK = $(CXXLD) $(ustacks_CXXFLAGS) $(CXXFLAGS) \
@@ -299,58 +262,20 @@ am__nobase_list = $(am__nobase_strip_setup); \
am__base_list = \
sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__uninstall_files_from_dir = { \
- test -z "$$files" \
- || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
- || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
- $(am__cd) "$$dir" && rm -f $$files; }; \
- }
SCRIPTS = $(dist_bin_SCRIPTS) $(dist_noinst_SCRIPTS)
-AM_V_P = $(am__v_P_ at AM_V@)
-am__v_P_ = $(am__v_P_ at AM_DEFAULT_V@)
-am__v_P_0 = false
-am__v_P_1 = :
-AM_V_GEN = $(am__v_GEN_ at AM_V@)
-am__v_GEN_ = $(am__v_GEN_ at AM_DEFAULT_V@)
-am__v_GEN_0 = @echo " GEN " $@;
-am__v_GEN_1 =
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-am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
-am__v_at_0 = @
-am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@
depcomp = $(SHELL) $(top_srcdir)/config/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
-AM_V_lt = $(am__v_lt_ at AM_V@)
-am__v_lt_ = $(am__v_lt_ at AM_DEFAULT_V@)
-am__v_lt_0 = --silent
-am__v_lt_1 =
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
-AM_V_CXX = $(am__v_CXX_ at AM_V@)
-am__v_CXX_ = $(am__v_CXX_ at AM_DEFAULT_V@)
-am__v_CXX_0 = @echo " CXX " $@;
-am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
-AM_V_CXXLD = $(am__v_CXXLD_ at AM_V@)
-am__v_CXXLD_ = $(am__v_CXXLD_ at AM_DEFAULT_V@)
-am__v_CXXLD_0 = @echo " CXXLD " $@;
-am__v_CXXLD_1 =
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-AM_V_CC = $(am__v_CC_ at AM_V@)
-am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
-am__v_CC_0 = @echo " CC " $@;
-am__v_CC_1 =
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
-am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
-am__v_CCLD_0 = @echo " CCLD " $@;
-am__v_CCLD_1 =
SOURCES = $(clone_filter_SOURCES) $(cstacks_SOURCES) \
$(estacks_SOURCES) $(genotypes_SOURCES) $(hstacks_SOURCES) \
$(kmer_filter_SOURCES) $(phasedstacks_SOURCES) \
@@ -363,240 +288,80 @@ DIST_SOURCES = $(clone_filter_SOURCES) $(cstacks_SOURCES) \
$(populations_SOURCES) $(process_radtags_SOURCES) \
$(process_shortreads_SOURCES) $(pstacks_SOURCES) \
$(rxstacks_SOURCES) $(sstacks_SOURCES) $(ustacks_SOURCES)
-RECURSIVE_TARGETS = all-recursive check-recursive cscopelist-recursive \
- ctags-recursive dvi-recursive html-recursive info-recursive \
- install-data-recursive install-dvi-recursive \
- install-exec-recursive install-html-recursive \
- install-info-recursive install-pdf-recursive \
- install-ps-recursive install-recursive installcheck-recursive \
- installdirs-recursive pdf-recursive ps-recursive \
- tags-recursive uninstall-recursive
-am__can_run_installinfo = \
- case $$AM_UPDATE_INFO_DIR in \
- n|no|NO) false;; \
- *) (install-info --version) >/dev/null 2>&1;; \
- esac
+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
+ html-recursive info-recursive install-data-recursive \
+ install-dvi-recursive install-exec-recursive \
+ install-html-recursive install-info-recursive \
+ install-pdf-recursive install-ps-recursive install-recursive \
+ installcheck-recursive installdirs-recursive pdf-recursive \
+ ps-recursive uninstall-recursive
DATA = $(nobase_pkgdata_DATA)
RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
distclean-recursive maintainer-clean-recursive
-am__recursive_targets = \
- $(RECURSIVE_TARGETS) \
- $(RECURSIVE_CLEAN_TARGETS) \
- $(am__extra_recursive_targets)
-AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
- cscope check recheck distdir dist dist-all distcheck
-am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \
- $(LISP)config.h.in
-# Read a list of newline-separated strings from the standard input,
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- unique=`for i in $$list; do \
- if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
- done | $(am__uniquify_input)`
+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+ $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
+ check check-html recheck recheck-html distdir dist dist-all \
+ distcheck
ETAGS = etags
CTAGS = ctags
-CSCOPE = cscope
-am__tty_colors_dummy = \
- mgn= red= grn= lgn= blu= brg= std=; \
- am__color_tests=no
-am__tty_colors = { \
- $(am__tty_colors_dummy); \
- if test "X$(AM_COLOR_TESTS)" = Xno; then \
- am__color_tests=no; \
- elif test "X$(AM_COLOR_TESTS)" = Xalways; then \
- am__color_tests=yes; \
- elif test "X$$TERM" != Xdumb && { test -t 1; } 2>/dev/null; then \
- am__color_tests=yes; \
- fi; \
- if test $$am__color_tests = yes; then \
- red='[0;31m'; \
- grn='[0;32m'; \
- lgn='[1;32m'; \
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- mgn='[0;35m'; \
- brg='[1m'; \
- std='[m'; \
- fi; \
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-am__recheck_rx = ^[ ]*:recheck:[ ]*
-am__global_test_result_rx = ^[ ]*:global-test-result:[ ]*
-am__copy_in_global_log_rx = ^[ ]*:copy-in-global-log:[ ]*
-# A command that, given a newline-separated list of test names on the
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-am__list_recheck_tests = $(AWK) '{ \
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- { \
- break; \
- } \
- }; \
- if (recheck) \
- print $$0; \
- close ($$0 ".trs"); \
- close ($$0 ".log"); \
+am__tty_colors = \
+red=; grn=; lgn=; blu=; std=
+# Restructured Text title and section.
+am__rst_title = sed 's/.*/ & /;h;s/./=/g;p;x;p;g;p;s/.*//'
+am__rst_section = sed 'p;s/./=/g;p;g'
+# Put stdin (possibly several lines separated by ". ") in a box.
+am__text_box = $(AWK) '{ \
+ n = split($$0, lines, "\\. "); max = 0; \
+ for (i = 1; i <= n; ++i) \
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+ max = length(lines[i]); \
+ for (i = 0; i < max; ++i) line = line "="; \
+ print line; \
+ for (i = 1; i <= n; ++i) if (lines[i]) print lines[i];\
+ print line; \
}'
-# A command that, given a newline-separated list of test names on the
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# Solaris 10 'make', and several other traditional 'make' implementations,
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+# pass "-e" to $(SHELL). This contradicts POSIX. Work around the problem
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am__sh_e_setup = case $$- in *e*) set +e;; esac
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-# containing $f, in $tst the test, in $log the log. Executes the
-# developer- defined test setup AM_TESTS_ENVIRONMENT (if any), and
-# passes TESTS_ENVIRONMENT. Set up options for the wrapper that
-# will run the test scripts (or their associated LOG_COMPILER, if
-# thy have one).
+# containing $f, in $tst the test, in $log the log, and passes
+# TESTS_ENVIRONMENT. Save and restore TERM around use of
+# TESTS_ENVIRONMENT, in case that unsets it.
am__check_pre = \
$(am__sh_e_setup); \
$(am__vpath_adj_setup) $(am__vpath_adj) \
-$(am__tty_colors); \
srcdir=$(srcdir); export srcdir; \
-case "$@" in \
- */*) am__odir=`echo "./$@" | sed 's|/[^/]*$$||'`;; \
- *) am__odir=.;; \
-esac; \
-test "x$$am__odir" = x"." || test -d "$$am__odir" \
- || $(MKDIR_P) "$$am__odir" || exit $$?; \
+rm -f $@-t; \
+trap 'st=$$?; rm -f '\''$(abs_builddir)/$@-t'\''; (exit $$st); exit $$st' \
+ 1 2 13 15; \
+am__odir=`echo "./$@" | sed 's|/[^/]*$$||'`; \
+test "x$$am__odir" = x. || $(MKDIR_P) "$$am__odir" || exit $$?; \
if test -f "./$$f"; then dir=./; \
elif test -f "$$f"; then dir=; \
else dir="$(srcdir)/"; fi; \
-tst=$$dir$$f; log='$@'; \
-if test -n '$(DISABLE_HARD_ERRORS)'; then \
- am__enable_hard_errors=no; \
-else \
- am__enable_hard_errors=yes; \
-fi; \
-case " $(XFAIL_TESTS) " in \
- *[\ \ ]$$f[\ \ ]* | *[\ \ ]$$dir$$f[\ \ ]*) \
- am__expect_failure=yes;; \
- *) \
- am__expect_failure=no;; \
-esac; \
-$(AM_TESTS_ENVIRONMENT) $(TESTS_ENVIRONMENT)
-# A shell command to get the names of the tests scripts with any registered
-# extension removed (i.e., equivalently, the names of the test logs, with
-# the '.log' extension removed). The result is saved in the shell variable
-# '$bases'. This honors runtime overriding of TESTS and TEST_LOGS. Sadly,
-# we cannot use something simpler, involving e.g., "$(TEST_LOGS:.log=)",
-# since that might cause problem with VPATH rewrites for suffix-less tests.
-# See also 'test-harness-vpath-rewrite.sh' and 'test-trs-basic.sh'.
-am__set_TESTS_bases = \
- bases='$(TEST_LOGS)'; \
- bases=`for i in $$bases; do echo $$i; done | sed 's/\.log$$//'`; \
- bases=`echo $$bases`
+tst=$$dir$$f; log='$@'; __SAVED_TERM=$$TERM; \
+$(TESTS_ENVIRONMENT)
RECHECK_LOGS = $(TEST_LOGS)
TEST_SUITE_LOG = test-suite.log
+TEST_SUITE_HTML = $(TEST_SUITE_LOG:.log=.html)
TEST_EXTENSIONS = @EXEEXT@ .test
LOG_COMPILE = $(LOG_COMPILER) $(AM_LOG_FLAGS) $(LOG_FLAGS)
-am__set_b = \
- case '$@' in \
- */*) \
- case '$*' in \
- */*) b='$*';; \
- *) b=`echo '$@' | sed 's/\.log$$//'`; \
- esac;; \
- *) \
- b='$*';; \
- esac
am__test_logs1 = $(TESTS:=.log)
am__test_logs2 = $(am__test_logs1:@EXEEXT at .log=.log)
TEST_LOGS = $(am__test_logs2:.test.log=.log)
-TEST_LOG_DRIVER = $(SHELL) $(top_srcdir)/config/test-driver
TEST_LOG_COMPILE = $(TEST_LOG_COMPILER) $(AM_TEST_LOG_FLAGS) \
$(TEST_LOG_FLAGS)
+TEST_LOGS_TMP = $(TEST_LOGS:.log=.log-t)
DIST_SUBDIRS = $(SUBDIRS)
-am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in \
- $(top_srcdir)/config/compile $(top_srcdir)/config/depcomp \
- $(top_srcdir)/config/install-sh $(top_srcdir)/config/missing \
- $(top_srcdir)/config/test-driver ChangeLog INSTALL README \
- config/compile config/depcomp config/install-sh config/missing
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
distdir = $(PACKAGE)-$(VERSION)
top_distdir = $(distdir)
am__remove_distdir = \
- if test -d "$(distdir)"; then \
- find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
- && rm -rf "$(distdir)" \
- || { sleep 5 && rm -rf "$(distdir)"; }; \
- else :; fi
-am__post_remove_distdir = $(am__remove_distdir)
+ { test ! -d "$(distdir)" \
+ || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
+ && rm -fr "$(distdir)"; }; }
am__relativize = \
dir0=`pwd`; \
sed_first='s,^\([^/]*\)/.*$$,\1,'; \
@@ -624,14 +389,10 @@ am__relativize = \
reldir="$$dir2"
DIST_ARCHIVES = $(distdir).tar.gz
GZIP_ENV = --best
-DIST_TARGETS = dist-gzip
distuninstallcheck_listfiles = find . -type f -print
-am__distuninstallcheck_listfiles = $(distuninstallcheck_listfiles) \
- | sed 's|^\./|$(prefix)/|' | grep -v '$(infodir)/dir$$'
distcleancheck_listfiles = find . -type f -print
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
-AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -674,7 +435,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
PACKAGE_NAME = @PACKAGE_NAME@
PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
SET_MAKE = @SET_MAKE@
@@ -725,7 +485,7 @@ target_alias = @target_alias@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
-ustacks_SOURCES = src/ustacks.h src/ustacks.cc src/stacks.h src/stacks.cc src/constants.h \
+ustacks_SOURCES = src/ustacks.h src/ustacks.cc src/stacks.h src/stacks.cc src/constants.h src/constants.cc \
src/mstack.h src/mstack.cc src/mst.h src/mst.cc src/cmb.h src/cmb.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
src/models.h src/models.cc src/utils.h src/utils.cc \
@@ -733,50 +493,52 @@ ustacks_SOURCES = src/ustacks.h src/ustacks.cc src/stacks.h src/stacks.cc src/co
src/input.h src/input.cc src/Tsv.h src/BowtieI.h src/FastaI.h src/FastqI.h src/SamI.h \
src/gzFasta.h src/gzFastq.h
-pstacks_SOURCES = src/pstacks.h src/pstacks.cc src/stacks.h src/stacks.cc src/constants.h \
- src/mstack.h src/mstack.cc \
+pstacks_SOURCES = src/pstacks.h src/pstacks.cc src/stacks.h src/stacks.cc src/constants.h src/constants.cc \
+ src/mstack.h src/mstack.cc src/log_utils.h src/log_utils.cc \
src/DNANSeq.h src/DNANSeq.cc src/DNASeq.h src/DNASeq.cc \
- src/models.h src/models.cc src/utils.h src/utils.cc \
+ src/models.h src/models.cc src/utils.h src/utils.cc src/aln_utils.h src/aln_utils.cc \
src/input.h src/input.cc src/Tsv.h src/BowtieI.h src/FastaI.h src/FastqI.h src/SamI.h \
src/BamI.h
-estacks_SOURCES = src/estacks.h src/estacks.cc src/stacks.h src/stacks.cc src/constants.h \
+estacks_SOURCES = src/estacks.h src/estacks.cc src/stacks.h src/stacks.cc src/constants.h src/constants.cc \
src/mstack.h src/mstack.cc \
- src/models.h src/models.cc src/utils.h src/utils.cc \
+ src/models.h src/models.cc src/utils.h src/utils.cc src/aln_utils.h src/aln_utils.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
src/input.h src/input.cc src/Tsv.h src/BowtieI.h src/FastaI.h src/FastqI.h src/SamI.h
-cstacks_SOURCES = src/cstacks.h src/cstacks.cc src/constants.h \
+cstacks_SOURCES = src/cstacks.h src/cstacks.cc src/constants.h src/constants.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
src/kmers.h src/kmers.cc src/utils.h src/utils.cc \
src/GappedAln.h src/aln_utils.h src/aln_utils.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
- src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
+ src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
+ src/MetaPopInfo.h src/MetaPopInfo.cc
-hstacks_SOURCES = src/hstacks.h src/hstacks.cc src/constants.h \
+hstacks_SOURCES = src/hstacks.h src/hstacks.cc src/constants.h src/constants.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
src/kmers.h src/kmers.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
src/utils.h src/utils.cc \
src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
-sstacks_SOURCES = src/sstacks.h src/sstacks.cc src/constants.h \
+sstacks_SOURCES = src/sstacks.h src/sstacks.cc src/constants.h src/constants.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
src/kmers.h src/kmers.cc \
src/GappedAln.h src/aln_utils.h src/aln_utils.cc \
src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc src/utils.h src/utils.cc \
- src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
+ src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/catalog_utils.cc \
+ src/MetaPopInfo.h src/MetaPopInfo.cc
-rxstacks_SOURCES = src/rxstacks.h src/rxstacks.cc src/constants.h \
+rxstacks_SOURCES = src/rxstacks.h src/rxstacks.cc src/constants.h src/constants.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
src/DNANSeq.h src/DNANSeq.cc src/DNASeq.h src/DNASeq.cc \
src/mst.h src/mst.cc \
src/models.h src/models.cc \
src/aln_utils.h src/aln_utils.cc src/utils.h src/utils.cc \
- src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
+ src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/catalog_utils.cc \
src/MetaPopInfo.h src/MetaPopInfo.cc
-process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/constants.h \
+process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/constants.h src/constants.cc \
src/utils.h src/utils.cc src/log_utils.h src/log_utils.cc \
src/write.h src/write.cc \
src/clean.h src/clean.cc \
@@ -784,7 +546,7 @@ process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/const
src/input.h src/input.cc src/BustardI.h src/BamUnalignedI.h src/FastqI.h src/gzFastq.h \
src/renz.h src/renz.cc
-process_shortreads_SOURCES = src/process_shortreads.h src/process_shortreads.cc src/constants.h \
+process_shortreads_SOURCES = src/process_shortreads.h src/process_shortreads.cc src/constants.h src/constants.cc \
src/clean.h src/clean.cc \
src/file_io.h src/file_io.cc \
src/utils.h src/utils.cc src/log_utils.h src/log_utils.cc \
@@ -792,14 +554,14 @@ process_shortreads_SOURCES = src/process_shortreads.h src/process_shortreads.cc
src/kmers.h src/kmers.cc \
src/input.h src/input.cc src/BustardI.h src/BamUnalignedI.h src/FastqI.h src/gzFastq.h
-kmer_filter_SOURCES = src/kmer_filter.h src/kmer_filter.cc src/constants.h \
+kmer_filter_SOURCES = src/kmer_filter.h src/kmer_filter.cc src/constants.h src/constants.cc \
src/utils.h src/utils.cc \
src/write.h src/write.cc \
src/kmers.h src/kmers.cc \
src/input.h src/input.cc src/BustardI.h src/FastqI.h src/FastaI.h \
src/gzFastq.h src/gzFasta.h
-clone_filter_SOURCES = src/clone_filter.h src/clone_filter.cc src/constants.h \
+clone_filter_SOURCES = src/clone_filter.h src/clone_filter.cc src/constants.h src/constants.cc \
src/kmers.h src/kmers.cc \
src/utils.h src/utils.cc \
src/write.h src/write.cc \
@@ -807,7 +569,7 @@ clone_filter_SOURCES = src/clone_filter.h src/clone_filter.cc src/constants.h \
src/input.h src/input.cc src/BustardI.h src/FastqI.h src/FastaI.h \
src/gzFastq.h src/gzFasta.h
-genotypes_SOURCES = src/genotypes.h src/genotypes.cc src/constants.h \
+genotypes_SOURCES = src/genotypes.h src/genotypes.cc src/constants.h src/constants.cc \
src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc \
src/log_utils.h src/log_utils.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
@@ -817,7 +579,7 @@ genotypes_SOURCES = src/genotypes.h src/genotypes.cc src/constants.h \
src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/renz.h src/renz.cc \
src/MetaPopInfo.h src/MetaPopInfo.cc
-populations_SOURCES = src/populations.h src/populations.cc src/constants.h \
+populations_SOURCES = src/populations.h src/populations.cc src/constants.h src/constants.cc \
src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc \
src/log_utils.h src/log_utils.cc \
src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
@@ -828,7 +590,7 @@ populations_SOURCES = src/populations.h src/populations.cc src/constants.h \
src/export_formats.h src/export_formats.cc \
src/MetaPopInfo.h src/MetaPopInfo.cc src/Vcf.h src/Vcf.cc
-phasedstacks_SOURCES = src/phasedstacks.h src/phasedstacks.cc src/constants.h \
+phasedstacks_SOURCES = src/phasedstacks.h src/phasedstacks.cc src/constants.h src/constants.cc \
src/locus.h src/locus.cc \
src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
src/log_utils.h src/log_utils.cc \
@@ -839,8 +601,9 @@ ustacks_LDFLAGS = $(OPENMP_CFLAGS)
pstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS) $(SPARSEHASH_CFLAGS)
pstacks_LDFLAGS = $(OPENMP_CFLAGS)
pstacks_LDADD = $(BAM_LIBS)
-estacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)
+estacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS) $(BAM_CFLAGS)
estacks_LDFLAGS = $(OPENMP_CFLAGS)
+estacks_LDADD = $(BAM_LIBS)
cstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)
cstacks_LDFLAGS = $(OPENMP_CFLAGS)
hstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)
@@ -869,7 +632,7 @@ clone_filter_LDADD = $(BAM_LIBS)
dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl scripts/export_sql.pl \
scripts/sort_read_pairs.pl scripts/exec_velvet.pl scripts/load_sequences.pl \
scripts/index_radtags.pl scripts/load_radtags.pl scripts/stacks_export_notify.pl \
- scripts/integrate_alignments.py
+ scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py
dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl
nobase_pkgdata_DATA = sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql \
@@ -892,8 +655,8 @@ all: config.h
$(MAKE) $(AM_MAKEFLAGS) all-recursive
.SUFFIXES:
-.SUFFIXES: .cc .log .o .obj .test .test$(EXEEXT) .trs
-am--refresh: Makefile
+.SUFFIXES: .cc .html .log .o .obj .test .test$(EXEEXT)
+am--refresh:
@:
$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
@for dep in $?; do \
@@ -908,6 +671,7 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --foreign Makefile
+.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
@@ -928,8 +692,10 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
config.h: stamp-h1
- @test -f $@ || rm -f stamp-h1
- @test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1
+ @if test ! -f $@; then \
+ rm -f stamp-h1; \
+ $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
+ else :; fi
stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
@rm -f stamp-h1
@@ -943,18 +709,14 @@ distclean-hdr:
-rm -f config.h stamp-h1
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
+ test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
- if test -n "$$list"; then \
- echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
- $(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
- fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
- while read p p1; do if test -f $$p \
- ; then echo "$$p"; echo "$$p"; else :; fi; \
+ while read p p1; do if test -f $$p; \
+ then echo "$$p"; echo "$$p"; else :; fi; \
done | \
- sed -e 'p;s,.*/,,;n;h' \
- -e 's|.*|.|' \
+ sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -975,8 +737,7 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
- -e 's/$$/$(EXEEXT)/' \
- `; \
+ -e 's/$$/$(EXEEXT)/' `; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
@@ -991,6 +752,8 @@ src/$(DEPDIR)/$(am__dirstamp):
@: > src/$(DEPDIR)/$(am__dirstamp)
src/clone_filter-clone_filter.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/clone_filter-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/clone_filter-kmers.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/clone_filter-utils.$(OBJEXT): src/$(am__dirstamp) \
@@ -1003,12 +766,13 @@ src/clone_filter-file_io.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/clone_filter-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-clone_filter$(EXEEXT): $(clone_filter_OBJECTS) $(clone_filter_DEPENDENCIES) $(EXTRA_clone_filter_DEPENDENCIES)
+clone_filter$(EXEEXT): $(clone_filter_OBJECTS) $(clone_filter_DEPENDENCIES)
@rm -f clone_filter$(EXEEXT)
- $(AM_V_CXXLD)$(clone_filter_LINK) $(clone_filter_OBJECTS) $(clone_filter_LDADD) $(LIBS)
+ $(clone_filter_LINK) $(clone_filter_OBJECTS) $(clone_filter_LDADD) $(LIBS)
src/cstacks-cstacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/cstacks-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/cstacks-stacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/cstacks-locus.$(OBJEXT): src/$(am__dirstamp) \
@@ -1027,32 +791,38 @@ src/cstacks-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/cstacks-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-cstacks$(EXEEXT): $(cstacks_OBJECTS) $(cstacks_DEPENDENCIES) $(EXTRA_cstacks_DEPENDENCIES)
+src/cstacks-MetaPopInfo.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
+cstacks$(EXEEXT): $(cstacks_OBJECTS) $(cstacks_DEPENDENCIES)
@rm -f cstacks$(EXEEXT)
- $(AM_V_CXXLD)$(cstacks_LINK) $(cstacks_OBJECTS) $(cstacks_LDADD) $(LIBS)
+ $(cstacks_LINK) $(cstacks_OBJECTS) $(cstacks_LDADD) $(LIBS)
src/estacks-estacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/estacks-stacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/estacks-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/estacks-mstack.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/estacks-models.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/estacks-utils.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/estacks-aln_utils.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/estacks-DNASeq.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/estacks-DNANSeq.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/estacks-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-estacks$(EXEEXT): $(estacks_OBJECTS) $(estacks_DEPENDENCIES) $(EXTRA_estacks_DEPENDENCIES)
+estacks$(EXEEXT): $(estacks_OBJECTS) $(estacks_DEPENDENCIES)
@rm -f estacks$(EXEEXT)
- $(AM_V_CXXLD)$(estacks_LINK) $(estacks_OBJECTS) $(estacks_LDADD) $(LIBS)
+ $(estacks_LINK) $(estacks_OBJECTS) $(estacks_LDADD) $(LIBS)
src/genotypes-genotypes.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/genotypes-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/genotypes-utils.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/genotypes-catalog_utils.$(OBJEXT): src/$(am__dirstamp) \
@@ -1079,12 +849,13 @@ src/genotypes-renz.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/genotypes-MetaPopInfo.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-genotypes$(EXEEXT): $(genotypes_OBJECTS) $(genotypes_DEPENDENCIES) $(EXTRA_genotypes_DEPENDENCIES)
+genotypes$(EXEEXT): $(genotypes_OBJECTS) $(genotypes_DEPENDENCIES)
@rm -f genotypes$(EXEEXT)
- $(AM_V_CXXLD)$(genotypes_LINK) $(genotypes_OBJECTS) $(genotypes_LDADD) $(LIBS)
+ $(genotypes_LINK) $(genotypes_OBJECTS) $(genotypes_LDADD) $(LIBS)
src/hstacks-hstacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/hstacks-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/hstacks-stacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/hstacks-locus.$(OBJEXT): src/$(am__dirstamp) \
@@ -1101,12 +872,13 @@ src/hstacks-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/hstacks-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-hstacks$(EXEEXT): $(hstacks_OBJECTS) $(hstacks_DEPENDENCIES) $(EXTRA_hstacks_DEPENDENCIES)
+hstacks$(EXEEXT): $(hstacks_OBJECTS) $(hstacks_DEPENDENCIES)
@rm -f hstacks$(EXEEXT)
- $(AM_V_CXXLD)$(hstacks_LINK) $(hstacks_OBJECTS) $(hstacks_LDADD) $(LIBS)
+ $(hstacks_LINK) $(hstacks_OBJECTS) $(hstacks_LDADD) $(LIBS)
src/kmer_filter-kmer_filter.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/kmer_filter-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/kmer_filter-utils.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/kmer_filter-write.$(OBJEXT): src/$(am__dirstamp) \
@@ -1115,12 +887,13 @@ src/kmer_filter-kmers.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/kmer_filter-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-kmer_filter$(EXEEXT): $(kmer_filter_OBJECTS) $(kmer_filter_DEPENDENCIES) $(EXTRA_kmer_filter_DEPENDENCIES)
+kmer_filter$(EXEEXT): $(kmer_filter_OBJECTS) $(kmer_filter_DEPENDENCIES)
@rm -f kmer_filter$(EXEEXT)
- $(AM_V_CXXLD)$(kmer_filter_LINK) $(kmer_filter_OBJECTS) $(kmer_filter_LDADD) $(LIBS)
+ $(kmer_filter_LINK) $(kmer_filter_OBJECTS) $(kmer_filter_LDADD) $(LIBS)
src/phasedstacks-phasedstacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/phasedstacks-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/phasedstacks-locus.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/phasedstacks-input.$(OBJEXT): src/$(am__dirstamp) \
@@ -1133,12 +906,13 @@ src/phasedstacks-utils.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/phasedstacks-catalog_utils.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-phasedstacks$(EXEEXT): $(phasedstacks_OBJECTS) $(phasedstacks_DEPENDENCIES) $(EXTRA_phasedstacks_DEPENDENCIES)
+phasedstacks$(EXEEXT): $(phasedstacks_OBJECTS) $(phasedstacks_DEPENDENCIES)
@rm -f phasedstacks$(EXEEXT)
- $(AM_V_CXXLD)$(phasedstacks_LINK) $(phasedstacks_OBJECTS) $(phasedstacks_LDADD) $(LIBS)
+ $(phasedstacks_LINK) $(phasedstacks_OBJECTS) $(phasedstacks_LDADD) $(LIBS)
src/populations-populations.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/populations-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/populations-utils.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/populations-catalog_utils.$(OBJEXT): src/$(am__dirstamp) \
@@ -1169,12 +943,13 @@ src/populations-MetaPopInfo.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/populations-Vcf.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-populations$(EXEEXT): $(populations_OBJECTS) $(populations_DEPENDENCIES) $(EXTRA_populations_DEPENDENCIES)
+populations$(EXEEXT): $(populations_OBJECTS) $(populations_DEPENDENCIES)
@rm -f populations$(EXEEXT)
- $(AM_V_CXXLD)$(populations_LINK) $(populations_OBJECTS) $(populations_LDADD) $(LIBS)
+ $(populations_LINK) $(populations_OBJECTS) $(populations_LDADD) $(LIBS)
src/process_radtags-process_radtags.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/process_radtags-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/process_radtags-utils.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/process_radtags-log_utils.$(OBJEXT): src/$(am__dirstamp) \
@@ -1189,12 +964,13 @@ src/process_radtags-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/process_radtags-renz.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-process_radtags$(EXEEXT): $(process_radtags_OBJECTS) $(process_radtags_DEPENDENCIES) $(EXTRA_process_radtags_DEPENDENCIES)
+process_radtags$(EXEEXT): $(process_radtags_OBJECTS) $(process_radtags_DEPENDENCIES)
@rm -f process_radtags$(EXEEXT)
- $(AM_V_CXXLD)$(process_radtags_LINK) $(process_radtags_OBJECTS) $(process_radtags_LDADD) $(LIBS)
+ $(process_radtags_LINK) $(process_radtags_OBJECTS) $(process_radtags_LDADD) $(LIBS)
src/process_shortreads-process_shortreads.$(OBJEXT): \
src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/process_shortreads-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/process_shortreads-clean.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/process_shortreads-file_io.$(OBJEXT): src/$(am__dirstamp) \
@@ -1209,16 +985,19 @@ src/process_shortreads-kmers.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/process_shortreads-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-process_shortreads$(EXEEXT): $(process_shortreads_OBJECTS) $(process_shortreads_DEPENDENCIES) $(EXTRA_process_shortreads_DEPENDENCIES)
+process_shortreads$(EXEEXT): $(process_shortreads_OBJECTS) $(process_shortreads_DEPENDENCIES)
@rm -f process_shortreads$(EXEEXT)
- $(AM_V_CXXLD)$(process_shortreads_LINK) $(process_shortreads_OBJECTS) $(process_shortreads_LDADD) $(LIBS)
+ $(process_shortreads_LINK) $(process_shortreads_OBJECTS) $(process_shortreads_LDADD) $(LIBS)
src/pstacks-pstacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/pstacks-stacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/pstacks-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/pstacks-mstack.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/pstacks-log_utils.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/pstacks-DNANSeq.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/pstacks-DNASeq.$(OBJEXT): src/$(am__dirstamp) \
@@ -1227,14 +1006,17 @@ src/pstacks-models.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/pstacks-utils.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/pstacks-aln_utils.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/pstacks-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-pstacks$(EXEEXT): $(pstacks_OBJECTS) $(pstacks_DEPENDENCIES) $(EXTRA_pstacks_DEPENDENCIES)
+pstacks$(EXEEXT): $(pstacks_OBJECTS) $(pstacks_DEPENDENCIES)
@rm -f pstacks$(EXEEXT)
- $(AM_V_CXXLD)$(pstacks_LINK) $(pstacks_OBJECTS) $(pstacks_LDADD) $(LIBS)
+ $(pstacks_LINK) $(pstacks_OBJECTS) $(pstacks_LDADD) $(LIBS)
src/rxstacks-rxstacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/rxstacks-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/rxstacks-stacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/rxstacks-locus.$(OBJEXT): src/$(am__dirstamp) \
@@ -1255,14 +1037,17 @@ src/rxstacks-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/rxstacks-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/rxstacks-catalog_utils.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/rxstacks-MetaPopInfo.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-rxstacks$(EXEEXT): $(rxstacks_OBJECTS) $(rxstacks_DEPENDENCIES) $(EXTRA_rxstacks_DEPENDENCIES)
+rxstacks$(EXEEXT): $(rxstacks_OBJECTS) $(rxstacks_DEPENDENCIES)
@rm -f rxstacks$(EXEEXT)
- $(AM_V_CXXLD)$(rxstacks_LINK) $(rxstacks_OBJECTS) $(rxstacks_LDADD) $(LIBS)
+ $(rxstacks_LINK) $(rxstacks_OBJECTS) $(rxstacks_LDADD) $(LIBS)
src/sstacks-sstacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/sstacks-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/sstacks-stacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/sstacks-locus.$(OBJEXT): src/$(am__dirstamp) \
@@ -1281,14 +1066,19 @@ src/sstacks-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/sstacks-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-sstacks$(EXEEXT): $(sstacks_OBJECTS) $(sstacks_DEPENDENCIES) $(EXTRA_sstacks_DEPENDENCIES)
+src/sstacks-catalog_utils.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
+src/sstacks-MetaPopInfo.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
+sstacks$(EXEEXT): $(sstacks_OBJECTS) $(sstacks_DEPENDENCIES)
@rm -f sstacks$(EXEEXT)
- $(AM_V_CXXLD)$(sstacks_LINK) $(sstacks_OBJECTS) $(sstacks_LDADD) $(LIBS)
+ $(sstacks_LINK) $(sstacks_OBJECTS) $(sstacks_LDADD) $(LIBS)
src/ustacks-ustacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/ustacks-stacks.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
+src/ustacks-constants.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
src/ustacks-mstack.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/ustacks-mst.$(OBJEXT): src/$(am__dirstamp) \
@@ -1309,17 +1099,13 @@ src/ustacks-aln_utils.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/ustacks-input.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-
-ustacks$(EXEEXT): $(ustacks_OBJECTS) $(ustacks_DEPENDENCIES) $(EXTRA_ustacks_DEPENDENCIES)
+ustacks$(EXEEXT): $(ustacks_OBJECTS) $(ustacks_DEPENDENCIES)
@rm -f ustacks$(EXEEXT)
- $(AM_V_CXXLD)$(ustacks_LINK) $(ustacks_OBJECTS) $(ustacks_LDADD) $(LIBS)
+ $(ustacks_LINK) $(ustacks_OBJECTS) $(ustacks_LDADD) $(LIBS)
install-dist_binSCRIPTS: $(dist_bin_SCRIPTS)
@$(NORMAL_INSTALL)
+ test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
@list='$(dist_bin_SCRIPTS)'; test -n "$(bindir)" || list=; \
- if test -n "$$list"; then \
- echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
- $(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
- fi; \
for p in $$list; do \
if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
if test -f "$$d$$p"; then echo "$$d$$p"; echo "$$p"; else :; fi; \
@@ -1347,17 +1133,174 @@ uninstall-dist_binSCRIPTS:
@list='$(dist_bin_SCRIPTS)'; test -n "$(bindir)" || exit 0; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 's,.*/,,;$(transform)'`; \
- dir='$(DESTDIR)$(bindir)'; $(am__uninstall_files_from_dir)
+ test -n "$$list" || exit 0; \
+ echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+ cd "$(DESTDIR)$(bindir)" && rm -f $$files
mostlyclean-compile:
-rm -f *.$(OBJEXT)
- -rm -f src/*.$(OBJEXT)
+ -rm -f src/clone_filter-clean.$(OBJEXT)
+ -rm -f src/clone_filter-clone_filter.$(OBJEXT)
+ -rm -f src/clone_filter-constants.$(OBJEXT)
+ -rm -f src/clone_filter-file_io.$(OBJEXT)
+ -rm -f src/clone_filter-input.$(OBJEXT)
+ -rm -f src/clone_filter-kmers.$(OBJEXT)
+ -rm -f src/clone_filter-utils.$(OBJEXT)
+ -rm -f src/clone_filter-write.$(OBJEXT)
+ -rm -f src/cstacks-DNANSeq.$(OBJEXT)
+ -rm -f src/cstacks-DNASeq.$(OBJEXT)
+ -rm -f src/cstacks-MetaPopInfo.$(OBJEXT)
+ -rm -f src/cstacks-aln_utils.$(OBJEXT)
+ -rm -f src/cstacks-constants.$(OBJEXT)
+ -rm -f src/cstacks-cstacks.$(OBJEXT)
+ -rm -f src/cstacks-input.$(OBJEXT)
+ -rm -f src/cstacks-kmers.$(OBJEXT)
+ -rm -f src/cstacks-locus.$(OBJEXT)
+ -rm -f src/cstacks-sql_utilities.$(OBJEXT)
+ -rm -f src/cstacks-stacks.$(OBJEXT)
+ -rm -f src/cstacks-utils.$(OBJEXT)
+ -rm -f src/estacks-DNANSeq.$(OBJEXT)
+ -rm -f src/estacks-DNASeq.$(OBJEXT)
+ -rm -f src/estacks-aln_utils.$(OBJEXT)
+ -rm -f src/estacks-constants.$(OBJEXT)
+ -rm -f src/estacks-estacks.$(OBJEXT)
+ -rm -f src/estacks-input.$(OBJEXT)
+ -rm -f src/estacks-models.$(OBJEXT)
+ -rm -f src/estacks-mstack.$(OBJEXT)
+ -rm -f src/estacks-stacks.$(OBJEXT)
+ -rm -f src/estacks-utils.$(OBJEXT)
+ -rm -f src/genotypes-DNANSeq.$(OBJEXT)
+ -rm -f src/genotypes-DNASeq.$(OBJEXT)
+ -rm -f src/genotypes-MetaPopInfo.$(OBJEXT)
+ -rm -f src/genotypes-aln_utils.$(OBJEXT)
+ -rm -f src/genotypes-catalog_utils.$(OBJEXT)
+ -rm -f src/genotypes-constants.$(OBJEXT)
+ -rm -f src/genotypes-genotype_dictionaries.$(OBJEXT)
+ -rm -f src/genotypes-genotypes.$(OBJEXT)
+ -rm -f src/genotypes-input.$(OBJEXT)
+ -rm -f src/genotypes-locus.$(OBJEXT)
+ -rm -f src/genotypes-log_utils.$(OBJEXT)
+ -rm -f src/genotypes-renz.$(OBJEXT)
+ -rm -f src/genotypes-sql_utilities.$(OBJEXT)
+ -rm -f src/genotypes-stacks.$(OBJEXT)
+ -rm -f src/genotypes-utils.$(OBJEXT)
+ -rm -f src/hstacks-DNANSeq.$(OBJEXT)
+ -rm -f src/hstacks-DNASeq.$(OBJEXT)
+ -rm -f src/hstacks-constants.$(OBJEXT)
+ -rm -f src/hstacks-hstacks.$(OBJEXT)
+ -rm -f src/hstacks-input.$(OBJEXT)
+ -rm -f src/hstacks-kmers.$(OBJEXT)
+ -rm -f src/hstacks-locus.$(OBJEXT)
+ -rm -f src/hstacks-sql_utilities.$(OBJEXT)
+ -rm -f src/hstacks-stacks.$(OBJEXT)
+ -rm -f src/hstacks-utils.$(OBJEXT)
+ -rm -f src/kmer_filter-constants.$(OBJEXT)
+ -rm -f src/kmer_filter-input.$(OBJEXT)
+ -rm -f src/kmer_filter-kmer_filter.$(OBJEXT)
+ -rm -f src/kmer_filter-kmers.$(OBJEXT)
+ -rm -f src/kmer_filter-utils.$(OBJEXT)
+ -rm -f src/kmer_filter-write.$(OBJEXT)
+ -rm -f src/phasedstacks-catalog_utils.$(OBJEXT)
+ -rm -f src/phasedstacks-constants.$(OBJEXT)
+ -rm -f src/phasedstacks-input.$(OBJEXT)
+ -rm -f src/phasedstacks-locus.$(OBJEXT)
+ -rm -f src/phasedstacks-log_utils.$(OBJEXT)
+ -rm -f src/phasedstacks-phasedstacks.$(OBJEXT)
+ -rm -f src/phasedstacks-sql_utilities.$(OBJEXT)
+ -rm -f src/phasedstacks-utils.$(OBJEXT)
+ -rm -f src/populations-DNANSeq.$(OBJEXT)
+ -rm -f src/populations-DNASeq.$(OBJEXT)
+ -rm -f src/populations-MetaPopInfo.$(OBJEXT)
+ -rm -f src/populations-Vcf.$(OBJEXT)
+ -rm -f src/populations-aln_utils.$(OBJEXT)
+ -rm -f src/populations-catalog_utils.$(OBJEXT)
+ -rm -f src/populations-constants.$(OBJEXT)
+ -rm -f src/populations-export_formats.$(OBJEXT)
+ -rm -f src/populations-genotype_dictionaries.$(OBJEXT)
+ -rm -f src/populations-input.$(OBJEXT)
+ -rm -f src/populations-locus.$(OBJEXT)
+ -rm -f src/populations-log_utils.$(OBJEXT)
+ -rm -f src/populations-populations.$(OBJEXT)
+ -rm -f src/populations-renz.$(OBJEXT)
+ -rm -f src/populations-sql_utilities.$(OBJEXT)
+ -rm -f src/populations-stacks.$(OBJEXT)
+ -rm -f src/populations-utils.$(OBJEXT)
+ -rm -f src/process_radtags-clean.$(OBJEXT)
+ -rm -f src/process_radtags-constants.$(OBJEXT)
+ -rm -f src/process_radtags-file_io.$(OBJEXT)
+ -rm -f src/process_radtags-input.$(OBJEXT)
+ -rm -f src/process_radtags-log_utils.$(OBJEXT)
+ -rm -f src/process_radtags-process_radtags.$(OBJEXT)
+ -rm -f src/process_radtags-renz.$(OBJEXT)
+ -rm -f src/process_radtags-utils.$(OBJEXT)
+ -rm -f src/process_radtags-write.$(OBJEXT)
+ -rm -f src/process_shortreads-clean.$(OBJEXT)
+ -rm -f src/process_shortreads-constants.$(OBJEXT)
+ -rm -f src/process_shortreads-file_io.$(OBJEXT)
+ -rm -f src/process_shortreads-input.$(OBJEXT)
+ -rm -f src/process_shortreads-kmers.$(OBJEXT)
+ -rm -f src/process_shortreads-log_utils.$(OBJEXT)
+ -rm -f src/process_shortreads-process_shortreads.$(OBJEXT)
+ -rm -f src/process_shortreads-utils.$(OBJEXT)
+ -rm -f src/process_shortreads-write.$(OBJEXT)
+ -rm -f src/pstacks-DNANSeq.$(OBJEXT)
+ -rm -f src/pstacks-DNASeq.$(OBJEXT)
+ -rm -f src/pstacks-aln_utils.$(OBJEXT)
+ -rm -f src/pstacks-constants.$(OBJEXT)
+ -rm -f src/pstacks-input.$(OBJEXT)
+ -rm -f src/pstacks-log_utils.$(OBJEXT)
+ -rm -f src/pstacks-models.$(OBJEXT)
+ -rm -f src/pstacks-mstack.$(OBJEXT)
+ -rm -f src/pstacks-pstacks.$(OBJEXT)
+ -rm -f src/pstacks-stacks.$(OBJEXT)
+ -rm -f src/pstacks-utils.$(OBJEXT)
+ -rm -f src/rxstacks-DNANSeq.$(OBJEXT)
+ -rm -f src/rxstacks-DNASeq.$(OBJEXT)
+ -rm -f src/rxstacks-MetaPopInfo.$(OBJEXT)
+ -rm -f src/rxstacks-aln_utils.$(OBJEXT)
+ -rm -f src/rxstacks-catalog_utils.$(OBJEXT)
+ -rm -f src/rxstacks-constants.$(OBJEXT)
+ -rm -f src/rxstacks-input.$(OBJEXT)
+ -rm -f src/rxstacks-locus.$(OBJEXT)
+ -rm -f src/rxstacks-models.$(OBJEXT)
+ -rm -f src/rxstacks-mst.$(OBJEXT)
+ -rm -f src/rxstacks-rxstacks.$(OBJEXT)
+ -rm -f src/rxstacks-sql_utilities.$(OBJEXT)
+ -rm -f src/rxstacks-stacks.$(OBJEXT)
+ -rm -f src/rxstacks-utils.$(OBJEXT)
+ -rm -f src/sstacks-DNANSeq.$(OBJEXT)
+ -rm -f src/sstacks-DNASeq.$(OBJEXT)
+ -rm -f src/sstacks-MetaPopInfo.$(OBJEXT)
+ -rm -f src/sstacks-aln_utils.$(OBJEXT)
+ -rm -f src/sstacks-catalog_utils.$(OBJEXT)
+ -rm -f src/sstacks-constants.$(OBJEXT)
+ -rm -f src/sstacks-input.$(OBJEXT)
+ -rm -f src/sstacks-kmers.$(OBJEXT)
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+ -rm -f src/sstacks-sstacks.$(OBJEXT)
+ -rm -f src/sstacks-stacks.$(OBJEXT)
+ -rm -f src/sstacks-utils.$(OBJEXT)
+ -rm -f src/ustacks-DNANSeq.$(OBJEXT)
+ -rm -f src/ustacks-DNASeq.$(OBJEXT)
+ -rm -f src/ustacks-aln_utils.$(OBJEXT)
+ -rm -f src/ustacks-cmb.$(OBJEXT)
+ -rm -f src/ustacks-constants.$(OBJEXT)
+ -rm -f src/ustacks-input.$(OBJEXT)
+ -rm -f src/ustacks-kmers.$(OBJEXT)
+ -rm -f src/ustacks-models.$(OBJEXT)
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distclean-compile:
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src/cstacks-sql_utilities.o: src/sql_utilities.cc
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src/genotypes-DNASeq.o: src/DNASeq.cc
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src/hstacks-stacks.o: src/stacks.cc
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src/hstacks-locus.o: src/locus.cc
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src/hstacks-kmers.o: src/kmers.cc
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src/pstacks-pstacks.o: src/pstacks.cc
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src/pstacks-pstacks.obj: src/pstacks.cc
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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src/pstacks-stacks.o: src/stacks.cc
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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src/pstacks-stacks.obj: src/stacks.cc
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+
+src/pstacks-constants.o: src/constants.cc
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pstacks_CXXFLAGS) $(CXXFLAGS) -MT src/pstacks-constants.o -MD -MP -MF src/$(DEPDIR)/pstacks-constants.Tpo -c -o src/pstacks-constants.o `test -f 'src/constants.cc' || echo '$(srcdir)/'`src/constants.cc
+ at am__fastdepCXX_TRUE@ $(am__mv) src/$(DEPDIR)/pstacks-constants.Tpo src/$(DEPDIR)/pstacks-constants.Po
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+
+src/pstacks-constants.obj: src/constants.cc
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pstacks_CXXFLAGS) $(CXXFLAGS) -MT src/pstacks-constants.obj -MD -MP -MF src/$(DEPDIR)/pstacks-constants.Tpo -c -o src/pstacks-constants.obj `if test -f 'src/constants.cc'; then $(CYGPATH_W) 'src/constants.cc'; else $(CYGPATH_W) '$(srcdir)/src/constants.cc'; fi`
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src/pstacks-mstack.o: src/mstack.cc
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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src/pstacks-mstack.obj: src/mstack.cc
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+
+src/pstacks-log_utils.o: src/log_utils.cc
+ at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pstacks_CXXFLAGS) $(CXXFLAGS) -MT src/pstacks-log_utils.o -MD -MP -MF src/$(DEPDIR)/pstacks-log_utils.Tpo -c -o src/pstacks-log_utils.o `test -f 'src/log_utils.cc' || echo '$(srcdir)/'`src/log_utils.cc
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+src/pstacks-log_utils.obj: src/log_utils.cc
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src/pstacks-DNANSeq.o: src/DNANSeq.cc
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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src/pstacks-DNANSeq.obj: src/DNANSeq.cc
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src/pstacks-DNASeq.o: src/DNASeq.cc
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src/pstacks-models.o: src/models.cc
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src/pstacks-models.obj: src/models.cc
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src/pstacks-utils.o: src/utils.cc
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src/pstacks-input.o: src/input.cc
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src/pstacks-input.obj: src/input.cc
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src/rxstacks-rxstacks.o: src/rxstacks.cc
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src/rxstacks-rxstacks.obj: src/rxstacks.cc
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src/rxstacks-stacks.o: src/stacks.cc
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src/rxstacks-stacks.obj: src/stacks.cc
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src/rxstacks-locus.o: src/locus.cc
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src/rxstacks-locus.obj: src/locus.cc
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src/rxstacks-DNANSeq.o: src/DNANSeq.cc
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src/rxstacks-DNANSeq.obj: src/DNANSeq.cc
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src/rxstacks-DNASeq.o: src/DNASeq.cc
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src/rxstacks-DNASeq.obj: src/DNASeq.cc
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src/rxstacks-mst.o: src/mst.cc
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src/rxstacks-sql_utilities.obj: src/sql_utilities.cc
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src/rxstacks-MetaPopInfo.o: src/MetaPopInfo.cc
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src/rxstacks-MetaPopInfo.obj: src/MetaPopInfo.cc
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src/sstacks-sstacks.o: src/sstacks.cc
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src/sstacks-stacks.o: src/stacks.cc
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src/sstacks-stacks.obj: src/stacks.cc
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src/sstacks-locus.o: src/locus.cc
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src/sstacks-locus.obj: src/locus.cc
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src/sstacks-kmers.o: src/kmers.cc
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src/sstacks-aln_utils.o: src/aln_utils.cc
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src/sstacks-aln_utils.obj: src/aln_utils.cc
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src/sstacks-DNASeq.o: src/DNASeq.cc
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src/sstacks-DNASeq.obj: src/DNASeq.cc
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src/sstacks-DNANSeq.o: src/DNANSeq.cc
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src/sstacks-utils.o: src/utils.cc
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src/sstacks-utils.obj: src/utils.cc
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src/sstacks-input.o: src/input.cc
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src/sstacks-input.obj: src/input.cc
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src/sstacks-sql_utilities.o: src/sql_utilities.cc
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src/sstacks-sql_utilities.obj: src/sql_utilities.cc
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src/ustacks-ustacks.o: src/ustacks.cc
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src/ustacks-ustacks.obj: src/ustacks.cc
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src/ustacks-stacks.o: src/stacks.cc
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src/ustacks-stacks.obj: src/stacks.cc
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src/ustacks-mstack.o: src/mstack.cc
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src/ustacks-mstack.obj: src/mstack.cc
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src/ustacks-mst.o: src/mst.cc
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src/ustacks-mst.obj: src/mst.cc
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src/ustacks-cmb.o: src/cmb.cc
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src/ustacks-cmb.obj: src/cmb.cc
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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src/ustacks-DNASeq.o: src/DNASeq.cc
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src/ustacks-DNASeq.obj: src/DNASeq.cc
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+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(ustacks_CXXFLAGS) $(CXXFLAGS) -c -o src/ustacks-aln_utils.obj `if test -f 'src/aln_utils.cc'; then $(CYGPATH_W) 'src/aln_utils.cc'; else $(CYGPATH_W) '$(srcdir)/src/aln_utils.cc'; fi`
src/ustacks-input.o: src/input.cc
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+ at am__fastdepCXX_TRUE@ $(am__mv) src/$(DEPDIR)/ustacks-input.Tpo src/$(DEPDIR)/ustacks-input.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='src/input.cc' object='src/ustacks-input.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(ustacks_CXXFLAGS) $(CXXFLAGS) -c -o src/ustacks-input.o `test -f 'src/input.cc' || echo '$(srcdir)/'`src/input.cc
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+ at am__fastdepCXX_TRUE@ $(am__mv) src/$(DEPDIR)/ustacks-input.Tpo src/$(DEPDIR)/ustacks-input.Po
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+ at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(ustacks_CXXFLAGS) $(CXXFLAGS) -c -o src/ustacks-input.obj `if test -f 'src/input.cc'; then $(CYGPATH_W) 'src/input.cc'; else $(CYGPATH_W) '$(srcdir)/src/input.cc'; fi`
install-nobase_pkgdataDATA: $(nobase_pkgdata_DATA)
@$(NORMAL_INSTALL)
+ test -z "$(pkgdatadir)" || $(MKDIR_P) "$(DESTDIR)$(pkgdatadir)"
@list='$(nobase_pkgdata_DATA)'; test -n "$(pkgdatadir)" || list=; \
- if test -n "$$list"; then \
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- $(MKDIR_P) "$(DESTDIR)$(pkgdatadir)" || exit 1; \
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$(am__nobase_list) | while read dir files; do \
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else xfiles="$$xfiles $(srcdir)/$$file"; fi; done; \
test -z "$$xfiles" || { \
test "x$$dir" = x. || { \
- echo " $(MKDIR_P) '$(DESTDIR)$(pkgdatadir)/$$dir'"; \
+ echo "$(MKDIR_P) '$(DESTDIR)$(pkgdatadir)/$$dir'"; \
$(MKDIR_P) "$(DESTDIR)$(pkgdatadir)/$$dir"; }; \
echo " $(INSTALL_DATA) $$xfiles '$(DESTDIR)$(pkgdatadir)/$$dir'"; \
$(INSTALL_DATA) $$xfiles "$(DESTDIR)$(pkgdatadir)/$$dir" || exit $$?; }; \
@@ -3405,28 +3659,27 @@ uninstall-nobase_pkgdataDATA:
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$(am__nobase_strip_setup); files=`$(am__nobase_strip)`; \
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+ cd "$(DESTDIR)$(pkgdatadir)" && rm -f $$files
# This directory's subdirectories are mostly independent; you can cd
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-$(am__recursive_targets):
- @fail=; \
- if $(am__make_keepgoing); then \
- failcom='fail=yes'; \
- else \
- failcom='exit 1'; \
- fi; \
+# into them and run `make' without going through this Makefile.
+# To change the values of `make' variables: instead of editing Makefiles,
+# (1) if the variable is set in `config.status', edit `config.status'
+# (which will cause the Makefiles to be regenerated when you run `make');
+# (2) otherwise, pass the desired values on the `make' command line.
+$(RECURSIVE_TARGETS):
+ @fail= failcom='exit 1'; \
+ for f in x $$MAKEFLAGS; do \
+ case $$f in \
+ *=* | --[!k]*);; \
+ *k*) failcom='fail=yes';; \
+ esac; \
+ done; \
dot_seen=no; \
target=`echo $@ | sed s/-recursive//`; \
- case "$@" in \
- distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
- *) list='$(SUBDIRS)' ;; \
- esac; \
- for subdir in $$list; do \
+ list='$(SUBDIRS)'; for subdir in $$list; do \
echo "Making $$target in $$subdir"; \
if test "$$subdir" = "."; then \
dot_seen=yes; \
@@ -3441,12 +3694,57 @@ $(am__recursive_targets):
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fi; test -z "$$fail"
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- $(am__define_uniq_tagged_files); mkid -fID $$unique
-tags: tags-recursive
-TAGS: tags
+$(RECURSIVE_CLEAN_TARGETS):
+ @fail= failcom='exit 1'; \
+ for f in x $$MAKEFLAGS; do \
+ case $$f in \
+ *=* | --[!k]*);; \
+ *k*) failcom='fail=yes';; \
+ esac; \
+ done; \
+ dot_seen=no; \
+ case "$@" in \
+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
+ *) list='$(SUBDIRS)' ;; \
+ esac; \
+ rev=''; for subdir in $$list; do \
+ if test "$$subdir" = "."; then :; else \
+ rev="$$subdir $$rev"; \
+ fi; \
+ done; \
+ rev="$$rev ."; \
+ target=`echo $@ | sed s/-recursive//`; \
+ for subdir in $$rev; do \
+ echo "Making $$target in $$subdir"; \
+ if test "$$subdir" = "."; then \
+ local_target="$$target-am"; \
+ else \
+ local_target="$$target"; \
+ fi; \
+ ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+ || eval $$failcom; \
+ done && test -z "$$fail"
+tags-recursive:
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+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+ done
+ctags-recursive:
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
+ done
-tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in files) print i; }; }'`; \
+ mkid -fID $$unique
+tags: TAGS
+
+TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
set x; \
here=`pwd`; \
if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
@@ -3462,7 +3760,12 @@ tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
fi; \
done; \
- $(am__define_uniq_tagged_files); \
+ list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in files) print i; }; }'`; \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
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-CTAGS: ctags
-ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
- $(am__define_uniq_tagged_files); \
+ctags: CTAGS
+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
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test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
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- @list='$(RECHECK_LOGS)'; test -z "$$list" || rm -f $$list
- @list='$(RECHECK_LOGS:.log=.trs)'; test -z "$$list" || rm -f $$list
- @test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
- @set +e; $(am__set_TESTS_bases); \
- log_list=`for i in $$bases; do echo $$i.log; done`; \
- trs_list=`for i in $$bases; do echo $$i.trs; done`; \
- log_list=`echo $$log_list`; trs_list=`echo $$trs_list`; \
- $(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) TEST_LOGS="$$log_list"; \
- exit $$?;
-recheck: all
+ @list='$(RECHECK_LOGS)'; test -z "$$list" || rm -f $$list
@test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
- @set +e; $(am__set_TESTS_bases); \
- bases=`for i in $$bases; do echo $$i; done \
- | $(am__list_recheck_tests)` || exit 1; \
- log_list=`for i in $$bases; do echo $$i.log; done`; \
- log_list=`echo $$log_list`; \
- $(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) \
- am__force_recheck=am--force-recheck \
- TEST_LOGS="$$log_list"; \
- exit $$?
+ @list='$(TEST_LOGS)'; \
+ list=`for f in $$list; do \
+ test .log = $$f || echo $$f; \
+ done | tr '\012\015' ' '`; \
+ $(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) TEST_LOGS="$$list"
+
+.log.html:
+ @list='$(RST2HTML) $$RST2HTML rst2html rst2html.py'; \
+ for r2h in $$list; do \
+ if ($$r2h --version) >/dev/null 2>&1; then \
+ R2H=$$r2h; \
+ fi; \
+ done; \
+ if test -z "$$R2H"; then \
+ echo >&2 "cannot find rst2html, cannot create $@"; \
+ exit 2; \
+ fi; \
+ $$R2H $< >$@.tmp
+ @mv $@.tmp $@
+
+# Be sure to run check first, and then to convert the result.
+# Beware of concurrent executions. Run "check" not "check-TESTS", as
+# check-SCRIPTS and other dependencies are rebuilt by the former only.
+# And expect check to fail.
+check-html:
+ @if $(MAKE) $(AM_MAKEFLAGS) check; then \
+ rv=0; else rv=$$?; \
+ fi; \
+ $(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_HTML) || exit 4; \
+ exit $$rv
+recheck recheck-html:
+ @target=`echo $@ | sed 's,^re,,'`; \
+ list='$(TEST_LOGS)'; \
+ list=`for f in $$list; do \
+ test -f $$f || continue; \
+ if read line < $$f; then \
+ case $$line in FAIL*|XPASS*) echo $$f;; esac; \
+ else echo $$f; fi; \
+ done | tr '\012\015' ' '`; \
+ $(MAKE) $(AM_MAKEFLAGS) $$target AM_MAKEFLAGS='$(AM_MAKEFLAGS) TEST_LOGS="'"$$list"'"'
tests/process_radtags.t.log: tests/process_radtags.t
- @p='tests/process_radtags.t'; \
- b='tests/process_radtags.t'; \
- $(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
- --log-file $$b.log --trs-file $$b.trs \
- $(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
- "$$tst" $(AM_TESTS_FD_REDIRECT)
+ @p='tests/process_radtags.t'; $(am__check_pre) $(LOG_COMPILE) "$$tst" $(am__check_post)
tests/kmer_filter.t.log: tests/kmer_filter.t
- @p='tests/kmer_filter.t'; \
- b='tests/kmer_filter.t'; \
- $(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
- --log-file $$b.log --trs-file $$b.trs \
- $(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
- "$$tst" $(AM_TESTS_FD_REDIRECT)
+ @p='tests/kmer_filter.t'; $(am__check_pre) $(LOG_COMPILE) "$$tst" $(am__check_post)
tests/ustacks.t.log: tests/ustacks.t
- @p='tests/ustacks.t'; \
- b='tests/ustacks.t'; \
- $(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
- --log-file $$b.log --trs-file $$b.trs \
- $(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
- "$$tst" $(AM_TESTS_FD_REDIRECT)
+ @p='tests/ustacks.t'; $(am__check_pre) $(LOG_COMPILE) "$$tst" $(am__check_post)
tests/pstacks.t.log: tests/pstacks.t
- @p='tests/pstacks.t'; \
- b='tests/pstacks.t'; \
- $(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
- --log-file $$b.log --trs-file $$b.trs \
- $(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
- "$$tst" $(AM_TESTS_FD_REDIRECT)
+ @p='tests/pstacks.t'; $(am__check_pre) $(LOG_COMPILE) "$$tst" $(am__check_post)
.test.log:
- @p='$<'; \
- $(am__set_b); \
- $(am__check_pre) $(TEST_LOG_DRIVER) --test-name "$$f" \
- --log-file $$b.log --trs-file $$b.trs \
- $(am__common_driver_flags) $(AM_TEST_LOG_DRIVER_FLAGS) $(TEST_LOG_DRIVER_FLAGS) -- $(TEST_LOG_COMPILE) \
- "$$tst" $(AM_TESTS_FD_REDIRECT)
+ @p='$<'; $(am__check_pre) $(TEST_LOG_COMPILE) "$$tst" $(am__check_post)
@am__EXEEXT_TRUE at .test$(EXEEXT).log:
- at am__EXEEXT_TRUE@ @p='$<'; \
- at am__EXEEXT_TRUE@ $(am__set_b); \
- at am__EXEEXT_TRUE@ $(am__check_pre) $(TEST_LOG_DRIVER) --test-name "$$f" \
- at am__EXEEXT_TRUE@ --log-file $$b.log --trs-file $$b.trs \
- at am__EXEEXT_TRUE@ $(am__common_driver_flags) $(AM_TEST_LOG_DRIVER_FLAGS) $(TEST_LOG_DRIVER_FLAGS) -- $(TEST_LOG_COMPILE) \
- at am__EXEEXT_TRUE@ "$$tst" $(AM_TESTS_FD_REDIRECT)
+ at am__EXEEXT_TRUE@ @p='$<'; $(am__check_pre) $(TEST_LOG_COMPILE) "$$tst" $(am__check_post)
distdir: $(DISTFILES)
$(am__remove_distdir)
@@ -3731,10 +3997,13 @@ distdir: $(DISTFILES)
done
@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
if test "$$subdir" = .; then :; else \
- $(am__make_dryrun) \
- || test -d "$(distdir)/$$subdir" \
- || $(MKDIR_P) "$(distdir)/$$subdir" \
- || exit 1; \
+ test -d "$(distdir)/$$subdir" \
+ || $(MKDIR_P) "$(distdir)/$$subdir" \
+ || exit 1; \
+ fi; \
+ done
+ @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+ if test "$$subdir" = .; then :; else \
dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
$(am__relativize); \
new_distdir=$$reldir; \
@@ -3763,42 +4032,36 @@ distdir: $(DISTFILES)
|| chmod -R a+r "$(distdir)"
dist-gzip: distdir
tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
- $(am__post_remove_distdir)
+ $(am__remove_distdir)
dist-bzip2: distdir
- tardir=$(distdir) && $(am__tar) | BZIP2=$${BZIP2--9} bzip2 -c >$(distdir).tar.bz2
- $(am__post_remove_distdir)
+ tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
+ $(am__remove_distdir)
-dist-lzip: distdir
- tardir=$(distdir) && $(am__tar) | lzip -c $${LZIP_OPT--9} >$(distdir).tar.lz
- $(am__post_remove_distdir)
+dist-lzma: distdir
+ tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
+ $(am__remove_distdir)
dist-xz: distdir
- tardir=$(distdir) && $(am__tar) | XZ_OPT=$${XZ_OPT--e} xz -c >$(distdir).tar.xz
- $(am__post_remove_distdir)
+ tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz
+ $(am__remove_distdir)
dist-tarZ: distdir
- @echo WARNING: "Support for distribution archives compressed with" \
- "legacy program 'compress' is deprecated." >&2
- @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
- $(am__post_remove_distdir)
+ $(am__remove_distdir)
dist-shar: distdir
- @echo WARNING: "Support for shar distribution archives is" \
- "deprecated." >&2
- @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
- $(am__post_remove_distdir)
+ $(am__remove_distdir)
dist-zip: distdir
-rm -f $(distdir).zip
zip -rq $(distdir).zip $(distdir)
- $(am__post_remove_distdir)
+ $(am__remove_distdir)
-dist dist-all:
- $(MAKE) $(AM_MAKEFLAGS) $(DIST_TARGETS) am__post_remove_distdir='@:'
- $(am__post_remove_distdir)
+dist dist-all: distdir
+ tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+ $(am__remove_distdir)
# This target untars the dist file and tries a VPATH configuration. Then
# it guarantees that the distribution is self-contained by making another
@@ -3809,8 +4072,8 @@ distcheck: dist
GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
*.tar.bz2*) \
bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
- *.tar.lz*) \
- lzip -dc $(distdir).tar.lz | $(am__untar) ;;\
+ *.tar.lzma*) \
+ lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
*.tar.xz*) \
xz -dc $(distdir).tar.xz | $(am__untar) ;;\
*.tar.Z*) \
@@ -3820,19 +4083,17 @@ distcheck: dist
*.zip*) \
unzip $(distdir).zip ;;\
esac
- chmod -R a-w $(distdir)
- chmod u+w $(distdir)
- mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
+ chmod -R a-w $(distdir); chmod u+w $(distdir)
+ mkdir $(distdir)/_build
+ mkdir $(distdir)/_inst
chmod a-w $(distdir)
test -d $(distdir)/_build || exit 0; \
dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
&& dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
&& am__cwd=`pwd` \
- && $(am__cd) $(distdir)/_build/sub \
- && ../../configure \
- $(AM_DISTCHECK_CONFIGURE_FLAGS) \
+ && $(am__cd) $(distdir)/_build \
+ && ../configure --srcdir=.. --prefix="$$dc_install_base" \
$(DISTCHECK_CONFIGURE_FLAGS) \
- --srcdir=../.. --prefix="$$dc_install_base" \
&& $(MAKE) $(AM_MAKEFLAGS) \
&& $(MAKE) $(AM_MAKEFLAGS) dvi \
&& $(MAKE) $(AM_MAKEFLAGS) check \
@@ -3855,21 +4116,13 @@ distcheck: dist
&& $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
&& cd "$$am__cwd" \
|| exit 1
- $(am__post_remove_distdir)
+ $(am__remove_distdir)
@(echo "$(distdir) archives ready for distribution: "; \
list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
distuninstallcheck:
- @test -n '$(distuninstallcheck_dir)' || { \
- echo 'ERROR: trying to run $@ with an empty' \
- '$$(distuninstallcheck_dir)' >&2; \
- exit 1; \
- }; \
- $(am__cd) '$(distuninstallcheck_dir)' || { \
- echo 'ERROR: cannot chdir into $(distuninstallcheck_dir)' >&2; \
- exit 1; \
- }; \
- test `$(am__distuninstallcheck_listfiles) | wc -l` -eq 0 \
+ @$(am__cd) '$(distuninstallcheck_dir)' \
+ && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
|| { echo "ERROR: files left after uninstall:" ; \
if test -n "$(DESTDIR)"; then \
echo " (check DESTDIR support)"; \
@@ -3904,18 +4157,14 @@ install-am: all-am
installcheck: installcheck-recursive
install-strip:
- if test -z '$(STRIP)'; then \
- $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
- install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
- install; \
- else \
- $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
- install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
- "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
- fi
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
mostlyclean-generic:
-test -z "$(TEST_LOGS)" || rm -f $(TEST_LOGS)
- -test -z "$(TEST_LOGS:.log=.trs)" || rm -f $(TEST_LOGS:.log=.trs)
+ -test -z "$(TEST_LOGS_TMP)" || rm -f $(TEST_LOGS_TMP)
+ -test -z "$(TEST_SUITE_HTML)" || rm -f $(TEST_SUITE_HTML)
-test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
clean-generic:
@@ -4004,13 +4253,14 @@ uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
uninstall-nobase_pkgdataDATA
@$(NORMAL_INSTALL)
$(MAKE) $(AM_MAKEFLAGS) uninstall-hook
-.MAKE: $(am__recursive_targets) all check-am install-am \
- install-data-am install-strip uninstall-am
-
-.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
- am--refresh check check-TESTS check-am clean clean-binPROGRAMS \
- clean-cscope clean-generic cscope cscopelist-am ctags ctags-am \
- dist dist-all dist-bzip2 dist-gzip dist-lzip dist-shar \
+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all check-am \
+ check-html ctags-recursive install-am install-data-am \
+ install-strip recheck recheck-html tags-recursive uninstall-am
+
+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
+ all all-am am--refresh check check-TESTS check-am check-html \
+ clean clean-binPROGRAMS clean-generic ctags ctags-recursive \
+ dist dist-all dist-bzip2 dist-gzip dist-lzma dist-shar \
dist-tarZ dist-xz dist-zip distcheck distclean \
distclean-compile distclean-generic distclean-hdr \
distclean-tags distcleancheck distdir distuninstallcheck dvi \
@@ -4023,13 +4273,11 @@ uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
install-ps install-ps-am install-strip installcheck \
installcheck-am installdirs installdirs-am maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am recheck tags tags-am \
- uninstall uninstall-am uninstall-binPROGRAMS \
- uninstall-dist_binSCRIPTS uninstall-hook \
+ mostlyclean-generic pdf pdf-am ps ps-am recheck recheck-html \
+ tags tags-recursive uninstall uninstall-am \
+ uninstall-binPROGRAMS uninstall-dist_binSCRIPTS uninstall-hook \
uninstall-nobase_pkgdataDATA
-.PRECIOUS: Makefile
-
debug:
$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++0x"
diff --git a/aclocal.m4 b/aclocal.m4
index 8b1f091..ed46330 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,7 +1,7 @@
-# generated automatically by aclocal 1.15 -*- Autoconf -*-
-
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# generated automatically by aclocal 1.11.1 -*- Autoconf -*-
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
+# 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -11,16 +11,15 @@
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.
-m4_ifndef([AC_CONFIG_MACRO_DIRS], [m4_defun([_AM_CONFIG_MACRO_DIRS], [])m4_defun([AC_CONFIG_MACRO_DIRS], [_AM_CONFIG_MACRO_DIRS($@)])])
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.69],,
-[m4_warning([this file was generated for autoconf 2.69.
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.63],,
+[m4_warning([this file was generated for autoconf 2.63.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
-To do so, use the procedure documented by the package, typically 'autoreconf'.])])
+To do so, use the procedure documented by the package, typically `autoreconf'.])])
-# Copyright (C) 2002-2014 Free Software Foundation, Inc.
+# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -32,10 +31,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
# generated from the m4 files accompanying Automake X.Y.
# (This private macro should not be called outside this file.)
AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.15'
+[am__api_version='1.11'
dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
dnl require some minimum version. Point them to the right macro.
-m4_if([$1], [1.15], [],
+m4_if([$1], [1.11.1], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -51,22 +50,22 @@ m4_define([_AM_AUTOCONF_VERSION], [])
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.15])dnl
+[AM_AUTOMAKE_VERSION([1.11.1])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets
-# $ac_aux_dir to '$srcdir/foo'. In other projects, it is set to
-# '$srcdir', '$srcdir/..', or '$srcdir/../..'.
+# $ac_aux_dir to `$srcdir/foo'. In other projects, it is set to
+# `$srcdir', `$srcdir/..', or `$srcdir/../..'.
#
# Of course, Automake must honor this variable whenever it calls a
# tool from the auxiliary directory. The problem is that $srcdir (and
@@ -85,7 +84,7 @@ _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
#
# The reason of the latter failure is that $top_srcdir and $ac_aux_dir
# are both prefixed by $srcdir. In an in-source build this is usually
-# harmless because $srcdir is '.', but things will broke when you
+# harmless because $srcdir is `.', but things will broke when you
# start a VPATH build or use an absolute $srcdir.
#
# So we could use something similar to $top_srcdir/$ac_aux_dir/missing,
@@ -103,26 +102,30 @@ _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
# configured tree to be moved without reconfiguration.
AC_DEFUN([AM_AUX_DIR_EXPAND],
-[AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl
-# Expand $ac_aux_dir to an absolute path.
-am_aux_dir=`cd "$ac_aux_dir" && pwd`
+[dnl Rely on autoconf to set up CDPATH properly.
+AC_PREREQ([2.50])dnl
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
])
# AM_CONDITIONAL -*- Autoconf -*-
-# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006, 2008
+# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 9
+
# AM_CONDITIONAL(NAME, SHELL-CONDITION)
# -------------------------------------
# Define a conditional.
AC_DEFUN([AM_CONDITIONAL],
-[AC_PREREQ([2.52])dnl
- m4_if([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])],
- [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
+[AC_PREREQ(2.52)dnl
+ ifelse([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])],
+ [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
AC_SUBST([$1_TRUE])dnl
AC_SUBST([$1_FALSE])dnl
_AM_SUBST_NOTMAKE([$1_TRUE])dnl
@@ -141,14 +144,16 @@ AC_CONFIG_COMMANDS_PRE(
Usually this means the macro was only invoked conditionally.]])
fi])])
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009
+# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 10
-# There are a few dirty hacks below to avoid letting 'AC_PROG_CC' be
+# There are a few dirty hacks below to avoid letting `AC_PROG_CC' be
# written in clear, in which case automake, when reading aclocal.m4,
# will think it sees a *use*, and therefore will trigger all it's
# C support machinery. Also note that it means that autoscan, seeing
@@ -158,7 +163,7 @@ fi])])
# _AM_DEPENDENCIES(NAME)
# ----------------------
# See how the compiler implements dependency checking.
-# NAME is "CC", "CXX", "OBJC", "OBJCXX", "UPC", or "GJC".
+# NAME is "CC", "CXX", "GCJ", or "OBJC".
# We try a few techniques and use that to set a single cache variable.
#
# We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was
@@ -171,13 +176,12 @@ AC_REQUIRE([AM_OUTPUT_DEPENDENCY_COMMANDS])dnl
AC_REQUIRE([AM_MAKE_INCLUDE])dnl
AC_REQUIRE([AM_DEP_TRACK])dnl
-m4_if([$1], [CC], [depcc="$CC" am_compiler_list=],
- [$1], [CXX], [depcc="$CXX" am_compiler_list=],
- [$1], [OBJC], [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
- [$1], [OBJCXX], [depcc="$OBJCXX" am_compiler_list='gcc3 gcc'],
- [$1], [UPC], [depcc="$UPC" am_compiler_list=],
- [$1], [GCJ], [depcc="$GCJ" am_compiler_list='gcc3 gcc'],
- [depcc="$$1" am_compiler_list=])
+ifelse([$1], CC, [depcc="$CC" am_compiler_list=],
+ [$1], CXX, [depcc="$CXX" am_compiler_list=],
+ [$1], OBJC, [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
+ [$1], UPC, [depcc="$UPC" am_compiler_list=],
+ [$1], GCJ, [depcc="$GCJ" am_compiler_list='gcc3 gcc'],
+ [depcc="$$1" am_compiler_list=])
AC_CACHE_CHECK([dependency style of $depcc],
[am_cv_$1_dependencies_compiler_type],
@@ -185,9 +189,8 @@ AC_CACHE_CHECK([dependency style of $depcc],
# We make a subdir and do the tests there. Otherwise we can end up
# making bogus files that we don't know about and never remove. For
# instance it was reported that on HP-UX the gcc test will end up
- # making a dummy file named 'D' -- because '-MD' means "put the output
- # in D".
- rm -rf conftest.dir
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
mkdir conftest.dir
# Copy depcomp to subdir because otherwise we won't find it if we're
# using a relative directory.
@@ -226,16 +229,16 @@ AC_CACHE_CHECK([dependency style of $depcc],
: > sub/conftest.c
for i in 1 2 3 4 5 6; do
echo '#include "conftst'$i'.h"' >> sub/conftest.c
- # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
- # Solaris 10 /bin/sh.
- echo '/* dummy */' > sub/conftst$i.h
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
done
echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
- # We check with '-c' and '-o' for the sake of the "dashmstdout"
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
# mode. It turns out that the SunPro C++ compiler does not properly
- # handle '-M -o', and we need to detect this. Also, some Intel
- # versions had trouble with output in subdirs.
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
am__obj=sub/conftest.${OBJEXT-o}
am__minus_obj="-o $am__obj"
case $depmode in
@@ -244,16 +247,16 @@ AC_CACHE_CHECK([dependency style of $depcc],
test "$am__universal" = false || continue
;;
nosideeffect)
- # After this tag, mechanisms are not by side-effect, so they'll
- # only be used when explicitly requested.
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
if test "x$enable_dependency_tracking" = xyes; then
continue
else
break
fi
;;
- msvc7 | msvc7msys | msvisualcpp | msvcmsys)
- # This compiler won't grok '-c -o', but also, the minuso test has
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
# not run yet. These depmodes are late enough in the game, and
# so weak that their functioning should not be impacted.
am__obj=conftest.${OBJEXT-o}
@@ -301,7 +304,7 @@ AM_CONDITIONAL([am__fastdep$1], [
# AM_SET_DEPDIR
# -------------
# Choose a directory name for dependency files.
-# This macro is AC_REQUIREd in _AM_DEPENDENCIES.
+# This macro is AC_REQUIREd in _AM_DEPENDENCIES
AC_DEFUN([AM_SET_DEPDIR],
[AC_REQUIRE([AM_SET_LEADING_DOT])dnl
AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
@@ -311,39 +314,34 @@ AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
# AM_DEP_TRACK
# ------------
AC_DEFUN([AM_DEP_TRACK],
-[AC_ARG_ENABLE([dependency-tracking], [dnl
-AS_HELP_STRING(
- [--enable-dependency-tracking],
- [do not reject slow dependency extractors])
-AS_HELP_STRING(
- [--disable-dependency-tracking],
- [speeds up one-time build])])
+[AC_ARG_ENABLE(dependency-tracking,
+[ --disable-dependency-tracking speeds up one-time build
+ --enable-dependency-tracking do not reject slow dependency extractors])
if test "x$enable_dependency_tracking" != xno; then
am_depcomp="$ac_aux_dir/depcomp"
AMDEPBACKSLASH='\'
- am__nodep='_no'
fi
AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno])
AC_SUBST([AMDEPBACKSLASH])dnl
_AM_SUBST_NOTMAKE([AMDEPBACKSLASH])dnl
-AC_SUBST([am__nodep])dnl
-_AM_SUBST_NOTMAKE([am__nodep])dnl
])
# Generate code to set up dependency tracking. -*- Autoconf -*-
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+#serial 5
# _AM_OUTPUT_DEPENDENCY_COMMANDS
# ------------------------------
AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
[{
- # Older Autoconf quotes --file arguments for eval, but not when files
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
# are listed without --file. Let's play safe and only enable the eval
# if we detect the quoting.
case $CONFIG_FILES in
@@ -356,7 +354,7 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
# Strip MF so we end up with the name of the file.
mf=`echo "$mf" | sed -e 's/:.*$//'`
# Check whether this is an Automake generated Makefile or not.
- # We used to match only the files named 'Makefile.in', but
+ # We used to match only the files named `Makefile.in', but
# some people rename them; so instead we look at the file content.
# Grep'ing the first line is not enough: some people post-process
# each Makefile.in and add a new line on top of each file to say so.
@@ -368,19 +366,21 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
continue
fi
# Extract the definition of DEPDIR, am__include, and am__quote
- # from the Makefile without running 'make'.
+ # from the Makefile without running `make'.
DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
test -z "$DEPDIR" && continue
am__include=`sed -n 's/^am__include = //p' < "$mf"`
- test -z "$am__include" && continue
+ test -z "am__include" && continue
am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
# Find all dependency output files, they are included files with
# $(DEPDIR) in their names. We invoke sed twice because it is the
# simplest approach to changing $(DEPDIR) to its actual value in the
# expansion.
for file in `sed -n "
s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
- sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
# Make sure the directory exists.
test -f "$dirpart/$file" && continue
fdir=`AS_DIRNAME(["$file"])`
@@ -398,7 +398,7 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
# This macro should only be invoked once -- use via AC_REQUIRE.
#
# This code is only required when automatic dependency tracking
-# is enabled. FIXME. This creates each '.P' file that we will
+# is enabled. FIXME. This creates each `.P' file that we will
# need in order to bootstrap the dependency handling code.
AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
[AC_CONFIG_COMMANDS([depfiles],
@@ -408,21 +408,18 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# Do all the work for Automake. -*- Autoconf -*-
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
+# 2005, 2006, 2008, 2009 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 16
+
# This macro actually does too much. Some checks are only needed if
# your package does certain things. But this isn't really a big deal.
-dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.
-m4_define([AC_PROG_CC],
-m4_defn([AC_PROG_CC])
-[_AM_PROG_CC_C_O
-])
-
# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
# AM_INIT_AUTOMAKE([OPTIONS])
# -----------------------------------------------
@@ -435,7 +432,7 @@ m4_defn([AC_PROG_CC])
# arguments mandatory, and then we can depend on a new Autoconf
# release and drop the old call support.
AC_DEFUN([AM_INIT_AUTOMAKE],
-[AC_PREREQ([2.65])dnl
+[AC_PREREQ([2.62])dnl
dnl Autoconf wants to disallow AM_ names. We explicitly allow
dnl the ones we care about.
m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
@@ -464,42 +461,33 @@ AC_SUBST([CYGPATH_W])
# Define the identity of the package.
dnl Distinguish between old-style and new-style calls.
m4_ifval([$2],
-[AC_DIAGNOSE([obsolete],
- [$0: two- and three-arguments forms are deprecated.])
-m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
+[m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
AC_SUBST([PACKAGE], [$1])dnl
AC_SUBST([VERSION], [$2])],
[_AM_SET_OPTIONS([$1])dnl
dnl Diagnose old-style AC_INIT with new-style AM_AUTOMAKE_INIT.
-m4_if(
- m4_ifdef([AC_PACKAGE_NAME], [ok]):m4_ifdef([AC_PACKAGE_VERSION], [ok]),
- [ok:ok],,
+m4_if(m4_ifdef([AC_PACKAGE_NAME], 1)m4_ifdef([AC_PACKAGE_VERSION], 1), 11,,
[m4_fatal([AC_INIT should be called with package and version arguments])])dnl
AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl
AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl
_AM_IF_OPTION([no-define],,
-[AC_DEFINE_UNQUOTED([PACKAGE], ["$PACKAGE"], [Name of package])
- AC_DEFINE_UNQUOTED([VERSION], ["$VERSION"], [Version number of package])])dnl
+[AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
+ AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package])])dnl
# Some tools Automake needs.
AC_REQUIRE([AM_SANITY_CHECK])dnl
AC_REQUIRE([AC_ARG_PROGRAM])dnl
-AM_MISSING_PROG([ACLOCAL], [aclocal-${am__api_version}])
-AM_MISSING_PROG([AUTOCONF], [autoconf])
-AM_MISSING_PROG([AUTOMAKE], [automake-${am__api_version}])
-AM_MISSING_PROG([AUTOHEADER], [autoheader])
-AM_MISSING_PROG([MAKEINFO], [makeinfo])
+AM_MISSING_PROG(ACLOCAL, aclocal-${am__api_version})
+AM_MISSING_PROG(AUTOCONF, autoconf)
+AM_MISSING_PROG(AUTOMAKE, automake-${am__api_version})
+AM_MISSING_PROG(AUTOHEADER, autoheader)
+AM_MISSING_PROG(MAKEINFO, makeinfo)
AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
-AC_REQUIRE([AC_PROG_MKDIR_P])dnl
-# For better backward compatibility. To be removed once Automake 1.9.x
-# dies out for good. For more background, see:
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
-AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
-# We need awk for the "check" target (and possibly the TAP driver). The
-# system "awk" is bad on some platforms.
+AC_REQUIRE([AM_PROG_MKDIR_P])dnl
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
AC_REQUIRE([AC_PROG_AWK])dnl
AC_REQUIRE([AC_PROG_MAKE_SET])dnl
AC_REQUIRE([AM_SET_LEADING_DOT])dnl
@@ -508,82 +496,34 @@ _AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])],
[_AM_PROG_TAR([v7])])])
_AM_IF_OPTION([no-dependencies],,
[AC_PROVIDE_IFELSE([AC_PROG_CC],
- [_AM_DEPENDENCIES([CC])],
- [m4_define([AC_PROG_CC],
- m4_defn([AC_PROG_CC])[_AM_DEPENDENCIES([CC])])])dnl
+ [_AM_DEPENDENCIES(CC)],
+ [define([AC_PROG_CC],
+ defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl
AC_PROVIDE_IFELSE([AC_PROG_CXX],
- [_AM_DEPENDENCIES([CXX])],
- [m4_define([AC_PROG_CXX],
- m4_defn([AC_PROG_CXX])[_AM_DEPENDENCIES([CXX])])])dnl
+ [_AM_DEPENDENCIES(CXX)],
+ [define([AC_PROG_CXX],
+ defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
AC_PROVIDE_IFELSE([AC_PROG_OBJC],
- [_AM_DEPENDENCIES([OBJC])],
- [m4_define([AC_PROG_OBJC],
- m4_defn([AC_PROG_OBJC])[_AM_DEPENDENCIES([OBJC])])])dnl
-AC_PROVIDE_IFELSE([AC_PROG_OBJCXX],
- [_AM_DEPENDENCIES([OBJCXX])],
- [m4_define([AC_PROG_OBJCXX],
- m4_defn([AC_PROG_OBJCXX])[_AM_DEPENDENCIES([OBJCXX])])])dnl
+ [_AM_DEPENDENCIES(OBJC)],
+ [define([AC_PROG_OBJC],
+ defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl
])
-AC_REQUIRE([AM_SILENT_RULES])dnl
-dnl The testsuite driver may need to know about EXEEXT, so add the
-dnl 'am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This
-dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.
+_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl
+dnl The `parallel-tests' driver may need to know about EXEEXT, so add the
+dnl `am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This macro
+dnl is hooked onto _AC_COMPILER_EXEEXT early, see below.
AC_CONFIG_COMMANDS_PRE(dnl
[m4_provide_if([_AM_COMPILER_EXEEXT],
[AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
-
-# POSIX will say in a future version that running "rm -f" with no argument
-# is OK; and we want to be able to make that assumption in our Makefile
-# recipes. So use an aggressive probe to check that the usage we want is
-# actually supported "in the wild" to an acceptable degree.
-# See automake bug#10828.
-# To make any issue more visible, cause the running configure to be aborted
-# by default if the 'rm' program in use doesn't match our expectations; the
-# user can still override this though.
-if rm -f && rm -fr && rm -rf; then : OK; else
- cat >&2 <<'END'
-Oops!
-
-Your 'rm' program seems unable to run without file operands specified
-on the command line, even when the '-f' option is present. This is contrary
-to the behaviour of most rm programs out there, and not conforming with
-the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
-
-Please tell bug-automake at gnu.org about your system, including the value
-of your $PATH and any error possibly output before this message. This
-can help us improve future automake versions.
-
-END
- if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
- echo 'Configuration will proceed anyway, since you have set the' >&2
- echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
- echo >&2
- else
- cat >&2 <<'END'
-Aborting the configuration process, to ensure you take notice of the issue.
-
-You can download and install GNU coreutils to get an 'rm' implementation
-that behaves properly: <http://www.gnu.org/software/coreutils/>.
-
-If you want to complete the configuration process using your problematic
-'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
-to "yes", and re-run configure.
-
-END
- AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
- fi
-fi
-dnl The trailing newline in this macro's definition is deliberate, for
-dnl backward compatibility and to allow trailing 'dnl'-style comments
-dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
])
-dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
+dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further
dnl mangled by Autoconf and run in a shell conditional statement.
m4_define([_AC_COMPILER_EXEEXT],
m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])
+
# When config.status generates a header, we must update the stamp-h file.
# This file resides in the same directory as the config header
# that is generated. The stamp files are numbered to have different names.
@@ -605,7 +545,7 @@ for _am_header in $config_headers :; do
done
echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2003, 2005, 2008 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -616,7 +556,7 @@ echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_co
# Define $install_sh.
AC_DEFUN([AM_PROG_INSTALL_SH],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-if test x"${install_sh+set}" != xset; then
+if test x"${install_sh}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
@@ -624,14 +564,16 @@ if test x"${install_sh+set}" != xset; then
install_sh="\${SHELL} $am_aux_dir/install-sh"
esac
fi
-AC_SUBST([install_sh])])
+AC_SUBST(install_sh)])
-# Copyright (C) 2003-2014 Free Software Foundation, Inc.
+# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 2
+
# Check whether the underlying file-system supports filenames
# with a leading dot. For instance MS-DOS doesn't.
AC_DEFUN([AM_SET_LEADING_DOT],
@@ -647,12 +589,14 @@ AC_SUBST([am__leading_dot])])
# Check to see how 'make' treats includes. -*- Autoconf -*-
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 4
+
# AM_MAKE_INCLUDE()
# -----------------
# Check to see how make treats includes.
@@ -670,7 +614,7 @@ am__quote=
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
-# Ignore all kinds of additional output from 'make'.
+# Ignore all kinds of additional output from `make'.
case `$am_make -s -f confmf 2> /dev/null` in #(
*the\ am__doit\ target*)
am__include=include
@@ -695,14 +639,52 @@ AC_MSG_RESULT([$_am_result])
rm -f confinc confmf
])
+# Copyright (C) 1999, 2000, 2001, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 6
+
+# AM_PROG_CC_C_O
+# --------------
+# Like AC_PROG_CC_C_O, but changed for automake.
+AC_DEFUN([AM_PROG_CC_C_O],
+[AC_REQUIRE([AC_PROG_CC_C_O])dnl
+AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([compile])dnl
+# FIXME: we rely on the cache variable name because
+# there is no other way.
+set dummy $CC
+am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+dnl Make sure AC_PROG_CC is never called again, or it will override our
+dnl setting of CC.
+m4_define([AC_PROG_CC],
+ [m4_fatal([AC_PROG_CC cannot be called after AM_PROG_CC_C_O])])
+])
+
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
-# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 6
+
# AM_MISSING_PROG(NAME, PROGRAM)
# ------------------------------
AC_DEFUN([AM_MISSING_PROG],
@@ -710,10 +692,11 @@ AC_DEFUN([AM_MISSING_PROG],
$1=${$1-"${am_missing_run}$2"}
AC_SUBST($1)])
+
# AM_MISSING_HAS_RUN
# ------------------
-# Define MISSING if not defined so far and test if it is modern enough.
-# If it is, set am_missing_run to use it, otherwise, to nothing.
+# Define MISSING if not defined so far and test if it supports --run.
+# If it does, set am_missing_run to use it, otherwise, to nothing.
AC_DEFUN([AM_MISSING_HAS_RUN],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
AC_REQUIRE_AUX_FILE([missing])dnl
@@ -726,35 +709,63 @@ if test x"${MISSING+set}" != xset; then
esac
fi
# Use eval to expand $SHELL
-if eval "$MISSING --is-lightweight"; then
- am_missing_run="$MISSING "
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
else
am_missing_run=
- AC_MSG_WARN(['missing' script is too old or missing])
+ AC_MSG_WARN([`missing' script is too old or missing])
fi
])
+# Copyright (C) 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_MKDIR_P
+# ---------------
+# Check for `mkdir -p'.
+AC_DEFUN([AM_PROG_MKDIR_P],
+[AC_PREREQ([2.60])dnl
+AC_REQUIRE([AC_PROG_MKDIR_P])dnl
+dnl Automake 1.8 to 1.9.6 used to define mkdir_p. We now use MKDIR_P,
+dnl while keeping a definition of mkdir_p for backward compatibility.
+dnl @MKDIR_P@ is magic: AC_OUTPUT adjusts its value for each Makefile.
+dnl However we cannot define mkdir_p as $(MKDIR_P) for the sake of
+dnl Makefile.ins that do not define MKDIR_P, so we do our own
+dnl adjustment using top_builddir (which is defined more often than
+dnl MKDIR_P).
+AC_SUBST([mkdir_p], ["$MKDIR_P"])dnl
+case $mkdir_p in
+ [[\\/$]]* | ?:[[\\/]]*) ;;
+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+])
+
# Helper functions for option handling. -*- Autoconf -*-
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2002, 2003, 2005, 2008 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 4
+
# _AM_MANGLE_OPTION(NAME)
# -----------------------
AC_DEFUN([_AM_MANGLE_OPTION],
[[_AM_OPTION_]m4_bpatsubst($1, [[^a-zA-Z0-9_]], [_])])
# _AM_SET_OPTION(NAME)
-# --------------------
+# ------------------------------
# Set option NAME. Presently that only means defining a flag for this option.
AC_DEFUN([_AM_SET_OPTION],
-[m4_define(_AM_MANGLE_OPTION([$1]), [1])])
+[m4_define(_AM_MANGLE_OPTION([$1]), 1)])
# _AM_SET_OPTIONS(OPTIONS)
-# ------------------------
+# ----------------------------------
# OPTIONS is a space-separated list of Automake options.
AC_DEFUN([_AM_SET_OPTIONS],
[m4_foreach_w([_AM_Option], [$1], [_AM_SET_OPTION(_AM_Option)])])
@@ -765,82 +776,24 @@ AC_DEFUN([_AM_SET_OPTIONS],
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# _AM_PROG_CC_C_O
-# ---------------
-# Like AC_PROG_CC_C_O, but changed for automake. We rewrite AC_PROG_CC
-# to automatically call this.
-AC_DEFUN([_AM_PROG_CC_C_O],
-[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-AC_REQUIRE_AUX_FILE([compile])dnl
-AC_LANG_PUSH([C])dnl
-AC_CACHE_CHECK(
- [whether $CC understands -c and -o together],
- [am_cv_prog_cc_c_o],
- [AC_LANG_CONFTEST([AC_LANG_PROGRAM([])])
- # Make sure it works both with $CC and with simple cc.
- # Following AC_PROG_CC_C_O, we do the test twice because some
- # compilers refuse to overwrite an existing .o file with -o,
- # though they will create one.
- am_cv_prog_cc_c_o=yes
- for am_i in 1 2; do
- if AM_RUN_LOG([$CC -c conftest.$ac_ext -o conftest2.$ac_objext]) \
- && test -f conftest2.$ac_objext; then
- : OK
- else
- am_cv_prog_cc_c_o=no
- break
- fi
- done
- rm -f core conftest*
- unset am_i])
-if test "$am_cv_prog_cc_c_o" != yes; then
- # Losing compiler, so override with the script.
- # FIXME: It is wrong to rewrite CC.
- # But if we don't then we get into trouble of one sort or another.
- # A longer-term fix would be to have automake use am__CC in this case,
- # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
- CC="$am_aux_dir/compile $CC"
-fi
-AC_LANG_POP([C])])
-
-# For backward compatibility.
-AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
-
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# AM_RUN_LOG(COMMAND)
-# -------------------
-# Run COMMAND, save the exit status in ac_status, and log it.
-# (This has been adapted from Autoconf's _AC_RUN_LOG macro.)
-AC_DEFUN([AM_RUN_LOG],
-[{ echo "$as_me:$LINENO: $1" >&AS_MESSAGE_LOG_FD
- ($1) >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
- (exit $ac_status); }])
-
# Check to make sure that the build environment is sane. -*- Autoconf -*-
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008
+# Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 5
+
# AM_SANITY_CHECK
# ---------------
AC_DEFUN([AM_SANITY_CHECK],
[AC_MSG_CHECKING([whether build environment is sane])
+# Just in case
+sleep 1
+echo timestamp > conftest.file
# Reject unsafe characters in $srcdir or the absolute working directory
# name. Accept space and tab only in the latter.
am_lf='
@@ -851,40 +804,32 @@ case `pwd` in
esac
case $srcdir in
*[[\\\"\#\$\&\'\`$am_lf\ \ ]]*)
- AC_MSG_ERROR([unsafe srcdir value: '$srcdir']);;
+ AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);;
esac
-# Do 'set' in a subshell so we don't clobber the current shell's
+# Do `set' in a subshell so we don't clobber the current shell's
# arguments. Must try -L first in case configure is actually a
# symlink; some systems play weird games with the mod time of symlinks
# (eg FreeBSD returns the mod time of the symlink's containing
# directory).
if (
- am_has_slept=no
- for am_try in 1 2; do
- echo "timestamp, slept: $am_has_slept" > conftest.file
- set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
- if test "$[*]" = "X"; then
- # -L didn't work.
- set X `ls -t "$srcdir/configure" conftest.file`
- fi
- if test "$[*]" != "X $srcdir/configure conftest.file" \
- && test "$[*]" != "X conftest.file $srcdir/configure"; then
-
- # If neither matched, then we have a broken ls. This can happen
- # if, for instance, CONFIG_SHELL is bash and it inherits a
- # broken ls alias from the environment. This has actually
- # happened. Such a system could not be considered "sane".
- AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
- alias in your environment])
- fi
- if test "$[2]" = conftest.file || test $am_try -eq 2; then
- break
- fi
- # Just in case.
- sleep 1
- am_has_slept=yes
- done
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$[*]" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$[*]" != "X $srcdir/configure conftest.file" \
+ && test "$[*]" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
+alias in your environment])
+ fi
+
test "$[2]" = conftest.file
)
then
@@ -894,85 +839,9 @@ else
AC_MSG_ERROR([newly created file is older than distributed files!
Check your system clock])
fi
-AC_MSG_RESULT([yes])
-# If we didn't sleep, we still need to ensure time stamps of config.status and
-# generated files are strictly newer.
-am_sleep_pid=
-if grep 'slept: no' conftest.file >/dev/null 2>&1; then
- ( sleep 1 ) &
- am_sleep_pid=$!
-fi
-AC_CONFIG_COMMANDS_PRE(
- [AC_MSG_CHECKING([that generated files are newer than configure])
- if test -n "$am_sleep_pid"; then
- # Hide warnings about reused PIDs.
- wait $am_sleep_pid 2>/dev/null
- fi
- AC_MSG_RESULT([done])])
-rm -f conftest.file
-])
-
-# Copyright (C) 2009-2014 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# AM_SILENT_RULES([DEFAULT])
-# --------------------------
-# Enable less verbose build rules; with the default set to DEFAULT
-# ("yes" being less verbose, "no" or empty being verbose).
-AC_DEFUN([AM_SILENT_RULES],
-[AC_ARG_ENABLE([silent-rules], [dnl
-AS_HELP_STRING(
- [--enable-silent-rules],
- [less verbose build output (undo: "make V=1")])
-AS_HELP_STRING(
- [--disable-silent-rules],
- [verbose build output (undo: "make V=0")])dnl
-])
-case $enable_silent_rules in @%:@ (((
- yes) AM_DEFAULT_VERBOSITY=0;;
- no) AM_DEFAULT_VERBOSITY=1;;
- *) AM_DEFAULT_VERBOSITY=m4_if([$1], [yes], [0], [1]);;
-esac
-dnl
-dnl A few 'make' implementations (e.g., NonStop OS and NextStep)
-dnl do not support nested variable expansions.
-dnl See automake bug#9928 and bug#10237.
-am_make=${MAKE-make}
-AC_CACHE_CHECK([whether $am_make supports nested variables],
- [am_cv_make_support_nested_variables],
- [if AS_ECHO([['TRUE=$(BAR$(V))
-BAR0=false
-BAR1=true
-V=1
-am__doit:
- @$(TRUE)
-.PHONY: am__doit']]) | $am_make -f - >/dev/null 2>&1; then
- am_cv_make_support_nested_variables=yes
-else
- am_cv_make_support_nested_variables=no
-fi])
-if test $am_cv_make_support_nested_variables = yes; then
- dnl Using '$V' instead of '$(V)' breaks IRIX make.
- AM_V='$(V)'
- AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
-else
- AM_V=$AM_DEFAULT_VERBOSITY
- AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
-fi
-AC_SUBST([AM_V])dnl
-AM_SUBST_NOTMAKE([AM_V])dnl
-AC_SUBST([AM_DEFAULT_V])dnl
-AM_SUBST_NOTMAKE([AM_DEFAULT_V])dnl
-AC_SUBST([AM_DEFAULT_VERBOSITY])dnl
-AM_BACKSLASH='\'
-AC_SUBST([AM_BACKSLASH])dnl
-_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
-])
+AC_MSG_RESULT(yes)])
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -980,32 +849,34 @@ _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
# AM_PROG_INSTALL_STRIP
# ---------------------
-# One issue with vendor 'install' (even GNU) is that you can't
+# One issue with vendor `install' (even GNU) is that you can't
# specify the program used to strip binaries. This is especially
# annoying in cross-compiling environments, where the build's strip
# is unlikely to handle the host's binaries.
# Fortunately install-sh will honor a STRIPPROG variable, so we
-# always use install-sh in "make install-strip", and initialize
+# always use install-sh in `make install-strip', and initialize
# STRIPPROG with the value of the STRIP variable (set by the user).
AC_DEFUN([AM_PROG_INSTALL_STRIP],
[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
-# Installed binaries are usually stripped using 'strip' when the user
-# run "make install-strip". However 'strip' might not be the right
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
# tool to use in cross-compilation environments, therefore Automake
-# will honor the 'STRIP' environment variable to overrule this program.
-dnl Don't test for $cross_compiling = yes, because it might be 'maybe'.
+# will honor the `STRIP' environment variable to overrule this program.
+dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
if test "$cross_compiling" != no; then
AC_CHECK_TOOL([STRIP], [strip], :)
fi
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
AC_SUBST([INSTALL_STRIP_PROGRAM])])
-# Copyright (C) 2006-2014 Free Software Foundation, Inc.
+# Copyright (C) 2006, 2008 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 2
+
# _AM_SUBST_NOTMAKE(VARIABLE)
# ---------------------------
# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
@@ -1013,22 +884,24 @@ AC_SUBST([INSTALL_STRIP_PROGRAM])])
AC_DEFUN([_AM_SUBST_NOTMAKE])
# AM_SUBST_NOTMAKE(VARIABLE)
-# --------------------------
+# ---------------------------
# Public sister of _AM_SUBST_NOTMAKE.
AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# Check how to create a tarball. -*- Autoconf -*-
-# Copyright (C) 2004-2014 Free Software Foundation, Inc.
+# Copyright (C) 2004, 2005 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
+# serial 2
+
# _AM_PROG_TAR(FORMAT)
# --------------------
# Check how to create a tarball in format FORMAT.
-# FORMAT should be one of 'v7', 'ustar', or 'pax'.
+# FORMAT should be one of `v7', `ustar', or `pax'.
#
# Substitute a variable $(am__tar) that is a command
# writing to stdout a FORMAT-tarball containing the directory
@@ -1038,114 +911,75 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# Substitute a variable $(am__untar) that extract such
# a tarball read from stdin.
# $(am__untar) < result.tar
-#
AC_DEFUN([_AM_PROG_TAR],
-[# Always define AMTAR for backward compatibility. Yes, it's still used
-# in the wild :-( We should find a proper way to deprecate it ...
-AC_SUBST([AMTAR], ['$${TAR-tar}'])
-
-# We'll loop over all known methods to create a tar archive until one works.
+[# Always define AMTAR for backward compatibility.
+AM_MISSING_PROG([AMTAR], [tar])
+m4_if([$1], [v7],
+ [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'],
+ [m4_case([$1], [ustar],, [pax],,
+ [m4_fatal([Unknown tar format])])
+AC_MSG_CHECKING([how to create a $1 tar archive])
+# Loop over all known methods to create a tar archive until one works.
_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
+_am_tools=${am_cv_prog_tar_$1-$_am_tools}
+# Do not fold the above two line into one, because Tru64 sh and
+# Solaris sh will not grok spaces in the rhs of `-'.
+for _am_tool in $_am_tools
+do
+ case $_am_tool in
+ gnutar)
+ for _am_tar in tar gnutar gtar;
+ do
+ AM_RUN_LOG([$_am_tar --version]) && break
+ done
+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+ am__untar="$_am_tar -xf -"
+ ;;
+ plaintar)
+ # Must skip GNU tar: if it does not support --format= it doesn't create
+ # ustar tarball either.
+ (tar --version) >/dev/null 2>&1 && continue
+ am__tar='tar chf - "$$tardir"'
+ am__tar_='tar chf - "$tardir"'
+ am__untar='tar xf -'
+ ;;
+ pax)
+ am__tar='pax -L -x $1 -w "$$tardir"'
+ am__tar_='pax -L -x $1 -w "$tardir"'
+ am__untar='pax -r'
+ ;;
+ cpio)
+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+ am__untar='cpio -i -H $1 -d'
+ ;;
+ none)
+ am__tar=false
+ am__tar_=false
+ am__untar=false
+ ;;
+ esac
-m4_if([$1], [v7],
- [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
-
- [m4_case([$1],
- [ustar],
- [# The POSIX 1988 'ustar' format is defined with fixed-size fields.
- # There is notably a 21 bits limit for the UID and the GID. In fact,
- # the 'pax' utility can hang on bigger UID/GID (see automake bug#8343
- # and bug#13588).
- am_max_uid=2097151 # 2^21 - 1
- am_max_gid=$am_max_uid
- # The $UID and $GID variables are not portable, so we need to resort
- # to the POSIX-mandated id(1) utility. Errors in the 'id' calls
- # below are definitely unexpected, so allow the users to see them
- # (that is, avoid stderr redirection).
- am_uid=`id -u || echo unknown`
- am_gid=`id -g || echo unknown`
- AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])
- if test $am_uid -le $am_max_uid; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
- _am_tools=none
- fi
- AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])
- if test $am_gid -le $am_max_gid; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
- _am_tools=none
- fi],
-
- [pax],
- [],
-
- [m4_fatal([Unknown tar format])])
-
- AC_MSG_CHECKING([how to create a $1 tar archive])
-
- # Go ahead even if we have the value already cached. We do so because we
- # need to set the values for the 'am__tar' and 'am__untar' variables.
- _am_tools=${am_cv_prog_tar_$1-$_am_tools}
-
- for _am_tool in $_am_tools; do
- case $_am_tool in
- gnutar)
- for _am_tar in tar gnutar gtar; do
- AM_RUN_LOG([$_am_tar --version]) && break
- done
- am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
- am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
- am__untar="$_am_tar -xf -"
- ;;
- plaintar)
- # Must skip GNU tar: if it does not support --format= it doesn't create
- # ustar tarball either.
- (tar --version) >/dev/null 2>&1 && continue
- am__tar='tar chf - "$$tardir"'
- am__tar_='tar chf - "$tardir"'
- am__untar='tar xf -'
- ;;
- pax)
- am__tar='pax -L -x $1 -w "$$tardir"'
- am__tar_='pax -L -x $1 -w "$tardir"'
- am__untar='pax -r'
- ;;
- cpio)
- am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
- am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
- am__untar='cpio -i -H $1 -d'
- ;;
- none)
- am__tar=false
- am__tar_=false
- am__untar=false
- ;;
- esac
+ # If the value was cached, stop now. We just wanted to have am__tar
+ # and am__untar set.
+ test -n "${am_cv_prog_tar_$1}" && break
- # If the value was cached, stop now. We just wanted to have am__tar
- # and am__untar set.
- test -n "${am_cv_prog_tar_$1}" && break
-
- # tar/untar a dummy directory, and stop if the command works.
- rm -rf conftest.dir
- mkdir conftest.dir
- echo GrepMe > conftest.dir/file
- AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
- rm -rf conftest.dir
- if test -s conftest.tar; then
- AM_RUN_LOG([$am__untar <conftest.tar])
- AM_RUN_LOG([cat conftest.dir/file])
- grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
- fi
- done
+ # tar/untar a dummy directory, and stop if the command works
rm -rf conftest.dir
+ mkdir conftest.dir
+ echo GrepMe > conftest.dir/file
+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ rm -rf conftest.dir
+ if test -s conftest.tar; then
+ AM_RUN_LOG([$am__untar <conftest.tar])
+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+ fi
+done
+rm -rf conftest.dir
- AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
- AC_MSG_RESULT([$am_cv_prog_tar_$1])])
-
+AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+AC_MSG_RESULT([$am_cv_prog_tar_$1])])
AC_SUBST([am__tar])
AC_SUBST([am__untar])
]) # _AM_PROG_TAR
diff --git a/config.h.in b/config.h.in
index b0dd76a..6d1f0c1 100644
--- a/config.h.in
+++ b/config.h.in
@@ -92,6 +92,9 @@
/* Define to 1 if the system has the type `_Bool'. */
#undef HAVE__BOOL
+/* Define to 1 if your C compiler doesn't accept -c and -o together. */
+#undef NO_MINUS_C_MINUS_O
+
/* Name of package */
#undef PACKAGE
@@ -107,12 +110,12 @@
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
-/* Define to the home page for this package. */
-#undef PACKAGE_URL
-
/* Define to the version of this package. */
#undef PACKAGE_VERSION
+/* Regular expressions are defined and implemented */
+#undef REGEX_FUNCTIONAL
+
/* Define to 1 if you have the ANSI C header files. */
#undef STDC_HEADERS
diff --git a/config/compile b/config/compile
index a85b723..c0096a7 100755
--- a/config/compile
+++ b/config/compile
@@ -1,9 +1,10 @@
#! /bin/sh
-# Wrapper for compilers which do not understand '-c -o'.
+# Wrapper for compilers which do not understand `-c -o'.
-scriptversion=2012-10-14.11; # UTC
+scriptversion=2009-10-06.20; # UTC
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2009 Free Software
+# Foundation, Inc.
# Written by Tom Tromey <tromey at cygnus.com>.
#
# This program is free software; you can redistribute it and/or modify
@@ -28,224 +29,21 @@ scriptversion=2012-10-14.11; # UTC
# bugs to <bug-automake at gnu.org> or send patches to
# <automake-patches at gnu.org>.
-nl='
-'
-
-# We need space, tab and new line, in precisely that order. Quoting is
-# there to prevent tools from complaining about whitespace usage.
-IFS=" "" $nl"
-
-file_conv=
-
-# func_file_conv build_file lazy
-# Convert a $build file to $host form and store it in $file
-# Currently only supports Windows hosts. If the determined conversion
-# type is listed in (the comma separated) LAZY, no conversion will
-# take place.
-func_file_conv ()
-{
- file=$1
- case $file in
- / | /[!/]*) # absolute file, and not a UNC file
- if test -z "$file_conv"; then
- # lazily determine how to convert abs files
- case `uname -s` in
- MINGW*)
- file_conv=mingw
- ;;
- CYGWIN*)
- file_conv=cygwin
- ;;
- *)
- file_conv=wine
- ;;
- esac
- fi
- case $file_conv/,$2, in
- *,$file_conv,*)
- ;;
- mingw/*)
- file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
- ;;
- cygwin/*)
- file=`cygpath -m "$file" || echo "$file"`
- ;;
- wine/*)
- file=`winepath -w "$file" || echo "$file"`
- ;;
- esac
- ;;
- esac
-}
-
-# func_cl_dashL linkdir
-# Make cl look for libraries in LINKDIR
-func_cl_dashL ()
-{
- func_file_conv "$1"
- if test -z "$lib_path"; then
- lib_path=$file
- else
- lib_path="$lib_path;$file"
- fi
- linker_opts="$linker_opts -LIBPATH:$file"
-}
-
-# func_cl_dashl library
-# Do a library search-path lookup for cl
-func_cl_dashl ()
-{
- lib=$1
- found=no
- save_IFS=$IFS
- IFS=';'
- for dir in $lib_path $LIB
- do
- IFS=$save_IFS
- if $shared && test -f "$dir/$lib.dll.lib"; then
- found=yes
- lib=$dir/$lib.dll.lib
- break
- fi
- if test -f "$dir/$lib.lib"; then
- found=yes
- lib=$dir/$lib.lib
- break
- fi
- if test -f "$dir/lib$lib.a"; then
- found=yes
- lib=$dir/lib$lib.a
- break
- fi
- done
- IFS=$save_IFS
-
- if test "$found" != yes; then
- lib=$lib.lib
- fi
-}
-
-# func_cl_wrapper cl arg...
-# Adjust compile command to suit cl
-func_cl_wrapper ()
-{
- # Assume a capable shell
- lib_path=
- shared=:
- linker_opts=
- for arg
- do
- if test -n "$eat"; then
- eat=
- else
- case $1 in
- -o)
- # configure might choose to run compile as 'compile cc -o foo foo.c'.
- eat=1
- case $2 in
- *.o | *.[oO][bB][jJ])
- func_file_conv "$2"
- set x "$@" -Fo"$file"
- shift
- ;;
- *)
- func_file_conv "$2"
- set x "$@" -Fe"$file"
- shift
- ;;
- esac
- ;;
- -I)
- eat=1
- func_file_conv "$2" mingw
- set x "$@" -I"$file"
- shift
- ;;
- -I*)
- func_file_conv "${1#-I}" mingw
- set x "$@" -I"$file"
- shift
- ;;
- -l)
- eat=1
- func_cl_dashl "$2"
- set x "$@" "$lib"
- shift
- ;;
- -l*)
- func_cl_dashl "${1#-l}"
- set x "$@" "$lib"
- shift
- ;;
- -L)
- eat=1
- func_cl_dashL "$2"
- ;;
- -L*)
- func_cl_dashL "${1#-L}"
- ;;
- -static)
- shared=false
- ;;
- -Wl,*)
- arg=${1#-Wl,}
- save_ifs="$IFS"; IFS=','
- for flag in $arg; do
- IFS="$save_ifs"
- linker_opts="$linker_opts $flag"
- done
- IFS="$save_ifs"
- ;;
- -Xlinker)
- eat=1
- linker_opts="$linker_opts $2"
- ;;
- -*)
- set x "$@" "$1"
- shift
- ;;
- *.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
- func_file_conv "$1"
- set x "$@" -Tp"$file"
- shift
- ;;
- *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
- func_file_conv "$1" mingw
- set x "$@" "$file"
- shift
- ;;
- *)
- set x "$@" "$1"
- shift
- ;;
- esac
- fi
- shift
- done
- if test -n "$linker_opts"; then
- linker_opts="-link$linker_opts"
- fi
- exec "$@" $linker_opts
- exit 1
-}
-
-eat=
-
case $1 in
'')
- echo "$0: No command. Try '$0 --help' for more information." 1>&2
+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
exit 1;
;;
-h | --h*)
cat <<\EOF
Usage: compile [--help] [--version] PROGRAM [ARGS]
-Wrapper for compilers which do not understand '-c -o'.
-Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
+Wrapper for compilers which do not understand `-c -o'.
+Remove `-o dest.o' from ARGS, run PROGRAM with the remaining
arguments, and rename the output as expected.
If you are trying to build a whole package this is not the
-right script to run: please start by reading the file 'INSTALL'.
+right script to run: please start by reading the file `INSTALL'.
Report bugs to <bug-automake at gnu.org>.
EOF
@@ -255,13 +53,11 @@ EOF
echo "compile $scriptversion"
exit $?
;;
- cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
- func_cl_wrapper "$@" # Doesn't return...
- ;;
esac
ofile=
cfile=
+eat=
for arg
do
@@ -270,8 +66,8 @@ do
else
case $1 in
-o)
- # configure might choose to run compile as 'compile cc -o foo foo.c'.
- # So we strip '-o arg' only if arg is an object.
+ # configure might choose to run compile as `compile cc -o foo foo.c'.
+ # So we strip `-o arg' only if arg is an object.
eat=1
case $2 in
*.o | *.obj)
@@ -298,10 +94,10 @@ do
done
if test -z "$ofile" || test -z "$cfile"; then
- # If no '-o' option was seen then we might have been invoked from a
+ # If no `-o' option was seen then we might have been invoked from a
# pattern rule where we don't need one. That is ok -- this is a
# normal compilation that the losing compiler can handle. If no
- # '.c' file was seen then we are probably linking. That is also
+ # `.c' file was seen then we are probably linking. That is also
# ok.
exec "$@"
fi
@@ -310,7 +106,7 @@ fi
cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
# Create the lock directory.
-# Note: use '[/\\:.-]' here to ensure that we don't use the same name
+# Note: use `[/\\:.-]' here to ensure that we don't use the same name
# that we are using for the .o file. Also, base the name on the expected
# object file name, since that is what matters with a parallel build.
lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
diff --git a/config/depcomp b/config/depcomp
index fc98710..df8eea7 100755
--- a/config/depcomp
+++ b/config/depcomp
@@ -1,9 +1,10 @@
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
-scriptversion=2013-05-30.07; # UTC
+scriptversion=2009-04-28.21; # UTC
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
+# Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -27,9 +28,9 @@ scriptversion=2013-05-30.07; # UTC
case $1 in
'')
- echo "$0: No command. Try '$0 --help' for more information." 1>&2
- exit 1;
- ;;
+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
@@ -39,11 +40,11 @@ as side-effects.
Environment variables:
depmode Dependency tracking mode.
- source Source file read by 'PROGRAMS ARGS'.
- object Object file output by 'PROGRAMS ARGS'.
+ source Source file read by `PROGRAMS ARGS'.
+ object Object file output by `PROGRAMS ARGS'.
DEPDIR directory where to store dependencies.
depfile Dependency file to output.
- tmpdepfile Temporary file to use when outputting dependencies.
+ tmpdepfile Temporary file to use when outputing dependencies.
libtool Whether libtool is used (yes/no).
Report bugs to <bug-automake at gnu.org>.
@@ -56,66 +57,6 @@ EOF
;;
esac
-# Get the directory component of the given path, and save it in the
-# global variables '$dir'. Note that this directory component will
-# be either empty or ending with a '/' character. This is deliberate.
-set_dir_from ()
-{
- case $1 in
- */*) dir=`echo "$1" | sed -e 's|/[^/]*$|/|'`;;
- *) dir=;;
- esac
-}
-
-# Get the suffix-stripped basename of the given path, and save it the
-# global variable '$base'.
-set_base_from ()
-{
- base=`echo "$1" | sed -e 's|^.*/||' -e 's/\.[^.]*$//'`
-}
-
-# If no dependency file was actually created by the compiler invocation,
-# we still have to create a dummy depfile, to avoid errors with the
-# Makefile "include basename.Plo" scheme.
-make_dummy_depfile ()
-{
- echo "#dummy" > "$depfile"
-}
-
-# Factor out some common post-processing of the generated depfile.
-# Requires the auxiliary global variable '$tmpdepfile' to be set.
-aix_post_process_depfile ()
-{
- # If the compiler actually managed to produce a dependency file,
- # post-process it.
- if test -f "$tmpdepfile"; then
- # Each line is of the form 'foo.o: dependency.h'.
- # Do two passes, one to just change these to
- # $object: dependency.h
- # and one to simply output
- # dependency.h:
- # which is needed to avoid the deleted-header problem.
- { sed -e "s,^.*\.[$lower]*:,$object:," < "$tmpdepfile"
- sed -e "s,^.*\.[$lower]*:[$tab ]*,," -e 's,$,:,' < "$tmpdepfile"
- } > "$depfile"
- rm -f "$tmpdepfile"
- else
- make_dummy_depfile
- fi
-}
-
-# A tabulation character.
-tab=' '
-# A newline character.
-nl='
-'
-# Character ranges might be problematic outside the C locale.
-# These definitions help.
-upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ
-lower=abcdefghijklmnopqrstuvwxyz
-digits=0123456789
-alpha=${upper}${lower}
-
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
exit 1
@@ -128,9 +69,6 @@ tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
rm -f "$tmpdepfile"
-# Avoid interferences from the environment.
-gccflag= dashmflag=
-
# Some modes work just like other modes, but use different flags. We
# parameterize here, but still list the modes in the big case below,
# to make depend.m4 easier to write. Note that we *cannot* use a case
@@ -142,32 +80,18 @@ if test "$depmode" = hp; then
fi
if test "$depmode" = dashXmstdout; then
- # This is just like dashmstdout with a different argument.
- dashmflag=-xM
- depmode=dashmstdout
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
fi
cygpath_u="cygpath -u -f -"
if test "$depmode" = msvcmsys; then
- # This is just like msvisualcpp but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvisualcpp
-fi
-
-if test "$depmode" = msvc7msys; then
- # This is just like msvc7 but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvc7
-fi
-
-if test "$depmode" = xlc; then
- # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information.
- gccflag=-qmakedep=gcc,-MF
- depmode=gcc
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u="sed s,\\\\\\\\,/,g"
+ depmode=msvisualcpp
fi
case "$depmode" in
@@ -190,7 +114,8 @@ gcc3)
done
"$@"
stat=$?
- if test $stat -ne 0; then
+ if test $stat -eq 0; then :
+ else
rm -f "$tmpdepfile"
exit $stat
fi
@@ -198,17 +123,13 @@ gcc3)
;;
gcc)
-## Note that this doesn't just cater to obsosete pre-3.x GCC compilers.
-## but also to in-use compilers like IMB xlc/xlC and the HP C compiler.
-## (see the conditional assignment to $gccflag above).
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-## -MM, not -M (despite what the docs say). Also, it might not be
-## supported by the other compilers which use the 'gcc' depmode.
+## -MM, not -M (despite what the docs say).
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
@@ -216,31 +137,31 @@ gcc)
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
- if test $stat -ne 0; then
+ if test $stat -eq 0; then :
+ else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
- # The second -e expression handles DOS-style file names with drive
- # letters.
+ alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-## This next piece of magic avoids the "deleted header file" problem.
+## This next piece of magic avoids the `deleted header file' problem.
## The problem is that when a header file which appears in a .P file
## is deleted, the dependency causes make to die (because there is
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
-## Some versions of gcc put a space before the ':'. On the theory
+ tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'. On the theory
## that the space means something, we add a space to the output as
-## well. hp depmode also adds that space, but also prefixes the VPATH
-## to the object. Take care to not repeat it in the output.
+## well.
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
@@ -258,7 +179,8 @@ sgi)
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
- if test $stat -ne 0; then
+ if test $stat -eq 0; then :
+ else
rm -f "$tmpdepfile"
exit $stat
fi
@@ -266,41 +188,43 @@ sgi)
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
echo "$object : \\" > "$depfile"
+
# Clip off the initial element (the dependent). Don't try to be
# clever and replace this with sed code, as IRIX sed won't handle
# lines with more than a fixed number of characters (4096 in
# IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
- # the IRIX cc adds comments like '#:fec' to the end of the
+ # the IRIX cc adds comments like `#:fec' to the end of the
# dependency line.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' \
- | tr "$nl" ' ' >> "$depfile"
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+ tr '
+' ' ' >> "$depfile"
echo >> "$depfile"
+
# The second pass generates a dummy entry for each header file.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
- >> "$depfile"
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> "$depfile"
else
- make_dummy_depfile
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
-xlc)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
aix)
# The C for AIX Compiler uses -M and outputs the dependencies
# in a .u file. In older versions, this file always lives in the
- # current directory. Also, the AIX compiler puts '$object:' at the
+ # current directory. Also, the AIX compiler puts `$object:' at the
# start of each line; $object doesn't have directory information.
# Version 6 uses the directory in both cases.
- set_dir_from "$object"
- set_base_from "$object"
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.u
tmpdepfile2=$base.u
@@ -313,7 +237,9 @@ aix)
"$@" -M
fi
stat=$?
- if test $stat -ne 0; then
+
+ if test $stat -eq 0; then :
+ else
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
exit $stat
fi
@@ -322,100 +248,44 @@ aix)
do
test -f "$tmpdepfile" && break
done
- aix_post_process_depfile
- ;;
-
-tcc)
- # tcc (Tiny C Compiler) understand '-MD -MF file' since version 0.9.26
- # FIXME: That version still under development at the moment of writing.
- # Make that this statement remains true also for stable, released
- # versions.
- # It will wrap lines (doesn't matter whether long or short) with a
- # trailing '\', as in:
- #
- # foo.o : \
- # foo.c \
- # foo.h \
- #
- # It will put a trailing '\' even on the last line, and will use leading
- # spaces rather than leading tabs (at least since its commit 0394caf7
- # "Emit spaces for -MD").
- "$@" -MD -MF "$tmpdepfile"
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
+ if test -f "$tmpdepfile"; then
+ # Each line is of the form `foo.o: dependent.h'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
fi
- rm -f "$depfile"
- # Each non-empty line is of the form 'foo.o : \' or ' dep.h \'.
- # We have to change lines of the first kind to '$object: \'.
- sed -e "s|.*:|$object :|" < "$tmpdepfile" > "$depfile"
- # And for each line of the second kind, we have to emit a 'dep.h:'
- # dummy dependency, to avoid the deleted-header problem.
- sed -n -e 's|^ *\(.*\) *\\$|\1:|p' < "$tmpdepfile" >> "$depfile"
rm -f "$tmpdepfile"
;;
-## The order of this option in the case statement is important, since the
-## shell code in configure will try each of these formats in the order
-## listed in this file. A plain '-MD' option would be understood by many
-## compilers, so we must ensure this comes after the gcc and icc options.
-pgcc)
- # Portland's C compiler understands '-MD'.
- # Will always output deps to 'file.d' where file is the root name of the
- # source file under compilation, even if file resides in a subdirectory.
- # The object file name does not affect the name of the '.d' file.
- # pgcc 10.2 will output
+icc)
+ # Intel's C compiler understands `-MD -MF file'. However on
+ # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+ # ICC 7.0 will fill foo.d with something like
+ # foo.o: sub/foo.c
+ # foo.o: sub/foo.h
+ # which is wrong. We want:
+ # sub/foo.o: sub/foo.c
+ # sub/foo.o: sub/foo.h
+ # sub/foo.c:
+ # sub/foo.h:
+ # ICC 7.1 will output
# foo.o: sub/foo.c sub/foo.h
- # and will wrap long lines using '\' :
+ # and will wrap long lines using \ :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
- set_dir_from "$object"
- # Use the source, not the object, to determine the base name, since
- # that's sadly what pgcc will do too.
- set_base_from "$source"
- tmpdepfile=$base.d
-
- # For projects that build the same source file twice into different object
- # files, the pgcc approach of using the *source* file root name can cause
- # problems in parallel builds. Use a locking strategy to avoid stomping on
- # the same $tmpdepfile.
- lockdir=$base.d-lock
- trap "
- echo '$0: caught signal, cleaning up...' >&2
- rmdir '$lockdir'
- exit 1
- " 1 2 13 15
- numtries=100
- i=$numtries
- while test $i -gt 0; do
- # mkdir is a portable test-and-set.
- if mkdir "$lockdir" 2>/dev/null; then
- # This process acquired the lock.
- "$@" -MD
- stat=$?
- # Release the lock.
- rmdir "$lockdir"
- break
- else
- # If the lock is being held by a different process, wait
- # until the winning process is done or we timeout.
- while test -d "$lockdir" && test $i -gt 0; do
- sleep 1
- i=`expr $i - 1`
- done
- fi
- i=`expr $i - 1`
- done
- trap - 1 2 13 15
- if test $i -le 0; then
- echo "$0: failed to acquire lock after $numtries attempts" >&2
- echo "$0: check lockdir '$lockdir'" >&2
- exit 1
- fi
- if test $stat -ne 0; then
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
rm -f "$tmpdepfile"
exit $stat
fi
@@ -427,8 +297,8 @@ pgcc)
sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
# Some versions of the HPUX 10.20 sed can't process this invocation
# correctly. Breaking it into two sed invocations is a workaround.
- sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" \
- | sed -e 's/$/ :/' >> "$depfile"
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+ sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
@@ -439,8 +309,9 @@ hp2)
# 'foo.d', which lands next to the object file, wherever that
# happens to be.
# Much of this is similar to the tru64 case; see comments there.
- set_dir_from "$object"
- set_base_from "$object"
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.d
tmpdepfile2=$dir.libs/$base.d
@@ -451,7 +322,8 @@ hp2)
"$@" +Maked
fi
stat=$?
- if test $stat -ne 0; then
+ if test $stat -eq 0; then :
+ else
rm -f "$tmpdepfile1" "$tmpdepfile2"
exit $stat
fi
@@ -461,107 +333,77 @@ hp2)
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[$lower]*:,$object:," "$tmpdepfile" > "$depfile"
- # Add 'dependent.h:' lines.
+ sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
+ # Add `dependent.h:' lines.
sed -ne '2,${
- s/^ *//
- s/ \\*$//
- s/$/:/
- p
- }' "$tmpdepfile" >> "$depfile"
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
else
- make_dummy_depfile
+ echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile" "$tmpdepfile2"
;;
tru64)
- # The Tru64 compiler uses -MD to generate dependencies as a side
- # effect. 'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'.
- # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
- # dependencies in 'foo.d' instead, so we check for that too.
- # Subdirectories are respected.
- set_dir_from "$object"
- set_base_from "$object"
-
- if test "$libtool" = yes; then
- # Libtool generates 2 separate objects for the 2 libraries. These
- # two compilations output dependencies in $dir.libs/$base.o.d and
- # in $dir$base.o.d. We have to check for both files, because
- # one of the two compilations can be disabled. We should prefer
- # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
- # automatically cleaned when .libs/ is deleted, while ignoring
- # the former would cause a distcleancheck panic.
- tmpdepfile1=$dir$base.o.d # libtool 1.5
- tmpdepfile2=$dir.libs/$base.o.d # Likewise.
- tmpdepfile3=$dir.libs/$base.d # Compaq CCC V6.2-504
- "$@" -Wc,-MD
- else
- tmpdepfile1=$dir$base.d
- tmpdepfile2=$dir$base.d
- tmpdepfile3=$dir$base.d
- "$@" -MD
- fi
-
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- do
- test -f "$tmpdepfile" && break
- done
- # Same post-processing that is required for AIX mode.
- aix_post_process_depfile
- ;;
-
-msvc7)
- if test "$libtool" = yes; then
- showIncludes=-Wc,-showIncludes
- else
- showIncludes=-showIncludes
- fi
- "$@" $showIncludes > "$tmpdepfile"
- stat=$?
- grep -v '^Note: including file: ' "$tmpdepfile"
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- # The first sed program below extracts the file names and escapes
- # backslashes for cygpath. The second sed program outputs the file
- # name when reading, but also accumulates all include files in the
- # hold buffer in order to output them again at the end. This only
- # works with sed implementations that can handle large buffers.
- sed < "$tmpdepfile" -n '
-/^Note: including file: *\(.*\)/ {
- s//\1/
- s/\\/\\\\/g
- p
-}' | $cygpath_u | sort -u | sed -n '
-s/ /\\ /g
-s/\(.*\)/'"$tab"'\1 \\/p
-s/.\(.*\) \\/\1:/
-H
-$ {
- s/.*/'"$tab"'/
- G
- p
-}' >> "$depfile"
- echo >> "$depfile" # make sure the fragment doesn't end with a backslash
- rm -f "$tmpdepfile"
- ;;
-
-msvc7msys)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in `foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+ if test "$libtool" = yes; then
+ # With Tru64 cc, shared objects can also be used to make a
+ # static library. This mechanism is used in libtool 1.4 series to
+ # handle both shared and static libraries in a single compilation.
+ # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
+ #
+ # With libtool 1.5 this exception was removed, and libtool now
+ # generates 2 separate objects for the 2 libraries. These two
+ # compilations output dependencies in $dir.libs/$base.o.d and
+ # in $dir$base.o.d. We have to check for both files, because
+ # one of the two compilations can be disabled. We should prefer
+ # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+ # automatically cleaned when .libs/ is deleted, while ignoring
+ # the former would cause a distcleancheck panic.
+ tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
+ tmpdepfile2=$dir$base.o.d # libtool 1.5
+ tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
+ tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1=$dir$base.o.d
+ tmpdepfile2=$dir$base.d
+ tmpdepfile3=$dir$base.d
+ tmpdepfile4=$dir$base.d
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
#nosideeffect)
# This comment above is used by automake to tell side-effect
@@ -580,7 +422,7 @@ dashmstdout)
shift
fi
- # Remove '-o $object'.
+ # Remove `-o $object'.
IFS=" "
for arg
do
@@ -600,18 +442,18 @@ dashmstdout)
done
test -z "$dashmflag" && dashmflag=-M
- # Require at least two characters before searching for ':'
+ # Require at least two characters before searching for `:'
# in the target name. This is to cope with DOS-style filenames:
- # a dependency such as 'c:/foo/bar' could be seen as target 'c' otherwise.
+ # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
"$@" $dashmflag |
- sed "s|^[$tab ]*[^:$tab ][^:][^:]*:[$tab ]*|$object: |" > "$tmpdepfile"
+ sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process this sed invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
+ tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
@@ -661,15 +503,12 @@ makedepend)
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
- # makedepend may prepend the VPATH from the source file name to the object.
- # No need to regex-escape $object, excess matching of '.' is harmless.
- sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process the last invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- sed '1,2d' "$tmpdepfile" \
- | tr ' ' "$nl" \
- | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
@@ -686,7 +525,7 @@ cpp)
shift
fi
- # Remove '-o $object'.
+ # Remove `-o $object'.
IFS=" "
for arg
do
@@ -705,10 +544,10 @@ cpp)
esac
done
- "$@" -E \
- | sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- | sed '$ s: \\$::' > "$tmpdepfile"
+ "$@" -E |
+ sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+ sed '$ s: \\$::' > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
cat < "$tmpdepfile" >> "$depfile"
@@ -740,23 +579,23 @@ msvisualcpp)
shift
;;
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
- set fnord "$@"
- shift
- shift
- ;;
+ set fnord "$@"
+ shift
+ shift
+ ;;
*)
- set fnord "$@" "$arg"
- shift
- shift
- ;;
+ set fnord "$@" "$arg"
+ shift
+ shift
+ ;;
esac
done
"$@" -E 2>/dev/null |
sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
- sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::'"$tab"'\1 \\:p' >> "$depfile"
- echo "$tab" >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
+ echo " " >> "$depfile"
sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
diff --git a/config/install-sh b/config/install-sh
index 0b0fdcb..6781b98 100755
--- a/config/install-sh
+++ b/config/install-sh
@@ -1,7 +1,7 @@
#!/bin/sh
# install - install a program, script, or datafile
-scriptversion=2013-12-25.23; # UTC
+scriptversion=2009-04-28.21; # UTC
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
@@ -35,21 +35,25 @@ scriptversion=2013-12-25.23; # UTC
# FSF changes to this file are in the public domain.
#
# Calling this script install-sh is preferred over install.sh, to prevent
-# 'make' implicit rules from creating a file called install from it
+# `make' implicit rules from creating a file called install from it
# when there is no Makefile.
#
# This script is compatible with the BSD install script, but was written
# from scratch.
-tab=' '
nl='
'
-IFS=" $tab$nl"
+IFS=" "" $nl"
-# Set DOITPROG to "echo" to test this script.
+# set DOITPROG to echo to test this script
+# Don't use :- since 4.3BSD and earlier shells don't like it.
doit=${DOITPROG-}
-doit_exec=${doit:-exec}
+if test -z "$doit"; then
+ doit_exec=exec
+else
+ doit_exec=$doit
+fi
# Put in absolute file names if you don't have them in your path;
# or use environment vars.
@@ -64,6 +68,17 @@ mvprog=${MVPROG-mv}
rmprog=${RMPROG-rm}
stripprog=${STRIPPROG-strip}
+posix_glob='?'
+initialize_posix_glob='
+ test "$posix_glob" != "?" || {
+ if (set -f) 2>/dev/null; then
+ posix_glob=
+ else
+ posix_glob=:
+ fi
+ }
+'
+
posix_mkdir=
# Desired mode of installed file.
@@ -82,7 +97,7 @@ dir_arg=
dst_arg=
copy_on_change=false
-is_target_a_directory=possibly
+no_target_directory=
usage="\
Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
@@ -122,57 +137,42 @@ while test $# -ne 0; do
-d) dir_arg=true;;
-g) chgrpcmd="$chgrpprog $2"
- shift;;
+ shift;;
--help) echo "$usage"; exit $?;;
-m) mode=$2
- case $mode in
- *' '* | *"$tab"* | *"$nl"* | *'*'* | *'?'* | *'['*)
- echo "$0: invalid mode: $mode" >&2
- exit 1;;
- esac
- shift;;
+ case $mode in
+ *' '* | *' '* | *'
+'* | *'*'* | *'?'* | *'['*)
+ echo "$0: invalid mode: $mode" >&2
+ exit 1;;
+ esac
+ shift;;
-o) chowncmd="$chownprog $2"
- shift;;
+ shift;;
-s) stripcmd=$stripprog;;
- -t)
- is_target_a_directory=always
- dst_arg=$2
- # Protect names problematic for 'test' and other utilities.
- case $dst_arg in
- -* | [=\(\)!]) dst_arg=./$dst_arg;;
- esac
- shift;;
+ -t) dst_arg=$2
+ shift;;
- -T) is_target_a_directory=never;;
+ -T) no_target_directory=true;;
--version) echo "$0 $scriptversion"; exit $?;;
- --) shift
- break;;
+ --) shift
+ break;;
- -*) echo "$0: invalid option: $1" >&2
- exit 1;;
+ -*) echo "$0: invalid option: $1" >&2
+ exit 1;;
*) break;;
esac
shift
done
-# We allow the use of options -d and -T together, by making -d
-# take the precedence; this is for compatibility with GNU install.
-
-if test -n "$dir_arg"; then
- if test -n "$dst_arg"; then
- echo "$0: target directory not allowed when installing a directory." >&2
- exit 1
- fi
-fi
-
if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
# When -d is used, all remaining arguments are directories to create.
# When -t is used, the destination is already specified.
@@ -186,10 +186,6 @@ if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
fi
shift # arg
dst_arg=$arg
- # Protect names problematic for 'test' and other utilities.
- case $dst_arg in
- -* | [=\(\)!]) dst_arg=./$dst_arg;;
- esac
done
fi
@@ -198,26 +194,13 @@ if test $# -eq 0; then
echo "$0: no input file specified." >&2
exit 1
fi
- # It's OK to call 'install-sh -d' without argument.
+ # It's OK to call `install-sh -d' without argument.
# This can happen when creating conditional directories.
exit 0
fi
if test -z "$dir_arg"; then
- if test $# -gt 1 || test "$is_target_a_directory" = always; then
- if test ! -d "$dst_arg"; then
- echo "$0: $dst_arg: Is not a directory." >&2
- exit 1
- fi
- fi
-fi
-
-if test -z "$dir_arg"; then
- do_exit='(exit $ret); exit $ret'
- trap "ret=129; $do_exit" 1
- trap "ret=130; $do_exit" 2
- trap "ret=141; $do_exit" 13
- trap "ret=143; $do_exit" 15
+ trap '(exit $?); exit' 1 2 13 15
# Set umask so as not to create temps with too-generous modes.
# However, 'strip' requires both read and write access to temps.
@@ -228,16 +211,16 @@ if test -z "$dir_arg"; then
*[0-7])
if test -z "$stripcmd"; then
- u_plus_rw=
+ u_plus_rw=
else
- u_plus_rw='% 200'
+ u_plus_rw='% 200'
fi
cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
*)
if test -z "$stripcmd"; then
- u_plus_rw=
+ u_plus_rw=
else
- u_plus_rw=,u+rw
+ u_plus_rw=,u+rw
fi
cp_umask=$mode$u_plus_rw;;
esac
@@ -245,9 +228,9 @@ fi
for src
do
- # Protect names problematic for 'test' and other utilities.
+ # Protect names starting with `-'.
case $src in
- -* | [=\(\)!]) src=./$src;;
+ -*) src=./$src;;
esac
if test -n "$dir_arg"; then
@@ -269,20 +252,51 @@ do
echo "$0: no destination specified." >&2
exit 1
fi
+
dst=$dst_arg
+ # Protect names starting with `-'.
+ case $dst in
+ -*) dst=./$dst;;
+ esac
# If destination is a directory, append the input filename; won't work
# if double slashes aren't ignored.
if test -d "$dst"; then
- if test "$is_target_a_directory" = never; then
- echo "$0: $dst_arg: Is a directory" >&2
- exit 1
+ if test -n "$no_target_directory"; then
+ echo "$0: $dst_arg: Is a directory" >&2
+ exit 1
fi
dstdir=$dst
dst=$dstdir/`basename "$src"`
dstdir_status=0
else
- dstdir=`dirname "$dst"`
+ # Prefer dirname, but fall back on a substitute if dirname fails.
+ dstdir=`
+ (dirname "$dst") 2>/dev/null ||
+ expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$dst" : 'X\(//\)[^/]' \| \
+ X"$dst" : 'X\(//\)$' \| \
+ X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+ echo X"$dst" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'
+ `
+
test -d "$dstdir"
dstdir_status=$?
fi
@@ -293,74 +307,74 @@ do
if test $dstdir_status != 0; then
case $posix_mkdir in
'')
- # Create intermediate dirs using mode 755 as modified by the umask.
- # This is like FreeBSD 'install' as of 1997-10-28.
- umask=`umask`
- case $stripcmd.$umask in
- # Optimize common cases.
- *[2367][2367]) mkdir_umask=$umask;;
- .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
-
- *[0-7])
- mkdir_umask=`expr $umask + 22 \
- - $umask % 100 % 40 + $umask % 20 \
- - $umask % 10 % 4 + $umask % 2
- `;;
- *) mkdir_umask=$umask,go-w;;
- esac
-
- # With -d, create the new directory with the user-specified mode.
- # Otherwise, rely on $mkdir_umask.
- if test -n "$dir_arg"; then
- mkdir_mode=-m$mode
- else
- mkdir_mode=
- fi
-
- posix_mkdir=false
- case $umask in
- *[123567][0-7][0-7])
- # POSIX mkdir -p sets u+wx bits regardless of umask, which
- # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
- ;;
- *)
- tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
- trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
-
- if (umask $mkdir_umask &&
- exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
- then
- if test -z "$dir_arg" || {
- # Check for POSIX incompatibilities with -m.
- # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
- # other-writable bit of parent directory when it shouldn't.
- # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
- ls_ld_tmpdir=`ls -ld "$tmpdir"`
- case $ls_ld_tmpdir in
- d????-?r-*) different_mode=700;;
- d????-?--*) different_mode=755;;
- *) false;;
- esac &&
- $mkdirprog -m$different_mode -p -- "$tmpdir" && {
- ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
- test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
- }
- }
- then posix_mkdir=:
- fi
- rmdir "$tmpdir/d" "$tmpdir"
- else
- # Remove any dirs left behind by ancient mkdir implementations.
- rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
- fi
- trap '' 0;;
- esac;;
+ # Create intermediate dirs using mode 755 as modified by the umask.
+ # This is like FreeBSD 'install' as of 1997-10-28.
+ umask=`umask`
+ case $stripcmd.$umask in
+ # Optimize common cases.
+ *[2367][2367]) mkdir_umask=$umask;;
+ .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+ *[0-7])
+ mkdir_umask=`expr $umask + 22 \
+ - $umask % 100 % 40 + $umask % 20 \
+ - $umask % 10 % 4 + $umask % 2
+ `;;
+ *) mkdir_umask=$umask,go-w;;
+ esac
+
+ # With -d, create the new directory with the user-specified mode.
+ # Otherwise, rely on $mkdir_umask.
+ if test -n "$dir_arg"; then
+ mkdir_mode=-m$mode
+ else
+ mkdir_mode=
+ fi
+
+ posix_mkdir=false
+ case $umask in
+ *[123567][0-7][0-7])
+ # POSIX mkdir -p sets u+wx bits regardless of umask, which
+ # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+ ;;
+ *)
+ tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+ trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+ if (umask $mkdir_umask &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+ then
+ if test -z "$dir_arg" || {
+ # Check for POSIX incompatibilities with -m.
+ # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+ # other-writeable bit of parent directory when it shouldn't.
+ # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+ ls_ld_tmpdir=`ls -ld "$tmpdir"`
+ case $ls_ld_tmpdir in
+ d????-?r-*) different_mode=700;;
+ d????-?--*) different_mode=755;;
+ *) false;;
+ esac &&
+ $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+ test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+ }
+ }
+ then posix_mkdir=:
+ fi
+ rmdir "$tmpdir/d" "$tmpdir"
+ else
+ # Remove any dirs left behind by ancient mkdir implementations.
+ rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+ fi
+ trap '' 0;;
+ esac;;
esac
if
$posix_mkdir && (
- umask $mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+ umask $mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
)
then :
else
@@ -370,51 +384,53 @@ do
# directory the slow way, step by step, checking for races as we go.
case $dstdir in
- /*) prefix='/';;
- [-=\(\)!]*) prefix='./';;
- *) prefix='';;
+ /*) prefix='/';;
+ -*) prefix='./';;
+ *) prefix='';;
esac
+ eval "$initialize_posix_glob"
+
oIFS=$IFS
IFS=/
- set -f
+ $posix_glob set -f
set fnord $dstdir
shift
- set +f
+ $posix_glob set +f
IFS=$oIFS
prefixes=
for d
do
- test X"$d" = X && continue
-
- prefix=$prefix$d
- if test -d "$prefix"; then
- prefixes=
- else
- if $posix_mkdir; then
- (umask=$mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
- # Don't fail if two instances are running concurrently.
- test -d "$prefix" || exit 1
- else
- case $prefix in
- *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
- *) qprefix=$prefix;;
- esac
- prefixes="$prefixes '$qprefix'"
- fi
- fi
- prefix=$prefix/
+ test -z "$d" && continue
+
+ prefix=$prefix$d
+ if test -d "$prefix"; then
+ prefixes=
+ else
+ if $posix_mkdir; then
+ (umask=$mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+ # Don't fail if two instances are running concurrently.
+ test -d "$prefix" || exit 1
+ else
+ case $prefix in
+ *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) qprefix=$prefix;;
+ esac
+ prefixes="$prefixes '$qprefix'"
+ fi
+ fi
+ prefix=$prefix/
done
if test -n "$prefixes"; then
- # Don't fail if two instances are running concurrently.
- (umask $mkdir_umask &&
- eval "\$doit_exec \$mkdirprog $prefixes") ||
- test -d "$dstdir" || exit 1
- obsolete_mkdir_used=true
+ # Don't fail if two instances are running concurrently.
+ (umask $mkdir_umask &&
+ eval "\$doit_exec \$mkdirprog $prefixes") ||
+ test -d "$dstdir" || exit 1
+ obsolete_mkdir_used=true
fi
fi
fi
@@ -449,12 +465,15 @@ do
# If -C, don't bother to copy if it wouldn't change the file.
if $copy_on_change &&
- old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
- new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
- set -f &&
+ old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
+ new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
+
+ eval "$initialize_posix_glob" &&
+ $posix_glob set -f &&
set X $old && old=:$2:$4:$5:$6 &&
set X $new && new=:$2:$4:$5:$6 &&
- set +f &&
+ $posix_glob set +f &&
+
test "$old" = "$new" &&
$cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
then
@@ -467,24 +486,24 @@ do
# to itself, or perhaps because mv is so ancient that it does not
# support -f.
{
- # Now remove or move aside any old file at destination location.
- # We try this two ways since rm can't unlink itself on some
- # systems and the destination file might be busy for other
- # reasons. In this case, the final cleanup might fail but the new
- # file should still install successfully.
- {
- test ! -f "$dst" ||
- $doit $rmcmd -f "$dst" 2>/dev/null ||
- { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
- { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
- } ||
- { echo "$0: cannot unlink or rename $dst" >&2
- (exit 1); exit 1
- }
- } &&
-
- # Now rename the file to the real destination.
- $doit $mvcmd "$dsttmp" "$dst"
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ test ! -f "$dst" ||
+ $doit $rmcmd -f "$dst" 2>/dev/null ||
+ { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+ { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+ } ||
+ { echo "$0: cannot unlink or rename $dst" >&2
+ (exit 1); exit 1
+ }
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dst"
}
fi || exit 1
diff --git a/config/missing b/config/missing
index f62bbae..28055d2 100755
--- a/config/missing
+++ b/config/missing
@@ -1,10 +1,11 @@
#! /bin/sh
-# Common wrapper for a few potentially missing GNU programs.
+# Common stub for a few missing GNU programs while installing.
-scriptversion=2013-10-28.13; # UTC
+scriptversion=2009-04-28.21; # UTC
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
-# Originally written by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -25,40 +26,69 @@ scriptversion=2013-10-28.13; # UTC
# the same distribution terms that you use for the rest of that program.
if test $# -eq 0; then
- echo 1>&2 "Try '$0 --help' for more information"
+ echo 1>&2 "Try \`$0 --help' for more information"
exit 1
fi
-case $1 in
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
- --is-lightweight)
- # Used by our autoconf macros to check whether the available missing
- # script is modern enough.
- exit 0
- ;;
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
- --run)
- # Back-compat with the calling convention used by older automake.
- shift
- ;;
+msg="missing on your system"
+
+case $1 in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
-h|--h|--he|--hel|--help)
echo "\
$0 [OPTION]... PROGRAM [ARGUMENT]...
-Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
-to PROGRAM being missing or too old.
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
Options:
-h, --help display this help and exit
-v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
Supported PROGRAM values:
- aclocal autoconf autoheader autom4te automake makeinfo
- bison yacc flex lex help2man
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ autom4te touch the output file, or create a stub one
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ tar try tar, gnutar, gtar, then tar without non-portable flags
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
-Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and
-'g' are ignored when checking the name.
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
Send bug reports to <bug-automake at gnu.org>."
exit $?
@@ -70,141 +100,272 @@ Send bug reports to <bug-automake at gnu.org>."
;;
-*)
- echo 1>&2 "$0: unknown '$1' option"
- echo 1>&2 "Try '$0 --help' for more information"
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
exit 1
;;
esac
-# Run the given program, remember its exit status.
-"$@"; st=$?
-
-# If it succeeded, we are done.
-test $st -eq 0 && exit 0
-
-# Also exit now if we it failed (or wasn't found), and '--version' was
-# passed; such an option is passed most likely to detect whether the
-# program is present and works.
-case $2 in --version|--help) exit $st;; esac
-
-# Exit code 63 means version mismatch. This often happens when the user
-# tries to use an ancient version of a tool on a file that requires a
-# minimum version.
-if test $st -eq 63; then
- msg="probably too old"
-elif test $st -eq 127; then
- # Program was missing.
- msg="missing on your system"
-else
- # Program was found and executed, but failed. Give up.
- exit $st
-fi
+# normalize program name to check for.
+program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+# Now exit if we have it, but it failed. Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program). This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+ lex*|yacc*)
+ # Not GNU programs, they don't have --version.
+ ;;
+
+ tar*)
+ if test -n "$run"; then
+ echo 1>&2 "ERROR: \`tar' requires --run"
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ exit 1
+ fi
+ ;;
+
+ *)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ # Could not run --version or --help. This is probably someone
+ # running `$TOOL --version' or `$TOOL --help' to check whether
+ # $TOOL exists and not knowing $TOOL uses missing.
+ exit 1
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+ aclocal*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case $f in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te*)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison*|yacc*)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f y.tab.h; then
+ echo >y.tab.h
+ fi
+ if test ! -f y.tab.c; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex*|flex*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f lex.yy.c; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit $?
+ fi
+ ;;
+
+ makeinfo*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ # The file to touch is that specified with -o ...
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -z "$file"; then
+ # ... or it is the one specified with @setfilename ...
+ infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '
+ /^@setfilename/{
+ s/.* \([^ ]*\) *$/\1/
+ p
+ q
+ }' $infile`
+ # ... or it is derived from the source name (dir/f.texi becomes f.info)
+ test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+ fi
+ # If the file does not exist, the user really needs makeinfo;
+ # let's fail without touching anything.
+ test -f $file || exit 1
+ touch $file
+ ;;
+
+ tar*)
+ shift
+
+ # We have already tried tar in the generic part.
+ # Look for gnutar/gtar before invocation to avoid ugly error
+ # messages.
+ if (gnutar --version > /dev/null 2>&1); then
+ gnutar "$@" && exit 0
+ fi
+ if (gtar --version > /dev/null 2>&1); then
+ gtar "$@" && exit 0
+ fi
+ firstarg="$1"
+ if shift; then
+ case $firstarg in
+ *o*)
+ firstarg=`echo "$firstarg" | sed s/o//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ case $firstarg in
+ *h*)
+ firstarg=`echo "$firstarg" | sed s/h//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ fi
+
+ echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+ You may want to install GNU tar or Free paxutils, or check the
+ command line arguments."
+ exit 1
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
-perl_URL=http://www.perl.org/
-flex_URL=http://flex.sourceforge.net/
-gnu_software_URL=http://www.gnu.org/software
-
-program_details ()
-{
- case $1 in
- aclocal|automake)
- echo "The '$1' program is part of the GNU Automake package:"
- echo "<$gnu_software_URL/automake>"
- echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
- echo "<$gnu_software_URL/autoconf>"
- echo "<$gnu_software_URL/m4/>"
- echo "<$perl_URL>"
- ;;
- autoconf|autom4te|autoheader)
- echo "The '$1' program is part of the GNU Autoconf package:"
- echo "<$gnu_software_URL/autoconf/>"
- echo "It also requires GNU m4 and Perl in order to run:"
- echo "<$gnu_software_URL/m4/>"
- echo "<$perl_URL>"
- ;;
- esac
-}
-
-give_advice ()
-{
- # Normalize program name to check for.
- normalized_program=`echo "$1" | sed '
- s/^gnu-//; t
- s/^gnu//; t
- s/^g//; t'`
-
- printf '%s\n' "'$1' is $msg."
-
- configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
- case $normalized_program in
- autoconf*)
- echo "You should only need it if you modified 'configure.ac',"
- echo "or m4 files included by it."
- program_details 'autoconf'
- ;;
- autoheader*)
- echo "You should only need it if you modified 'acconfig.h' or"
- echo "$configure_deps."
- program_details 'autoheader'
- ;;
- automake*)
- echo "You should only need it if you modified 'Makefile.am' or"
- echo "$configure_deps."
- program_details 'automake'
- ;;
- aclocal*)
- echo "You should only need it if you modified 'acinclude.m4' or"
- echo "$configure_deps."
- program_details 'aclocal'
- ;;
- autom4te*)
- echo "You might have modified some maintainer files that require"
- echo "the 'autom4te' program to be rebuilt."
- program_details 'autom4te'
- ;;
- bison*|yacc*)
- echo "You should only need it if you modified a '.y' file."
- echo "You may want to install the GNU Bison package:"
- echo "<$gnu_software_URL/bison/>"
- ;;
- lex*|flex*)
- echo "You should only need it if you modified a '.l' file."
- echo "You may want to install the Fast Lexical Analyzer package:"
- echo "<$flex_URL>"
- ;;
- help2man*)
- echo "You should only need it if you modified a dependency" \
- "of a man page."
- echo "You may want to install the GNU Help2man package:"
- echo "<$gnu_software_URL/help2man/>"
- ;;
- makeinfo*)
- echo "You should only need it if you modified a '.texi' file, or"
- echo "any other file indirectly affecting the aspect of the manual."
- echo "You might want to install the Texinfo package:"
- echo "<$gnu_software_URL/texinfo/>"
- echo "The spurious makeinfo call might also be the consequence of"
- echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
- echo "want to install GNU make:"
- echo "<$gnu_software_URL/make/>"
- ;;
- *)
- echo "You might have modified some files without having the proper"
- echo "tools for further handling them. Check the 'README' file, it"
- echo "often tells you about the needed prerequisites for installing"
- echo "this package. You may also peek at any GNU archive site, in"
- echo "case some other package contains this missing '$1' program."
- ;;
- esac
-}
-
-give_advice "$1" | sed -e '1s/^/WARNING: /' \
- -e '2,$s/^/ /' >&2
-
-# Propagate the correct exit status (expected to be 127 for a program
-# not found, 63 for a program that failed due to version mismatch).
-exit $st
+exit 0
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
diff --git a/config/test-driver b/config/test-driver
deleted file mode 100755
index 8e575b0..0000000
--- a/config/test-driver
+++ /dev/null
@@ -1,148 +0,0 @@
-#! /bin/sh
-# test-driver - basic testsuite driver script.
-
-scriptversion=2013-07-13.22; # UTC
-
-# Copyright (C) 2011-2014 Free Software Foundation, Inc.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# This file is maintained in Automake, please report
-# bugs to <bug-automake at gnu.org> or send patches to
-# <automake-patches at gnu.org>.
-
-# Make unconditional expansion of undefined variables an error. This
-# helps a lot in preventing typo-related bugs.
-set -u
-
-usage_error ()
-{
- echo "$0: $*" >&2
- print_usage >&2
- exit 2
-}
-
-print_usage ()
-{
- cat <<END
-Usage:
- test-driver --test-name=NAME --log-file=PATH --trs-file=PATH
- [--expect-failure={yes|no}] [--color-tests={yes|no}]
- [--enable-hard-errors={yes|no}] [--]
- TEST-SCRIPT [TEST-SCRIPT-ARGUMENTS]
-The '--test-name', '--log-file' and '--trs-file' options are mandatory.
-END
-}
-
-test_name= # Used for reporting.
-log_file= # Where to save the output of the test script.
-trs_file= # Where to save the metadata of the test run.
-expect_failure=no
-color_tests=no
-enable_hard_errors=yes
-while test $# -gt 0; do
- case $1 in
- --help) print_usage; exit $?;;
- --version) echo "test-driver $scriptversion"; exit $?;;
- --test-name) test_name=$2; shift;;
- --log-file) log_file=$2; shift;;
- --trs-file) trs_file=$2; shift;;
- --color-tests) color_tests=$2; shift;;
- --expect-failure) expect_failure=$2; shift;;
- --enable-hard-errors) enable_hard_errors=$2; shift;;
- --) shift; break;;
- -*) usage_error "invalid option: '$1'";;
- *) break;;
- esac
- shift
-done
-
-missing_opts=
-test x"$test_name" = x && missing_opts="$missing_opts --test-name"
-test x"$log_file" = x && missing_opts="$missing_opts --log-file"
-test x"$trs_file" = x && missing_opts="$missing_opts --trs-file"
-if test x"$missing_opts" != x; then
- usage_error "the following mandatory options are missing:$missing_opts"
-fi
-
-if test $# -eq 0; then
- usage_error "missing argument"
-fi
-
-if test $color_tests = yes; then
- # Keep this in sync with 'lib/am/check.am:$(am__tty_colors)'.
- red='[0;31m' # Red.
- grn='[0;32m' # Green.
- lgn='[1;32m' # Light green.
- blu='[1;34m' # Blue.
- mgn='[0;35m' # Magenta.
- std='[m' # No color.
-else
- red= grn= lgn= blu= mgn= std=
-fi
-
-do_exit='rm -f $log_file $trs_file; (exit $st); exit $st'
-trap "st=129; $do_exit" 1
-trap "st=130; $do_exit" 2
-trap "st=141; $do_exit" 13
-trap "st=143; $do_exit" 15
-
-# Test script is run here.
-"$@" >$log_file 2>&1
-estatus=$?
-
-if test $enable_hard_errors = no && test $estatus -eq 99; then
- tweaked_estatus=1
-else
- tweaked_estatus=$estatus
-fi
-
-case $tweaked_estatus:$expect_failure in
- 0:yes) col=$red res=XPASS recheck=yes gcopy=yes;;
- 0:*) col=$grn res=PASS recheck=no gcopy=no;;
- 77:*) col=$blu res=SKIP recheck=no gcopy=yes;;
- 99:*) col=$mgn res=ERROR recheck=yes gcopy=yes;;
- *:yes) col=$lgn res=XFAIL recheck=no gcopy=yes;;
- *:*) col=$red res=FAIL recheck=yes gcopy=yes;;
-esac
-
-# Report the test outcome and exit status in the logs, so that one can
-# know whether the test passed or failed simply by looking at the '.log'
-# file, without the need of also peaking into the corresponding '.trs'
-# file (automake bug#11814).
-echo "$res $test_name (exit status: $estatus)" >>$log_file
-
-# Report outcome to console.
-echo "${col}${res}${std}: $test_name"
-
-# Register the test result, and other relevant metadata.
-echo ":test-result: $res" > $trs_file
-echo ":global-test-result: $res" >> $trs_file
-echo ":recheck: $recheck" >> $trs_file
-echo ":copy-in-global-log: $gcopy" >> $trs_file
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:
diff --git a/configure b/configure
index 920893f..bfd0514 100755
--- a/configure
+++ b/configure
@@ -1,20 +1,18 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for Stacks 1.44.
-#
-#
-# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
-#
+# Generated by GNU Autoconf 2.63 for Stacks 1.46.
#
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
# This configure script is free software; the Free Software Foundation
# gives unlimited permission to copy, distribute and modify it.
-## -------------------- ##
-## M4sh Initialization. ##
-## -------------------- ##
+## --------------------- ##
+## M4sh Initialization. ##
+## --------------------- ##
# Be more Bourne compatible
DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
emulate sh
NULLCMD=:
# Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
@@ -22,15 +20,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
alias -g '${1+"$@"}'='"$@"'
setopt NO_GLOB_SUBST
else
- case `(set -o) 2>/dev/null` in #(
- *posix*) :
- set -o posix ;; #(
- *) :
- ;;
+ case `(set -o) 2>/dev/null` in
+ *posix*) set -o posix ;;
esac
+
fi
+
+
+# PATH needs CR
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
as_nl='
'
export as_nl
@@ -38,13 +44,7 @@ export as_nl
as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-# Prefer a ksh shell builtin over an external printf program on Solaris,
-# but without wasting forks for bash or zsh.
-if test -z "$BASH_VERSION$ZSH_VERSION" \
- && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
- as_echo='print -r --'
- as_echo_n='print -rn --'
-elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
as_echo='printf %s\n'
as_echo_n='printf %s'
else
@@ -55,7 +55,7 @@ else
as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
as_echo_n_body='eval
arg=$1;
- case $arg in #(
+ case $arg in
*"$as_nl"*)
expr "X$arg" : "X\\(.*\\)$as_nl";
arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
@@ -78,6 +78,13 @@ if test "${PATH_SEPARATOR+set}" != set; then
}
fi
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ as_unset=unset
+else
+ as_unset=false
+fi
+
# IFS
# We need space, tab and new line, in precisely that order. Quoting is
@@ -87,16 +94,15 @@ fi
IFS=" "" $as_nl"
# Find who we are. Look in the path if we contain no directory separator.
-as_myself=
-case $0 in #((
+case $0 in
*[\\/]* ) as_myself=$0 ;;
*) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
- done
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+done
IFS=$as_save_IFS
;;
@@ -108,16 +114,12 @@ if test "x$as_myself" = x; then
fi
if test ! -f "$as_myself"; then
$as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
- exit 1
+ { (exit 1); exit 1; }
fi
-# Unset variables that we do not need and which cause bugs (e.g. in
-# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
-# suppresses any "Segmentation fault" message there. '((' could
-# trigger a bug in pdksh 5.2.14.
-for as_var in BASH_ENV ENV MAIL MAILPATH
-do eval test x\${$as_var+set} = xset \
- && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+# Work around bugs in pre-3.0 UWIN ksh.
+for as_var in ENV MAIL MAILPATH
+do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
done
PS1='$ '
PS2='> '
@@ -129,293 +131,7 @@ export LC_ALL
LANGUAGE=C
export LANGUAGE
-# CDPATH.
-(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-
-# Use a proper internal environment variable to ensure we don't fall
- # into an infinite loop, continuously re-executing ourselves.
- if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then
- _as_can_reexec=no; export _as_can_reexec;
- # We cannot yet assume a decent shell, so we have to provide a
-# neutralization value for shells without unset; and this also
-# works around shells that cannot unset nonexistent variables.
-# Preserve -v and -x to the replacement shell.
-BASH_ENV=/dev/null
-ENV=/dev/null
-(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
-case $- in # ((((
- *v*x* | *x*v* ) as_opts=-vx ;;
- *v* ) as_opts=-v ;;
- *x* ) as_opts=-x ;;
- * ) as_opts= ;;
-esac
-exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
-# Admittedly, this is quite paranoid, since all the known shells bail
-# out after a failed `exec'.
-$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
-as_fn_exit 255
- fi
- # We don't want this to propagate to other subprocesses.
- { _as_can_reexec=; unset _as_can_reexec;}
-if test "x$CONFIG_SHELL" = x; then
- as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
- emulate sh
- NULLCMD=:
- # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
- # is contrary to our usage. Disable this feature.
- alias -g '\${1+\"\$@\"}'='\"\$@\"'
- setopt NO_GLOB_SUBST
-else
- case \`(set -o) 2>/dev/null\` in #(
- *posix*) :
- set -o posix ;; #(
- *) :
- ;;
-esac
-fi
-"
- as_required="as_fn_return () { (exit \$1); }
-as_fn_success () { as_fn_return 0; }
-as_fn_failure () { as_fn_return 1; }
-as_fn_ret_success () { return 0; }
-as_fn_ret_failure () { return 1; }
-
-exitcode=0
-as_fn_success || { exitcode=1; echo as_fn_success failed.; }
-as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
-as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
-as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
-if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
-
-else
- exitcode=1; echo positional parameters were not saved.
-fi
-test x\$exitcode = x0 || exit 1
-test -x / || exit 1"
- as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
- as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
- eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
- test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
-test \$(( 1 + 1 )) = 2 || exit 1"
- if (eval "$as_required") 2>/dev/null; then :
- as_have_required=yes
-else
- as_have_required=no
-fi
- if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
-
-else
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-as_found=false
-for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- as_found=:
- case $as_dir in #(
- /*)
- for as_base in sh bash ksh sh5; do
- # Try only shells that exist, to save several forks.
- as_shell=$as_dir/$as_base
- if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
- { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
- CONFIG_SHELL=$as_shell as_have_required=yes
- if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
- break 2
-fi
-fi
- done;;
- esac
- as_found=false
-done
-$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
- { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
- CONFIG_SHELL=$SHELL as_have_required=yes
-fi; }
-IFS=$as_save_IFS
-
-
- if test "x$CONFIG_SHELL" != x; then :
- export CONFIG_SHELL
- # We cannot yet assume a decent shell, so we have to provide a
-# neutralization value for shells without unset; and this also
-# works around shells that cannot unset nonexistent variables.
-# Preserve -v and -x to the replacement shell.
-BASH_ENV=/dev/null
-ENV=/dev/null
-(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
-case $- in # ((((
- *v*x* | *x*v* ) as_opts=-vx ;;
- *v* ) as_opts=-v ;;
- *x* ) as_opts=-x ;;
- * ) as_opts= ;;
-esac
-exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
-# Admittedly, this is quite paranoid, since all the known shells bail
-# out after a failed `exec'.
-$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
-exit 255
-fi
-
- if test x$as_have_required = xno; then :
- $as_echo "$0: This script requires a shell more modern than all"
- $as_echo "$0: the shells that I found on your system."
- if test x${ZSH_VERSION+set} = xset ; then
- $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
- $as_echo "$0: be upgraded to zsh 4.3.4 or later."
- else
- $as_echo "$0: Please tell bug-autoconf at gnu.org about your system,
-$0: including any error possibly output before this
-$0: message. Then install a modern shell, or manually run
-$0: the script under such a shell if you do have one."
- fi
- exit 1
-fi
-fi
-fi
-SHELL=${CONFIG_SHELL-/bin/sh}
-export SHELL
-# Unset more variables known to interfere with behavior of common tools.
-CLICOLOR_FORCE= GREP_OPTIONS=
-unset CLICOLOR_FORCE GREP_OPTIONS
-
-## --------------------- ##
-## M4sh Shell Functions. ##
-## --------------------- ##
-# as_fn_unset VAR
-# ---------------
-# Portably unset VAR.
-as_fn_unset ()
-{
- { eval $1=; unset $1;}
-}
-as_unset=as_fn_unset
-
-# as_fn_set_status STATUS
-# -----------------------
-# Set $? to STATUS, without forking.
-as_fn_set_status ()
-{
- return $1
-} # as_fn_set_status
-
-# as_fn_exit STATUS
-# -----------------
-# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
-as_fn_exit ()
-{
- set +e
- as_fn_set_status $1
- exit $1
-} # as_fn_exit
-
-# as_fn_mkdir_p
-# -------------
-# Create "$as_dir" as a directory, including parents if necessary.
-as_fn_mkdir_p ()
-{
-
- case $as_dir in #(
- -*) as_dir=./$as_dir;;
- esac
- test -d "$as_dir" || eval $as_mkdir_p || {
- as_dirs=
- while :; do
- case $as_dir in #(
- *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
- *) as_qdir=$as_dir;;
- esac
- as_dirs="'$as_qdir' $as_dirs"
- as_dir=`$as_dirname -- "$as_dir" ||
-$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$as_dir" : 'X\(//\)[^/]' \| \
- X"$as_dir" : 'X\(//\)$' \| \
- X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$as_dir" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
- test -d "$as_dir" && break
- done
- test -z "$as_dirs" || eval "mkdir $as_dirs"
- } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
-
-
-} # as_fn_mkdir_p
-
-# as_fn_executable_p FILE
-# -----------------------
-# Test if FILE is an executable regular file.
-as_fn_executable_p ()
-{
- test -f "$1" && test -x "$1"
-} # as_fn_executable_p
-# as_fn_append VAR VALUE
-# ----------------------
-# Append the text in VALUE to the end of the definition contained in VAR. Take
-# advantage of any shell optimizations that allow amortized linear growth over
-# repeated appends, instead of the typical quadratic growth present in naive
-# implementations.
-if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
- eval 'as_fn_append ()
- {
- eval $1+=\$2
- }'
-else
- as_fn_append ()
- {
- eval $1=\$$1\$2
- }
-fi # as_fn_append
-
-# as_fn_arith ARG...
-# ------------------
-# Perform arithmetic evaluation on the ARGs, and store the result in the
-# global $as_val. Take advantage of shells that can avoid forks. The arguments
-# must be portable across $(()) and expr.
-if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
- eval 'as_fn_arith ()
- {
- as_val=$(( $* ))
- }'
-else
- as_fn_arith ()
- {
- as_val=`expr "$@" || test $? -eq 1`
- }
-fi # as_fn_arith
-
-
-# as_fn_error STATUS ERROR [LINENO LOG_FD]
-# ----------------------------------------
-# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
-# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with STATUS, using 1 if that was 0.
-as_fn_error ()
-{
- as_status=$1; test $as_status -eq 0 && as_status=1
- if test "$4"; then
- as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
- fi
- $as_echo "$as_me: error: $2" >&2
- as_fn_exit $as_status
-} # as_fn_error
-
+# Required to use basename.
if expr a : '\(a\)' >/dev/null 2>&1 &&
test "X`expr 00001 : '.*\(...\)'`" = X001; then
as_expr=expr
@@ -429,12 +145,8 @@ else
as_basename=false
fi
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
- as_dirname=dirname
-else
- as_dirname=false
-fi
+# Name of the executable.
as_me=`$as_basename -- "$0" ||
$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
X"$0" : 'X\(//\)$' \| \
@@ -454,133 +166,437 @@ $as_echo X/"$0" |
}
s/.*/./; q'`
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
+# CDPATH.
+$as_unset CDPATH
- as_lineno_1=$LINENO as_lineno_1a=$LINENO
- as_lineno_2=$LINENO as_lineno_2a=$LINENO
- eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
- test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
- # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
- sed -n '
- p
- /[$]LINENO/=
- ' <$as_myself |
- sed '
- s/[$]LINENO.*/&-/
- t lineno
- b
- :lineno
- N
- :loop
- s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
- t loop
- s/-\n.*//
- ' >$as_me.lineno &&
- chmod +x "$as_me.lineno" ||
- { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+if test "x$CONFIG_SHELL" = x; then
+ if (eval ":") 2>/dev/null; then
+ as_have_required=yes
+else
+ as_have_required=no
+fi
- # If we had to re-execute with $CONFIG_SHELL, we're ensured to have
- # already done that, so ensure we don't try to do so again and fall
- # in an infinite loop. This has already happened in practice.
- _as_can_reexec=no; export _as_can_reexec
- # Don't try to exec as it changes $[0], causing all sort of problems
- # (the dirname of $[0] is not the place where we might find the
- # original and so on. Autoconf is especially sensitive to this).
- . "./$as_me.lineno"
- # Exit status is that of the last command.
- exit
+ if test $as_have_required = yes && (eval ":
+(as_func_return () {
+ (exit \$1)
+}
+as_func_success () {
+ as_func_return 0
+}
+as_func_failure () {
+ as_func_return 1
+}
+as_func_ret_success () {
+ return 0
+}
+as_func_ret_failure () {
+ return 1
}
-ECHO_C= ECHO_N= ECHO_T=
-case `echo -n x` in #(((((
--n*)
- case `echo 'xy\c'` in
- *c*) ECHO_T=' ';; # ECHO_T is single tab character.
- xy) ECHO_C='\c';;
- *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
- ECHO_T=' ';;
- esac;;
-*)
- ECHO_N='-n';;
-esac
-
-rm -f conf$$ conf$$.exe conf$$.file
-if test -d conf$$.dir; then
- rm -f conf$$.dir/conf$$.file
+exitcode=0
+if as_func_success; then
+ :
else
- rm -f conf$$.dir
- mkdir conf$$.dir 2>/dev/null
+ exitcode=1
+ echo as_func_success failed.
fi
-if (echo >conf$$.file) 2>/dev/null; then
- if ln -s conf$$.file conf$$ 2>/dev/null; then
- as_ln_s='ln -s'
- # ... but there are two gotchas:
- # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
- # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
- # In both cases, we have to default to `cp -pR'.
- ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
- as_ln_s='cp -pR'
- elif ln conf$$.file conf$$ 2>/dev/null; then
- as_ln_s=ln
- else
- as_ln_s='cp -pR'
- fi
-else
- as_ln_s='cp -pR'
+
+if as_func_failure; then
+ exitcode=1
+ echo as_func_failure succeeded.
fi
-rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
-rmdir conf$$.dir 2>/dev/null
-if mkdir -p . 2>/dev/null; then
- as_mkdir_p='mkdir -p "$as_dir"'
+if as_func_ret_success; then
+ :
else
- test -d ./-p && rmdir ./-p
- as_mkdir_p=false
+ exitcode=1
+ echo as_func_ret_success failed.
fi
-as_test_x='test -x'
-as_executable_p=as_fn_executable_p
+if as_func_ret_failure; then
+ exitcode=1
+ echo as_func_ret_failure succeeded.
+fi
-# Sed expression to map a string onto a valid CPP name.
-as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
+ :
+else
+ exitcode=1
+ echo positional parameters were not saved.
+fi
-# Sed expression to map a string onto a valid variable name.
-as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+test \$exitcode = 0) || { (exit 1); exit 1; }
+(
+ as_lineno_1=\$LINENO
+ as_lineno_2=\$LINENO
+ test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
+ test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
+") 2> /dev/null; then
+ :
+else
+ as_candidate_shells=
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ case $as_dir in
+ /*)
+ for as_base in sh bash ksh sh5; do
+ as_candidate_shells="$as_candidate_shells $as_dir/$as_base"
+ done;;
+ esac
+done
+IFS=$as_save_IFS
-test -n "$DJDIR" || exec 7<&0 </dev/null
-exec 6>&1
-# Name of the host.
-# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
-# so uname gets run too.
-ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+ for as_shell in $as_candidate_shells $SHELL; do
+ # Try only shells that exist, to save several forks.
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { ("$as_shell") 2> /dev/null <<\_ASEOF
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in
+ *posix*) set -o posix ;;
+esac
-#
-# Initializations.
-#
-ac_default_prefix=/usr/local
-ac_clean_files=
-ac_config_libobj_dir=.
-LIBOBJS=
-cross_compiling=no
-subdirs=
-MFLAGS=
-MAKEFLAGS=
+fi
-# Identity of this package.
-PACKAGE_NAME='Stacks'
-PACKAGE_TARNAME='stacks'
-PACKAGE_VERSION='1.44'
-PACKAGE_STRING='Stacks 1.44'
-PACKAGE_BUGREPORT=''
-PACKAGE_URL=''
+
+:
+_ASEOF
+}; then
+ CONFIG_SHELL=$as_shell
+ as_have_required=yes
+ if { "$as_shell" 2> /dev/null <<\_ASEOF
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in
+ *posix*) set -o posix ;;
+esac
+
+fi
+
+
+:
+(as_func_return () {
+ (exit $1)
+}
+as_func_success () {
+ as_func_return 0
+}
+as_func_failure () {
+ as_func_return 1
+}
+as_func_ret_success () {
+ return 0
+}
+as_func_ret_failure () {
+ return 1
+}
+
+exitcode=0
+if as_func_success; then
+ :
+else
+ exitcode=1
+ echo as_func_success failed.
+fi
+
+if as_func_failure; then
+ exitcode=1
+ echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+ :
+else
+ exitcode=1
+ echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+ exitcode=1
+ echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = "$1" ); then
+ :
+else
+ exitcode=1
+ echo positional parameters were not saved.
+fi
+
+test $exitcode = 0) || { (exit 1); exit 1; }
+
+(
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
+
+_ASEOF
+}; then
+ break
+fi
+
+fi
+
+ done
+
+ if test "x$CONFIG_SHELL" != x; then
+ for as_var in BASH_ENV ENV
+ do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+ done
+ export CONFIG_SHELL
+ exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
+fi
+
+
+ if test $as_have_required = no; then
+ echo This script requires a shell more modern than all the
+ echo shells that I found on your system. Please install a
+ echo modern shell, or manually run the script under such a
+ echo shell if you do have one.
+ { (exit 1); exit 1; }
+fi
+
+
+fi
+
+fi
+
+
+
+(eval "as_func_return () {
+ (exit \$1)
+}
+as_func_success () {
+ as_func_return 0
+}
+as_func_failure () {
+ as_func_return 1
+}
+as_func_ret_success () {
+ return 0
+}
+as_func_ret_failure () {
+ return 1
+}
+
+exitcode=0
+if as_func_success; then
+ :
+else
+ exitcode=1
+ echo as_func_success failed.
+fi
+
+if as_func_failure; then
+ exitcode=1
+ echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+ :
+else
+ exitcode=1
+ echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+ exitcode=1
+ echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
+ :
+else
+ exitcode=1
+ echo positional parameters were not saved.
+fi
+
+test \$exitcode = 0") || {
+ echo No shell found that supports shell functions.
+ echo Please tell bug-autoconf at gnu.org about your system,
+ echo including any error possibly output before this message.
+ echo This can help us improve future autoconf versions.
+ echo Configuration will now proceed without shell functions.
+}
+
+
+
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
+
+ # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
+ # uniformly replaced by the line number. The first 'sed' inserts a
+ # line-number line after each line using $LINENO; the second 'sed'
+ # does the real work. The second script uses 'N' to pair each
+ # line-number line with the line containing $LINENO, and appends
+ # trailing '-' during substitution so that $LINENO is not a special
+ # case at line end.
+ # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+ # scripts with optimization help from Paolo Bonzini. Blame Lee
+ # E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
+ { (exit 1); exit 1; }; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in
+-n*)
+ case `echo 'x\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ *) ECHO_C='\c';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p=:
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+
+exec 7<&0 </dev/null 6>&1
+
+# Name of the host.
+# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
+# so uname gets run too.
+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+#
+# Initializations.
+#
+ac_default_prefix=/usr/local
+ac_clean_files=
+ac_config_libobj_dir=.
+LIBOBJS=
+cross_compiling=no
+subdirs=
+MFLAGS=
+MAKEFLAGS=
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+# Identity of this package.
+PACKAGE_NAME='Stacks'
+PACKAGE_TARNAME='stacks'
+PACKAGE_VERSION='1.46'
+PACKAGE_STRING='Stacks 1.46'
+PACKAGE_BUGREPORT=''
ac_unique_file="src/ustacks.cc"
# Factoring default headers for most tests.
@@ -637,7 +653,6 @@ CC
am__fastdepCXX_FALSE
am__fastdepCXX_TRUE
CXXDEPMODE
-am__nodep
AMDEPBACKSLASH
AMDEP_FALSE
AMDEP_TRUE
@@ -654,10 +669,6 @@ CXX
SPARSEHASH_CFLAGS
BAM_LIBS
BAM_CFLAGS
-AM_BACKSLASH
-AM_DEFAULT_VERBOSITY
-AM_DEFAULT_V
-AM_V
am__untar
am__tar
AMTAR
@@ -711,7 +722,6 @@ bindir
program_transform_name
prefix
exec_prefix
-PACKAGE_URL
PACKAGE_BUGREPORT
PACKAGE_STRING
PACKAGE_VERSION
@@ -722,7 +732,6 @@ SHELL'
ac_subst_files=''
ac_user_opts='
enable_option_checking
-enable_silent_rules
enable_bam
enable_sparsehash
with_sparsehash_include_path
@@ -803,9 +812,8 @@ do
fi
case $ac_option in
- *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
- *=) ac_optarg= ;;
- *) ac_optarg=yes ;;
+ *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *) ac_optarg=yes ;;
esac
# Accept the important Cygnus configure options, so we can diagnose typos.
@@ -850,7 +858,8 @@ do
ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
# Reject names that are not valid shell variable names.
expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
- as_fn_error $? "invalid feature name: $ac_useropt"
+ { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2
+ { (exit 1); exit 1; }; }
ac_useropt_orig=$ac_useropt
ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
case $ac_user_opts in
@@ -876,7 +885,8 @@ do
ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
# Reject names that are not valid shell variable names.
expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
- as_fn_error $? "invalid feature name: $ac_useropt"
+ { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2
+ { (exit 1); exit 1; }; }
ac_useropt_orig=$ac_useropt
ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
case $ac_user_opts in
@@ -1080,7 +1090,8 @@ do
ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
# Reject names that are not valid shell variable names.
expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
- as_fn_error $? "invalid package name: $ac_useropt"
+ { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2
+ { (exit 1); exit 1; }; }
ac_useropt_orig=$ac_useropt
ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
case $ac_user_opts in
@@ -1096,7 +1107,8 @@ do
ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
# Reject names that are not valid shell variable names.
expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
- as_fn_error $? "invalid package name: $ac_useropt"
+ { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2
+ { (exit 1); exit 1; }; }
ac_useropt_orig=$ac_useropt
ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
case $ac_user_opts in
@@ -1126,17 +1138,17 @@ do
| --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
x_libraries=$ac_optarg ;;
- -*) as_fn_error $? "unrecognized option: \`$ac_option'
-Try \`$0 --help' for more information"
+ -*) { $as_echo "$as_me: error: unrecognized option: $ac_option
+Try \`$0 --help' for more information." >&2
+ { (exit 1); exit 1; }; }
;;
*=*)
ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
# Reject names that are not valid shell variable names.
- case $ac_envvar in #(
- '' | [0-9]* | *[!_$as_cr_alnum]* )
- as_fn_error $? "invalid variable name: \`$ac_envvar'" ;;
- esac
+ expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null &&
+ { $as_echo "$as_me: error: invalid variable name: $ac_envvar" >&2
+ { (exit 1); exit 1; }; }
eval $ac_envvar=\$ac_optarg
export $ac_envvar ;;
@@ -1145,7 +1157,7 @@ Try \`$0 --help' for more information"
$as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2
expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
$as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2
- : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}"
+ : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}
;;
esac
@@ -1153,13 +1165,15 @@ done
if test -n "$ac_prev"; then
ac_option=--`echo $ac_prev | sed 's/_/-/g'`
- as_fn_error $? "missing argument to $ac_option"
+ { $as_echo "$as_me: error: missing argument to $ac_option" >&2
+ { (exit 1); exit 1; }; }
fi
if test -n "$ac_unrecognized_opts"; then
case $enable_option_checking in
no) ;;
- fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;;
+ fatal) { $as_echo "$as_me: error: unrecognized options: $ac_unrecognized_opts" >&2
+ { (exit 1); exit 1; }; } ;;
*) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
esac
fi
@@ -1182,7 +1196,8 @@ do
[\\/$]* | ?:[\\/]* ) continue;;
NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
esac
- as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
+ { $as_echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2
+ { (exit 1); exit 1; }; }
done
# There might be people who depend on the old broken behavior: `$host'
@@ -1196,6 +1211,8 @@ target=$target_alias
if test "x$host_alias" != x; then
if test "x$build_alias" = x; then
cross_compiling=maybe
+ $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
+ If a cross compiler is detected then cross compile mode will be used." >&2
elif test "x$build_alias" != "x$host_alias"; then
cross_compiling=yes
fi
@@ -1210,9 +1227,11 @@ test "$silent" = yes && exec 6>/dev/null
ac_pwd=`pwd` && test -n "$ac_pwd" &&
ac_ls_di=`ls -di .` &&
ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
- as_fn_error $? "working directory cannot be determined"
+ { $as_echo "$as_me: error: working directory cannot be determined" >&2
+ { (exit 1); exit 1; }; }
test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
- as_fn_error $? "pwd does not report name of working directory"
+ { $as_echo "$as_me: error: pwd does not report name of working directory" >&2
+ { (exit 1); exit 1; }; }
# Find the source files, if location was not specified.
@@ -1251,11 +1270,13 @@ else
fi
if test ! -r "$srcdir/$ac_unique_file"; then
test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
- as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
+ { $as_echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2
+ { (exit 1); exit 1; }; }
fi
ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
ac_abs_confdir=`(
- cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
+ cd "$srcdir" && test -r "./$ac_unique_file" || { $as_echo "$as_me: error: $ac_msg" >&2
+ { (exit 1); exit 1; }; }
pwd)`
# When building in place, set srcdir=.
if test "$ac_abs_confdir" = "$ac_pwd"; then
@@ -1281,7 +1302,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures Stacks 1.44 to adapt to many kinds of systems.
+\`configure' configures Stacks 1.46 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1295,7 +1316,7 @@ Configuration:
--help=short display options specific to this package
--help=recursive display the short help of all the included packages
-V, --version display version information and exit
- -q, --quiet, --silent do not print \`checking ...' messages
+ -q, --quiet, --silent do not print \`checking...' messages
--cache-file=FILE cache test results in FILE [disabled]
-C, --config-cache alias for \`--cache-file=config.cache'
-n, --no-create do not create output files
@@ -1347,7 +1368,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of Stacks 1.44:";;
+ short | recursive ) echo "Configuration of Stacks 1.46:";;
esac
cat <<\_ACEOF
@@ -1355,15 +1376,11 @@ Optional Features:
--disable-option-checking ignore unrecognized --enable/--with options
--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
- --enable-silent-rules less verbose build output (undo: "make V=1")
- --disable-silent-rules verbose build output (undo: "make V=0")
--disable-bam Disable use of BAM files through HTSLib.
--enable-sparsehash Enable the use of Google Sparsehash (must be
installed).
- --enable-dependency-tracking
- do not reject slow dependency extractors
- --disable-dependency-tracking
- speeds up one-time build
+ --disable-dependency-tracking speeds up one-time build
+ --enable-dependency-tracking do not reject slow dependency extractors
--disable-openmp do not use OpenMP
Optional Packages:
@@ -1378,7 +1395,7 @@ Some influential environment variables:
LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir>
LIBS libraries to pass to the linker, e.g. -l<library>
- CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
+ CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
CC C compiler command
CFLAGS C compiler flags
@@ -1387,7 +1404,6 @@ Some influential environment variables:
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
-Report bugs to the package provider.
_ACEOF
ac_status=$?
fi
@@ -1450,502 +1466,59 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-Stacks configure 1.44
-generated by GNU Autoconf 2.69
+Stacks configure 1.46
+generated by GNU Autoconf 2.63
-Copyright (C) 2012 Free Software Foundation, Inc.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
This configure script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it.
_ACEOF
exit
fi
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
-## ------------------------ ##
-## Autoconf initialization. ##
-## ------------------------ ##
+It was created by Stacks $as_me 1.46, which was
+generated by GNU Autoconf 2.63. Invocation command line was
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-# ----------------------------
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-ac_fn_cxx_try_compile ()
-{
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- fi
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
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- ac_retval=0
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- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
+ $ $0 $@
- ac_retval=1
-fi
- eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
- as_fn_set_status $ac_retval
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
-} # ac_fn_cxx_try_compile
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
-# ac_fn_c_try_compile LINENO
-# --------------------------
-# Try to compile conftest.$ac_ext, and return whether this succeeded.
-ac_fn_c_try_compile ()
-{
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- rm -f conftest.$ac_objext
- if { { ac_try="$ac_compile"
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- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
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- eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
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+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
-} # ac_fn_c_try_compile
-
-# ac_fn_c_try_link LINENO
-# -----------------------
-# Try to link conftest.$ac_ext, and return whether this succeeded.
-ac_fn_c_try_link ()
-{
- as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- rm -f conftest.$ac_objext conftest$ac_exeext
- if { { ac_try="$ac_link"
-case "(($ac_try" in
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- *) ac_try_echo=$ac_try;;
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-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
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- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
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- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
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- # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
- # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
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- rm -rf conftest.dSYM conftest_ipa8_conftest.oo
- eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
- as_fn_set_status $ac_retval
-
-} # ac_fn_c_try_link
-
-# ac_fn_c_try_cpp LINENO
-# ----------------------
-# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
-ac_fn_c_try_cpp ()
-{
- as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- if { { ac_try="$ac_cpp conftest.$ac_ext"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
- ac_status=$?
- if test -s conftest.err; then
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- mv -f conftest.er1 conftest.err
- fi
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; } > conftest.i && {
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- }; then :
- ac_retval=0
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_retval=1
-fi
- eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
- as_fn_set_status $ac_retval
-
-} # ac_fn_c_try_cpp
-
-# ac_fn_c_try_run LINENO
-# ----------------------
-# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
-# that executables *can* be run.
-ac_fn_c_try_run ()
-{
- as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- if { { ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; } && { ac_try='./conftest$ac_exeext'
- { { case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }; }; then :
- ac_retval=0
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_retval=$ac_status
-fi
- rm -rf conftest.dSYM conftest_ipa8_conftest.oo
- eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
- as_fn_set_status $ac_retval
-
-} # ac_fn_c_try_run
-
-# ac_fn_c_check_header_mongrel LINENO HEADER VAR INCLUDES
-# -------------------------------------------------------
-# Tests whether HEADER exists, giving a warning if it cannot be compiled using
-# the include files in INCLUDES and setting the cache variable VAR
-# accordingly.
-ac_fn_c_check_header_mongrel ()
-{
- as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- if eval \${$3+:} false; then :
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-$as_echo_n "checking for $2... " >&6; }
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- $as_echo_n "(cached) " >&6
-fi
-eval ac_res=\$$3
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-else
- # Is the header compilable?
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
-$as_echo_n "checking $2 usability... " >&6; }
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-$4
-#include <$2>
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- ac_header_compiler=yes
-else
- ac_header_compiler=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
-$as_echo "$ac_header_compiler" >&6; }
-
-# Is the header present?
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5
-$as_echo_n "checking $2 presence... " >&6; }
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include <$2>
-_ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
- ac_header_preproc=yes
-else
- ac_header_preproc=no
-fi
-rm -f conftest.err conftest.i conftest.$ac_ext
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
-$as_echo "$ac_header_preproc" >&6; }
-
-# So? What about this header?
-case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in #((
- yes:no: )
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5
-$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;}
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
-$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
- ;;
- no:yes:* )
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5
-$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;}
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5
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- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5
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- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5
-$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
-$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
- ;;
-esac
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-$as_echo_n "checking for $2... " >&6; }
-if eval \${$3+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- eval "$3=\$ac_header_compiler"
-fi
-eval ac_res=\$$3
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-fi
- eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-
-} # ac_fn_c_check_header_mongrel
-
-# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES
-# -------------------------------------------------------
-# Tests whether HEADER exists and can be compiled using the include files in
-# INCLUDES, setting the cache variable VAR accordingly.
-ac_fn_c_check_header_compile ()
-{
- as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-$as_echo_n "checking for $2... " >&6; }
-if eval \${$3+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-$4
-#include <$2>
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- eval "$3=yes"
-else
- eval "$3=no"
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-eval ac_res=\$$3
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
- eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-
-} # ac_fn_c_check_header_compile
-
-# ac_fn_c_check_type LINENO TYPE VAR INCLUDES
-# -------------------------------------------
-# Tests whether TYPE exists after having included INCLUDES, setting cache
-# variable VAR accordingly.
-ac_fn_c_check_type ()
-{
- as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-$as_echo_n "checking for $2... " >&6; }
-if eval \${$3+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- eval "$3=no"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-$4
-int
-main ()
-{
-if (sizeof ($2))
- return 0;
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-$4
-int
-main ()
-{
-if (sizeof (($2)))
- return 0;
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-
-else
- eval "$3=yes"
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-eval ac_res=\$$3
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
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-
-} # ac_fn_c_check_type
-
-# ac_fn_c_check_func LINENO FUNC VAR
-# ----------------------------------
-# Tests whether FUNC exists, setting the cache variable VAR accordingly
-ac_fn_c_check_func ()
-{
- as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
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- $as_echo_n "(cached) " >&6
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- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
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-
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-
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-# include <limits.h>
-#else
-# include <assert.h>
-#endif
-
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-
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-#ifdef __cplusplus
-extern "C"
-#endif
-char $2 ();
-/* The GNU C library defines this for functions which it implements
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-#if defined __stub_$2 || defined __stub___$2
-choke me
-#endif
-
-int
-main ()
-{
-return $2 ();
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
- eval "$3=yes"
-else
- eval "$3=no"
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-fi
-eval ac_res=\$$3
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
- eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-
-} # ac_fn_c_check_func
-cat >config.log <<_ACEOF
-This file contains any messages produced by compilers while
-running configure, to aid debugging if configure makes a mistake.
-
-It was created by Stacks $as_me 1.44, which was
-generated by GNU Autoconf 2.69. Invocation command line was
-
- $ $0 $@
-
-_ACEOF
-exec 5>>config.log
-{
-cat <<_ASUNAME
-## --------- ##
-## Platform. ##
-## --------- ##
-
-hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
-uname -m = `(uname -m) 2>/dev/null || echo unknown`
-uname -r = `(uname -r) 2>/dev/null || echo unknown`
-uname -s = `(uname -s) 2>/dev/null || echo unknown`
-uname -v = `(uname -v) 2>/dev/null || echo unknown`
-
-/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
-/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
-
-/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
-/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
-/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
-/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
-/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
-/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
-/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
-
-_ASUNAME
+_ASUNAME
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- $as_echo "PATH: $as_dir"
- done
+ $as_echo "PATH: $as_dir"
+done
IFS=$as_save_IFS
} >&5
@@ -1982,9 +1555,9 @@ do
ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
esac
case $ac_pass in
- 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
+ 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;;
2)
- as_fn_append ac_configure_args1 " '$ac_arg'"
+ ac_configure_args1="$ac_configure_args1 '$ac_arg'"
if test $ac_must_keep_next = true; then
ac_must_keep_next=false # Got value, back to normal.
else
@@ -2000,13 +1573,13 @@ do
-* ) ac_must_keep_next=true ;;
esac
fi
- as_fn_append ac_configure_args " '$ac_arg'"
+ ac_configure_args="$ac_configure_args '$ac_arg'"
;;
esac
done
done
-{ ac_configure_args0=; unset ac_configure_args0;}
-{ ac_configure_args1=; unset ac_configure_args1;}
+$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; }
+$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; }
# When interrupted or exit'd, cleanup temporary files, and complete
# config.log. We remove comments because anyway the quotes in there
@@ -2018,9 +1591,11 @@ trap 'exit_status=$?
{
echo
- $as_echo "## ---------------- ##
+ cat <<\_ASBOX
+## ---------------- ##
## Cache variables. ##
-## ---------------- ##"
+## ---------------- ##
+_ASBOX
echo
# The following way of writing the cache mishandles newlines in values,
(
@@ -2029,13 +1604,13 @@ trap 'exit_status=$?
case $ac_val in #(
*${as_nl}*)
case $ac_var in #(
- *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+ *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5
$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
esac
case $ac_var in #(
_ | IFS | as_nl) ;; #(
BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
- *) { eval $ac_var=; unset $ac_var;} ;;
+ *) $as_unset $ac_var ;;
esac ;;
esac
done
@@ -2054,9 +1629,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
)
echo
- $as_echo "## ----------------- ##
+ cat <<\_ASBOX
+## ----------------- ##
## Output variables. ##
-## ----------------- ##"
+## ----------------- ##
+_ASBOX
echo
for ac_var in $ac_subst_vars
do
@@ -2069,9 +1646,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
echo
if test -n "$ac_subst_files"; then
- $as_echo "## ------------------- ##
+ cat <<\_ASBOX
+## ------------------- ##
## File substitutions. ##
-## ------------------- ##"
+## ------------------- ##
+_ASBOX
echo
for ac_var in $ac_subst_files
do
@@ -2085,9 +1664,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
fi
if test -s confdefs.h; then
- $as_echo "## ----------- ##
+ cat <<\_ASBOX
+## ----------- ##
## confdefs.h. ##
-## ----------- ##"
+## ----------- ##
+_ASBOX
echo
cat confdefs.h
echo
@@ -2101,39 +1682,37 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
exit $exit_status
' 0
for ac_signal in 1 2 13 15; do
- trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
+ trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal
done
ac_signal=0
# confdefs.h avoids OS command line length limits that DEFS can exceed.
rm -f -r conftest* confdefs.h
-$as_echo "/* confdefs.h */" > confdefs.h
-
# Predefined preprocessor variables.
cat >>confdefs.h <<_ACEOF
#define PACKAGE_NAME "$PACKAGE_NAME"
_ACEOF
+
cat >>confdefs.h <<_ACEOF
#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
_ACEOF
+
cat >>confdefs.h <<_ACEOF
#define PACKAGE_VERSION "$PACKAGE_VERSION"
_ACEOF
+
cat >>confdefs.h <<_ACEOF
#define PACKAGE_STRING "$PACKAGE_STRING"
_ACEOF
-cat >>confdefs.h <<_ACEOF
-#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
-_ACEOF
cat >>confdefs.h <<_ACEOF
-#define PACKAGE_URL "$PACKAGE_URL"
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
_ACEOF
@@ -2142,12 +1721,7 @@ _ACEOF
ac_site_file1=NONE
ac_site_file2=NONE
if test -n "$CONFIG_SITE"; then
- # We do not want a PATH search for config.site.
- case $CONFIG_SITE in #((
- -*) ac_site_file1=./$CONFIG_SITE;;
- */*) ac_site_file1=$CONFIG_SITE;;
- *) ac_site_file1=./$CONFIG_SITE;;
- esac
+ ac_site_file1=$CONFIG_SITE
elif test "x$prefix" != xNONE; then
ac_site_file1=$prefix/share/config.site
ac_site_file2=$prefix/etc/config.site
@@ -2158,23 +1732,19 @@ fi
for ac_site_file in "$ac_site_file1" "$ac_site_file2"
do
test "x$ac_site_file" = xNONE && continue
- if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
+ if test -r "$ac_site_file"; then
+ { $as_echo "$as_me:$LINENO: loading site script $ac_site_file" >&5
$as_echo "$as_me: loading site script $ac_site_file" >&6;}
sed 's/^/| /' "$ac_site_file" >&5
- . "$ac_site_file" \
- || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "failed to load site script $ac_site_file
-See \`config.log' for more details" "$LINENO" 5; }
+ . "$ac_site_file"
fi
done
if test -r "$cache_file"; then
- # Some versions of bash will fail to source /dev/null (special files
- # actually), so we avoid doing that. DJGPP emulates it as a regular file.
- if test /dev/null != "$cache_file" && test -f "$cache_file"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+ # Some versions of bash will fail to source /dev/null (special
+ # files actually), so we avoid doing that.
+ if test -f "$cache_file"; then
+ { $as_echo "$as_me:$LINENO: loading cache $cache_file" >&5
$as_echo "$as_me: loading cache $cache_file" >&6;}
case $cache_file in
[\\/]* | ?:[\\/]* ) . "$cache_file";;
@@ -2182,7 +1752,7 @@ $as_echo "$as_me: loading cache $cache_file" >&6;}
esac
fi
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+ { $as_echo "$as_me:$LINENO: creating cache $cache_file" >&5
$as_echo "$as_me: creating cache $cache_file" >&6;}
>$cache_file
fi
@@ -2197,11 +1767,11 @@ for ac_var in $ac_precious_vars; do
eval ac_new_val=\$ac_env_${ac_var}_value
case $ac_old_set,$ac_new_set in
set,)
- { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+ { $as_echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
ac_cache_corrupted=: ;;
,set)
- { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+ { $as_echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5
$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
ac_cache_corrupted=: ;;
,);;
@@ -2211,17 +1781,17 @@ $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
ac_old_val_w=`echo x $ac_old_val`
ac_new_val_w=`echo x $ac_new_val`
if test "$ac_old_val_w" != "$ac_new_val_w"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+ { $as_echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5
$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
ac_cache_corrupted=:
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+ { $as_echo "$as_me:$LINENO: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
eval $ac_var=\$ac_old_val
fi
- { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+ { $as_echo "$as_me:$LINENO: former value: \`$ac_old_val'" >&5
$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
- { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+ { $as_echo "$as_me:$LINENO: current value: \`$ac_new_val'" >&5
$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
fi;;
esac
@@ -2233,20 +1803,43 @@ $as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
esac
case " $ac_configure_args " in
*" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
- *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ *) ac_configure_args="$ac_configure_args '$ac_arg'" ;;
esac
fi
done
if $ac_cache_corrupted; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
- { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+ { $as_echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5
$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
- as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5
+$as_echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;}
+ { (exit 1); exit 1; }; }
fi
-## -------------------- ##
-## Main body of script. ##
-## -------------------- ##
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
@@ -2272,7 +1865,9 @@ for ac_dir in config "$srcdir"/config; do
fi
done
if test -z "$ac_aux_dir"; then
- as_fn_error $? "cannot find install-sh, install.sh, or shtool in config \"$srcdir\"/config" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in config \"$srcdir\"/config" >&5
+$as_echo "$as_me: error: cannot find install-sh or install.sh in config \"$srcdir\"/config" >&2;}
+ { (exit 1); exit 1; }; }
fi
# These three variables are undocumented and unsupported,
@@ -2284,7 +1879,7 @@ ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
-am__api_version='1.15'
+am__api_version='1.11'
# Find a good install program. We prefer a C program (faster),
# so one script is as good as another. But avoid the broken or
@@ -2300,10 +1895,10 @@ am__api_version='1.15'
# OS/2's system install, which has a completely different semantic
# ./install, which can be erroneously created by make from ./install.sh.
# Reject install programs that cannot install multiple files.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
+{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
$as_echo_n "checking for a BSD-compatible install... " >&6; }
if test -z "$INSTALL"; then
-if ${ac_cv_path_install+:} false; then :
+if test "${ac_cv_path_install+set}" = set; then
$as_echo_n "(cached) " >&6
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
@@ -2311,11 +1906,11 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- # Account for people who put trailing slashes in PATH elements.
-case $as_dir/ in #((
- ./ | .// | /[cC]/* | \
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in
+ ./ | .// | /cC/* | \
/etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
- ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
+ ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
/usr/ucb/* ) ;;
*)
# OSF1 and SCO ODT 3.0 have their own names for install.
@@ -2323,7 +1918,7 @@ case $as_dir/ in #((
# by default.
for ac_prog in ginstall scoinst install; do
for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
if test $ac_prog = install &&
grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
# AIX install. It has an incompatible calling convention.
@@ -2352,7 +1947,7 @@ case $as_dir/ in #((
;;
esac
- done
+done
IFS=$as_save_IFS
rm -rf conftest.one conftest.two conftest.dir
@@ -2368,7 +1963,7 @@ fi
INSTALL=$ac_install_sh
fi
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
+{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5
$as_echo "$INSTALL" >&6; }
# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
@@ -2379,73 +1974,68 @@ test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
+{ $as_echo "$as_me:$LINENO: checking whether build environment is sane" >&5
$as_echo_n "checking whether build environment is sane... " >&6; }
+# Just in case
+sleep 1
+echo timestamp > conftest.file
# Reject unsafe characters in $srcdir or the absolute working directory
# name. Accept space and tab only in the latter.
am_lf='
'
case `pwd` in
*[\\\"\#\$\&\'\`$am_lf]*)
- as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5;;
+ { { $as_echo "$as_me:$LINENO: error: unsafe absolute working directory name" >&5
+$as_echo "$as_me: error: unsafe absolute working directory name" >&2;}
+ { (exit 1); exit 1; }; };;
esac
case $srcdir in
*[\\\"\#\$\&\'\`$am_lf\ \ ]*)
- as_fn_error $? "unsafe srcdir value: '$srcdir'" "$LINENO" 5;;
+ { { $as_echo "$as_me:$LINENO: error: unsafe srcdir value: \`$srcdir'" >&5
+$as_echo "$as_me: error: unsafe srcdir value: \`$srcdir'" >&2;}
+ { (exit 1); exit 1; }; };;
esac
-# Do 'set' in a subshell so we don't clobber the current shell's
+# Do `set' in a subshell so we don't clobber the current shell's
# arguments. Must try -L first in case configure is actually a
# symlink; some systems play weird games with the mod time of symlinks
# (eg FreeBSD returns the mod time of the symlink's containing
# directory).
if (
- am_has_slept=no
- for am_try in 1 2; do
- echo "timestamp, slept: $am_has_slept" > conftest.file
- set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
- if test "$*" = "X"; then
- # -L didn't work.
- set X `ls -t "$srcdir/configure" conftest.file`
- fi
- if test "$*" != "X $srcdir/configure conftest.file" \
- && test "$*" != "X conftest.file $srcdir/configure"; then
-
- # If neither matched, then we have a broken ls. This can happen
- # if, for instance, CONFIG_SHELL is bash and it inherits a
- # broken ls alias from the environment. This has actually
- # happened. Such a system could not be considered "sane".
- as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
- alias in your environment" "$LINENO" 5
- fi
- if test "$2" = conftest.file || test $am_try -eq 2; then
- break
- fi
- # Just in case.
- sleep 1
- am_has_slept=yes
- done
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t "$srcdir/configure" conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ { { $as_echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken
+alias in your environment" >&5
+$as_echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken
+alias in your environment" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+
test "$2" = conftest.file
)
then
# Ok.
:
else
- as_fn_error $? "newly created file is older than distributed files!
-Check your system clock" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: newly created file is older than distributed files!
+Check your system clock" >&5
+$as_echo "$as_me: error: newly created file is older than distributed files!
+Check your system clock" >&2;}
+ { (exit 1); exit 1; }; }
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
-# If we didn't sleep, we still need to ensure time stamps of config.status and
-# generated files are strictly newer.
-am_sleep_pid=
-if grep 'slept: no' conftest.file >/dev/null 2>&1; then
- ( sleep 1 ) &
- am_sleep_pid=$!
-fi
-
-rm -f conftest.file
-
test "$program_prefix" != NONE &&
program_transform_name="s&^&$program_prefix&;$program_transform_name"
# Use a double $ so make ignores it.
@@ -2456,8 +2046,8 @@ test "$program_suffix" != NONE &&
ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
-# Expand $ac_aux_dir to an absolute path.
-am_aux_dir=`cd "$ac_aux_dir" && pwd`
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
if test x"${MISSING+set}" != xset; then
case $am_aux_dir in
@@ -2468,15 +2058,15 @@ if test x"${MISSING+set}" != xset; then
esac
fi
# Use eval to expand $SHELL
-if eval "$MISSING --is-lightweight"; then
- am_missing_run="$MISSING "
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
else
am_missing_run=
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: 'missing' script is too old or missing" >&5
-$as_echo "$as_me: WARNING: 'missing' script is too old or missing" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
fi
-if test x"${install_sh+set}" != xset; then
+if test x"${install_sh}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
@@ -2485,17 +2075,17 @@ if test x"${install_sh+set}" != xset; then
esac
fi
-# Installed binaries are usually stripped using 'strip' when the user
-# run "make install-strip". However 'strip' might not be the right
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
# tool to use in cross-compilation environments, therefore Automake
-# will honor the 'STRIP' environment variable to overrule this program.
+# will honor the `STRIP' environment variable to overrule this program.
if test "$cross_compiling" != no; then
if test -n "$ac_tool_prefix"; then
# Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
set dummy ${ac_tool_prefix}strip; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_STRIP+:} false; then :
+if test "${ac_cv_prog_STRIP+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$STRIP"; then
@@ -2506,24 +2096,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_STRIP="${ac_tool_prefix}strip"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
STRIP=$ac_cv_prog_STRIP
if test -n "$STRIP"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5
+ { $as_echo "$as_me:$LINENO: result: $STRIP" >&5
$as_echo "$STRIP" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -2533,9 +2123,9 @@ if test -z "$ac_cv_prog_STRIP"; then
ac_ct_STRIP=$STRIP
# Extract the first word of "strip", so it can be a program name with args.
set dummy strip; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_STRIP+:} false; then :
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$ac_ct_STRIP"; then
@@ -2546,24 +2136,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_ac_ct_STRIP="strip"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
if test -n "$ac_ct_STRIP"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5
$as_echo "$ac_ct_STRIP" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -2572,7 +2162,7 @@ fi
else
case $cross_compiling:$ac_tool_warned in
yes:)
-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
ac_tool_warned=yes ;;
esac
@@ -2585,10 +2175,10 @@ fi
fi
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
+{ $as_echo "$as_me:$LINENO: checking for a thread-safe mkdir -p" >&5
$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
if test -z "$MKDIR_P"; then
- if ${ac_cv_path_mkdir+:} false; then :
+ if test "${ac_cv_path_mkdir+set}" = set; then
$as_echo_n "(cached) " >&6
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
@@ -2596,9 +2186,9 @@ for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_prog in mkdir gmkdir; do
+ for ac_prog in mkdir gmkdir; do
for ac_exec_ext in '' $ac_executable_extensions; do
- as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext" || continue
+ { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
'mkdir (GNU coreutils) '* | \
'mkdir (coreutils) '* | \
@@ -2608,12 +2198,11 @@ do
esac
done
done
- done
+done
IFS=$as_save_IFS
fi
- test -d ./--version && rmdir ./--version
if test "${ac_cv_path_mkdir+set}" = set; then
MKDIR_P="$ac_cv_path_mkdir -p"
else
@@ -2621,19 +2210,26 @@ fi
# value for MKDIR_P within a source directory, because that will
# break other packages using the cache if that directory is
# removed, or if the value is a relative name.
+ test -d ./--version && rmdir ./--version
MKDIR_P="$ac_install_sh -d"
fi
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
+{ $as_echo "$as_me:$LINENO: result: $MKDIR_P" >&5
$as_echo "$MKDIR_P" >&6; }
+mkdir_p="$MKDIR_P"
+case $mkdir_p in
+ [\\/$]* | ?:[\\/]*) ;;
+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+
for ac_prog in gawk mawk nawk awk
do
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_AWK+:} false; then :
+if test "${ac_cv_prog_AWK+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$AWK"; then
@@ -2644,24 +2240,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_AWK="$ac_prog"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
AWK=$ac_cv_prog_AWK
if test -n "$AWK"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+ { $as_echo "$as_me:$LINENO: result: $AWK" >&5
$as_echo "$AWK" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -2669,11 +2265,11 @@ fi
test -n "$AWK" && break
done
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
set x ${MAKE-make}
ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
-if eval \${ac_cv_prog_make_${ac_make}_set+:} false; then :
+if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
cat >conftest.make <<\_ACEOF
@@ -2681,7 +2277,7 @@ SHELL = /bin/sh
all:
@echo '@@@%%%=$(MAKE)=@@@%%%'
_ACEOF
-# GNU make sometimes prints "make[1]: Entering ...", which would confuse us.
+# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
case `${MAKE-make} -f conftest.make 2>/dev/null` in
*@@@%%%=?*=@@@%%%*)
eval ac_cv_prog_make_${ac_make}_set=yes;;
@@ -2691,11 +2287,11 @@ esac
rm -f conftest.make
fi
if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
SET_MAKE=
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
SET_MAKE="MAKE=${MAKE-make}"
fi
@@ -2709,52 +2305,15 @@ else
fi
rmdir .tst 2>/dev/null
-# Check whether --enable-silent-rules was given.
-if test "${enable_silent_rules+set}" = set; then :
- enableval=$enable_silent_rules;
-fi
-
-case $enable_silent_rules in # (((
- yes) AM_DEFAULT_VERBOSITY=0;;
- no) AM_DEFAULT_VERBOSITY=1;;
- *) AM_DEFAULT_VERBOSITY=1;;
-esac
-am_make=${MAKE-make}
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $am_make supports nested variables" >&5
-$as_echo_n "checking whether $am_make supports nested variables... " >&6; }
-if ${am_cv_make_support_nested_variables+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if $as_echo 'TRUE=$(BAR$(V))
-BAR0=false
-BAR1=true
-V=1
-am__doit:
- @$(TRUE)
-.PHONY: am__doit' | $am_make -f - >/dev/null 2>&1; then
- am_cv_make_support_nested_variables=yes
-else
- am_cv_make_support_nested_variables=no
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_make_support_nested_variables" >&5
-$as_echo "$am_cv_make_support_nested_variables" >&6; }
-if test $am_cv_make_support_nested_variables = yes; then
- AM_V='$(V)'
- AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
-else
- AM_V=$AM_DEFAULT_VERBOSITY
- AM_DEFAULT_V=$AM_DEFAULT_VERBOSITY
-fi
-AM_BACKSLASH='\'
-
if test "`cd $srcdir && pwd`" != "`pwd`"; then
# Use -I$(srcdir) only when $(srcdir) != ., so that make's output
# is not polluted with repeated "-I."
am__isrc=' -I$(srcdir)'
# test to see if srcdir already configured
if test -f $srcdir/config.status; then
- as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
+$as_echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;}
+ { (exit 1); exit 1; }; }
fi
fi
@@ -2770,7 +2329,7 @@ fi
# Define the identity of the package.
PACKAGE='stacks'
- VERSION='1.44'
+ VERSION='1.46'
cat >>confdefs.h <<_ACEOF
@@ -2798,70 +2357,17 @@ AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
-# For better backward compatibility. To be removed once Automake 1.9.x
-# dies out for good. For more background, see:
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
-# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
-mkdir_p='$(MKDIR_P)'
-
-# We need awk for the "check" target (and possibly the TAP driver). The
-# system "awk" is bad on some platforms.
-# Always define AMTAR for backward compatibility. Yes, it's still used
-# in the wild :-( We should find a proper way to deprecate it ...
-AMTAR='$${TAR-tar}'
-
-
-# We'll loop over all known methods to create a tar archive until one works.
-_am_tools='gnutar pax cpio none'
-
-am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
+# Always define AMTAR for backward compatibility.
+AMTAR=${AMTAR-"${am_missing_run}tar"}
+am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
-# POSIX will say in a future version that running "rm -f" with no argument
-# is OK; and we want to be able to make that assumption in our Makefile
-# recipes. So use an aggressive probe to check that the usage we want is
-# actually supported "in the wild" to an acceptable degree.
-# See automake bug#10828.
-# To make any issue more visible, cause the running configure to be aborted
-# by default if the 'rm' program in use doesn't match our expectations; the
-# user can still override this though.
-if rm -f && rm -fr && rm -rf; then : OK; else
- cat >&2 <<'END'
-Oops!
-
-Your 'rm' program seems unable to run without file operands specified
-on the command line, even when the '-f' option is present. This is contrary
-to the behaviour of most rm programs out there, and not conforming with
-the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
-
-Please tell bug-automake at gnu.org about your system, including the value
-of your $PATH and any error possibly output before this message. This
-can help us improve future automake versions.
-
-END
- if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
- echo 'Configuration will proceed anyway, since you have set the' >&2
- echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
- echo >&2
- else
- cat >&2 <<'END'
-Aborting the configuration process, to ensure you take notice of the issue.
-
-You can download and install GNU coreutils to get an 'rm' implementation
-that behaves properly: <http://www.gnu.org/software/coreutils/>.
-
-If you want to complete the configuration process using your problematic
-'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
-to "yes", and re-run configure.
-
-END
- as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
- fi
-fi
ac_config_headers="$ac_config_headers config.h"
@@ -2872,15 +2378,17 @@ ac_config_headers="$ac_config_headers config.h"
# Get BAM, aka HTSLib library and include locations if requested
#
# Check whether --enable-bam was given.
-if test "${enable_bam+set}" = set; then :
+if test "${enable_bam+set}" = set; then
enableval=$enable_bam;
fi
-if test "x$enable_bam" != "xno"; then :
+if test "x$enable_bam" != "xno"; then
-$as_echo "#define HAVE_BAM 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BAM 1
+_ACEOF
BAM_CFLAGS='-I./htslib/htslib'
@@ -2891,23 +2399,26 @@ BAM_LIBS='./htslib/libhts.a'
fi
+
#
# Enable use of Google Sparsehash and get include location if requested.
#
# Check whether --enable-sparsehash was given.
-if test "${enable_sparsehash+set}" = set; then :
+if test "${enable_sparsehash+set}" = set; then
enableval=$enable_sparsehash;
fi
-if test "x$enable_sparsehash" = "xyes"; then :
+if test "x$enable_sparsehash" = "xyes"; then
-$as_echo "#define HAVE_SPARSEHASH 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_SPARSEHASH 1
+_ACEOF
# Check whether --with-sparsehash-include-path was given.
-if test "${with_sparsehash_include_path+set}" = set; then :
+if test "${with_sparsehash_include_path+set}" = set; then
withval=$with_sparsehash_include_path; SPARSEHASH_CFLAGS="-I$withval"
else
SPARSEHASH_CFLAGS=""
@@ -2918,6 +2429,7 @@ fi
fi
+
# Checks for programs.
ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
@@ -2933,9 +2445,9 @@ if test -z "$CXX"; then
do
# Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CXX+:} false; then :
+if test "${ac_cv_prog_CXX+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$CXX"; then
@@ -2946,24 +2458,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
CXX=$ac_cv_prog_CXX
if test -n "$CXX"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5
+ { $as_echo "$as_me:$LINENO: result: $CXX" >&5
$as_echo "$CXX" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -2977,9 +2489,9 @@ if test -z "$CXX"; then
do
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_CXX+:} false; then :
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$ac_ct_CXX"; then
@@ -2990,24 +2502,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_ac_ct_CXX="$ac_prog"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
if test -n "$ac_ct_CXX"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5
$as_echo "$ac_ct_CXX" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -3020,7 +2532,7 @@ done
else
case $cross_compiling:$ac_tool_warned in
yes:)
-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
ac_tool_warned=yes ;;
esac
@@ -3031,31 +2543,48 @@ fi
fi
fi
# Provide some information about the compiler.
-$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5
+$as_echo "$as_me:$LINENO: checking for C++ compiler version" >&5
set X $ac_compile
ac_compiler=$2
-for ac_option in --version -v -V -qversion; do
- { { ac_try="$ac_compiler $ac_option >&5"
+{ (ac_try="$ac_compiler --version >&5"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler --version >&5") 2>&5
ac_status=$?
- if test -s conftest.err; then
- sed '10a\
-... rest of stderr output deleted ...
- 10q' conftest.err >conftest.er1
- cat conftest.er1 >&5
- fi
- rm -f conftest.er1 conftest.err
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }
-done
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -v >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -V >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -3071,8 +2600,8 @@ ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
# Try to create an executable without -o first, disregard a.out.
# It will help us diagnose broken compilers, and finding out an intuition
# of exeext.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C++ compiler works" >&5
-$as_echo_n "checking whether the C++ compiler works... " >&6; }
+{ $as_echo "$as_me:$LINENO: checking for C++ compiler default output file name" >&5
+$as_echo_n "checking for C++ compiler default output file name... " >&6; }
ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
# The possible output files:
@@ -3088,17 +2617,17 @@ do
done
rm -f $ac_rmfiles
-if { { ac_try="$ac_link_default"
+if { (ac_try="$ac_link_default"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
(eval "$ac_link_default") 2>&5
ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }; then :
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
# Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
# in a Makefile. We should not override ac_cv_exeext if it was cached,
@@ -3115,7 +2644,7 @@ do
# certainly right.
break;;
*.* )
- if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
then :; else
ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
fi
@@ -3134,41 +2663,84 @@ test "$ac_cv_exeext" = no && ac_cv_exeext=
else
ac_file=''
fi
-if test -z "$ac_file"; then :
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-$as_echo "$as_me: failed program was:" >&5
+
+{ $as_echo "$as_me:$LINENO: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
+if test -z "$ac_file"; then
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error 77 "C++ compiler cannot create executables
-See \`config.log' for more details" "$LINENO" 5; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
+{ { $as_echo "$as_me:$LINENO: error: C++ compiler cannot create executables
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: C++ compiler cannot create executables
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler default output file name" >&5
-$as_echo_n "checking for C++ compiler default output file name... " >&6; }
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
-$as_echo "$ac_file" >&6; }
+
ac_exeext=$ac_cv_exeext
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:$LINENO: checking whether the C++ compiler works" >&5
+$as_echo_n "checking whether the C++ compiler works... " >&6; }
+# FIXME: These cross compiler hacks should be removed for Autoconf 3.0
+# If not cross compiling, check that we can run a simple program.
+if test "$cross_compiling" != yes; then
+ if { ac_try='./$ac_file'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot run C++ compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot run C++ compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
ac_clean_files=$ac_clean_files_save
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:$LINENO: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+{ $as_echo "$as_me:$LINENO: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+{ $as_echo "$as_me:$LINENO: checking for suffix of executables" >&5
$as_echo_n "checking for suffix of executables... " >&6; }
-if { { ac_try="$ac_link"
+if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
(eval "$ac_link") 2>&5
ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }; then :
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
# If both `conftest.exe' and `conftest' are `present' (well, observable)
# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
# work properly (i.e., refer to `conftest.exe'), while it won't with
@@ -3183,83 +2755,32 @@ for ac_file in conftest.exe conftest conftest.*; do
esac
done
else
- { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "cannot compute suffix of executables: cannot compile and link
-See \`config.log' for more details" "$LINENO" 5; }
+{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
fi
-rm -f conftest conftest$ac_cv_exeext
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
+
+rm -f conftest$ac_cv_exeext
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5
$as_echo "$ac_cv_exeext" >&6; }
rm -f conftest.$ac_ext
EXEEXT=$ac_cv_exeext
ac_exeext=$EXEEXT
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include <stdio.h>
-int
-main ()
-{
-FILE *f = fopen ("conftest.out", "w");
- return ferror (f) || fclose (f) != 0;
-
- ;
- return 0;
-}
-_ACEOF
-ac_clean_files="$ac_clean_files conftest.out"
-# Check that the compiler produces executables we can run. If not, either
-# the compiler is broken, or we cross compile.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
-$as_echo_n "checking whether we are cross compiling... " >&6; }
-if test "$cross_compiling" != yes; then
- { { ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }
- if { ac_try='./conftest$ac_cv_exeext'
- { { case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }; }; then
- cross_compiling=no
- else
- if test "$cross_compiling" = maybe; then
- cross_compiling=yes
- else
- { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "cannot run C++ compiled programs.
-If you meant to cross compile, use \`--host'.
-See \`config.log' for more details" "$LINENO" 5; }
- fi
- fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
-$as_echo "$cross_compiling" >&6; }
-
-rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
-ac_clean_files=$ac_clean_files_save
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
+{ $as_echo "$as_me:$LINENO: checking for suffix of object files" >&5
$as_echo_n "checking for suffix of object files... " >&6; }
-if ${ac_cv_objext+:} false; then :
+if test "${ac_cv_objext+set}" = set; then
$as_echo_n "(cached) " >&6
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -3271,17 +2792,17 @@ main ()
}
_ACEOF
rm -f conftest.o conftest.obj
-if { { ac_try="$ac_compile"
+if { (ac_try="$ac_compile"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
(eval "$ac_compile") 2>&5
ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }; then :
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
for ac_file in conftest.o conftest.obj conftest.*; do
test -f "$ac_file" || continue;
case $ac_file in
@@ -3294,23 +2815,31 @@ else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "cannot compute suffix of object files: cannot compile
-See \`config.log' for more details" "$LINENO" 5; }
+{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
fi
+
rm -f conftest.$ac_cv_objext conftest.$ac_ext
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_objext" >&5
$as_echo "$ac_cv_objext" >&6; }
OBJEXT=$ac_cv_objext
ac_objext=$OBJEXT
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5
+{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5
$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
-if ${ac_cv_cxx_compiler_gnu+:} false; then :
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then
$as_echo_n "(cached) " >&6
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -3324,16 +2853,37 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_compiler_gnu=yes
else
- ac_compiler_gnu=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_compiler_gnu=no
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5
$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
if test $ac_compiler_gnu = yes; then
GXX=yes
@@ -3342,16 +2892,20 @@ else
fi
ac_test_CXXFLAGS=${CXXFLAGS+set}
ac_save_CXXFLAGS=$CXXFLAGS
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5
+{ $as_echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5
$as_echo_n "checking whether $CXX accepts -g... " >&6; }
-if ${ac_cv_prog_cxx_g+:} false; then :
+if test "${ac_cv_prog_cxx_g+set}" = set; then
$as_echo_n "(cached) " >&6
else
ac_save_cxx_werror_flag=$ac_cxx_werror_flag
ac_cxx_werror_flag=yes
ac_cv_prog_cxx_g=no
CXXFLAGS="-g"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -3362,11 +2916,35 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_cv_prog_cxx_g=yes
else
- CXXFLAGS=""
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ CXXFLAGS=""
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -3377,12 +2955,36 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
-
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
else
- ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
CXXFLAGS="-g"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -3393,17 +2995,42 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_cv_prog_cxx_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
ac_cxx_werror_flag=$ac_save_cxx_werror_flag
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5
$as_echo "$ac_cv_prog_cxx_g" >&6; }
if test "$ac_test_CXXFLAGS" = set; then
CXXFLAGS=$ac_save_CXXFLAGS
@@ -3437,14 +3064,14 @@ am__doit:
.PHONY: am__doit
END
# If we don't find an include directive, just comment out the code.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
+{ $as_echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5
$as_echo_n "checking for style of include used by $am_make... " >&6; }
am__include="#"
am__quote=
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
-# Ignore all kinds of additional output from 'make'.
+# Ignore all kinds of additional output from `make'.
case `$am_make -s -f confmf 2> /dev/null` in #(
*the\ am__doit\ target*)
am__include=include
@@ -3465,19 +3092,18 @@ if test "$am__include" = "#"; then
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
+{ $as_echo "$as_me:$LINENO: result: $_am_result" >&5
$as_echo "$_am_result" >&6; }
rm -f confinc confmf
# Check whether --enable-dependency-tracking was given.
-if test "${enable_dependency_tracking+set}" = set; then :
+if test "${enable_dependency_tracking+set}" = set; then
enableval=$enable_dependency_tracking;
fi
if test "x$enable_dependency_tracking" != xno; then
am_depcomp="$ac_aux_dir/depcomp"
AMDEPBACKSLASH='\'
- am__nodep='_no'
fi
if test "x$enable_dependency_tracking" != xno; then
AMDEP_TRUE=
@@ -3491,18 +3117,17 @@ fi
depcc="$CXX" am_compiler_list=
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
$as_echo_n "checking dependency style of $depcc... " >&6; }
-if ${am_cv_CXX_dependencies_compiler_type+:} false; then :
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
# We make a subdir and do the tests there. Otherwise we can end up
# making bogus files that we don't know about and never remove. For
# instance it was reported that on HP-UX the gcc test will end up
- # making a dummy file named 'D' -- because '-MD' means "put the output
- # in D".
- rm -rf conftest.dir
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
mkdir conftest.dir
# Copy depcomp to subdir because otherwise we won't find it if we're
# using a relative directory.
@@ -3536,16 +3161,16 @@ else
: > sub/conftest.c
for i in 1 2 3 4 5 6; do
echo '#include "conftst'$i'.h"' >> sub/conftest.c
- # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
- # Solaris 10 /bin/sh.
- echo '/* dummy */' > sub/conftst$i.h
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
done
echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
- # We check with '-c' and '-o' for the sake of the "dashmstdout"
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
# mode. It turns out that the SunPro C++ compiler does not properly
- # handle '-M -o', and we need to detect this. Also, some Intel
- # versions had trouble with output in subdirs.
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
am__obj=sub/conftest.${OBJEXT-o}
am__minus_obj="-o $am__obj"
case $depmode in
@@ -3554,16 +3179,16 @@ else
test "$am__universal" = false || continue
;;
nosideeffect)
- # After this tag, mechanisms are not by side-effect, so they'll
- # only be used when explicitly requested.
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
if test "x$enable_dependency_tracking" = xyes; then
continue
else
break
fi
;;
- msvc7 | msvc7msys | msvisualcpp | msvcmsys)
- # This compiler won't grok '-c -o', but also, the minuso test has
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
# not run yet. These depmodes are late enough in the game, and
# so weak that their functioning should not be impacted.
am__obj=conftest.${OBJEXT-o}
@@ -3602,7 +3227,7 @@ else
fi
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5
+{ $as_echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5
$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
@@ -3625,9 +3250,9 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
if test -n "$ac_tool_prefix"; then
# Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
set dummy ${ac_tool_prefix}gcc; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CC+:} false; then :
+if test "${ac_cv_prog_CC+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
@@ -3638,24 +3263,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_CC="${ac_tool_prefix}gcc"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
$as_echo "$CC" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -3665,9 +3290,9 @@ if test -z "$ac_cv_prog_CC"; then
ac_ct_CC=$CC
# Extract the first word of "gcc", so it can be a program name with args.
set dummy gcc; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_CC+:} false; then :
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$ac_ct_CC"; then
@@ -3678,24 +3303,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_ac_ct_CC="gcc"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
ac_ct_CC=$ac_cv_prog_ac_ct_CC
if test -n "$ac_ct_CC"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
$as_echo "$ac_ct_CC" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -3704,7 +3329,7 @@ fi
else
case $cross_compiling:$ac_tool_warned in
yes:)
-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
ac_tool_warned=yes ;;
esac
@@ -3718,9 +3343,9 @@ if test -z "$CC"; then
if test -n "$ac_tool_prefix"; then
# Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
set dummy ${ac_tool_prefix}cc; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CC+:} false; then :
+if test "${ac_cv_prog_CC+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
@@ -3731,24 +3356,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_CC="${ac_tool_prefix}cc"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
$as_echo "$CC" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -3758,9 +3383,9 @@ fi
if test -z "$CC"; then
# Extract the first word of "cc", so it can be a program name with args.
set dummy cc; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CC+:} false; then :
+if test "${ac_cv_prog_CC+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
@@ -3772,18 +3397,18 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
ac_prog_rejected=yes
continue
fi
ac_cv_prog_CC="cc"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
if test $ac_prog_rejected = yes; then
@@ -3802,10 +3427,10 @@ fi
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
$as_echo "$CC" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -3817,9 +3442,9 @@ if test -z "$CC"; then
do
# Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_CC+:} false; then :
+if test "${ac_cv_prog_CC+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
@@ -3830,24 +3455,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
$as_echo "$CC" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -3861,9 +3486,9 @@ if test -z "$CC"; then
do
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_ac_ct_CC+:} false; then :
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$ac_ct_CC"; then
@@ -3874,24 +3499,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_ac_ct_CC="$ac_prog"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
ac_ct_CC=$ac_cv_prog_ac_ct_CC
if test -n "$ac_ct_CC"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
$as_echo "$ac_ct_CC" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -3904,7 +3529,7 @@ done
else
case $cross_compiling:$ac_tool_warned in
yes:)
-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
ac_tool_warned=yes ;;
esac
@@ -3915,42 +3540,62 @@ fi
fi
-test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "no acceptable C compiler found in \$PATH
-See \`config.log' for more details" "$LINENO" 5; }
+{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
# Provide some information about the compiler.
-$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+$as_echo "$as_me:$LINENO: checking for C compiler version" >&5
set X $ac_compile
ac_compiler=$2
-for ac_option in --version -v -V -qversion; do
- { { ac_try="$ac_compiler $ac_option >&5"
+{ (ac_try="$ac_compiler --version >&5"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler --version >&5") 2>&5
ac_status=$?
- if test -s conftest.err; then
- sed '10a\
-... rest of stderr output deleted ...
- 10q' conftest.err >conftest.er1
- cat conftest.er1 >&5
- fi
- rm -f conftest.er1 conftest.err
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }
-done
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -v >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -V >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
-if ${ac_cv_c_compiler_gnu+:} false; then :
+if test "${ac_cv_c_compiler_gnu+set}" = set; then
$as_echo_n "(cached) " >&6
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -3964,16 +3609,37 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_compiler_gnu=yes
else
- ac_compiler_gnu=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_compiler_gnu=no
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
ac_cv_c_compiler_gnu=$ac_compiler_gnu
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
$as_echo "$ac_cv_c_compiler_gnu" >&6; }
if test $ac_compiler_gnu = yes; then
GCC=yes
@@ -3982,16 +3648,20 @@ else
fi
ac_test_CFLAGS=${CFLAGS+set}
ac_save_CFLAGS=$CFLAGS
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
$as_echo_n "checking whether $CC accepts -g... " >&6; }
-if ${ac_cv_prog_cc_g+:} false; then :
+if test "${ac_cv_prog_cc_g+set}" = set; then
$as_echo_n "(cached) " >&6
else
ac_save_c_werror_flag=$ac_c_werror_flag
ac_c_werror_flag=yes
ac_cv_prog_cc_g=no
CFLAGS="-g"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -4002,11 +3672,35 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_cv_prog_cc_g=yes
else
- CFLAGS=""
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ CFLAGS=""
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -4017,12 +3711,36 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
-
-else
- ac_c_werror_flag=$ac_save_c_werror_flag
- CFLAGS="-g"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
@@ -4033,17 +3751,42 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_cv_prog_cc_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
ac_c_werror_flag=$ac_save_c_werror_flag
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
$as_echo "$ac_cv_prog_cc_g" >&6; }
if test "$ac_test_CFLAGS" = set; then
CFLAGS=$ac_save_CFLAGS
@@ -4060,18 +3803,23 @@ else
CFLAGS=
fi
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5
$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
-if ${ac_cv_prog_cc_c89+:} false; then :
+if test "${ac_cv_prog_cc_c89+set}" = set; then
$as_echo_n "(cached) " >&6
else
ac_cv_prog_cc_c89=no
ac_save_CC=$CC
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <stdarg.h>
#include <stdio.h>
-struct stat;
+#include <sys/types.h>
+#include <sys/stat.h>
/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
struct buf { int x; };
FILE * (*rcsopen) (struct buf *, struct stat *, int);
@@ -4123,9 +3871,32 @@ for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
-Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
do
CC="$ac_save_CC $ac_arg"
- if ac_fn_c_try_compile "$LINENO"; then :
+ rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_cv_prog_cc_c89=$ac_arg
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
fi
+
rm -f core conftest.err conftest.$ac_objext
test "x$ac_cv_prog_cc_c89" != "xno" && break
done
@@ -4136,99 +3907,37 @@ fi
# AC_CACHE_VAL
case "x$ac_cv_prog_cc_c89" in
x)
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+ { $as_echo "$as_me:$LINENO: result: none needed" >&5
$as_echo "none needed" >&6; } ;;
xno)
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+ { $as_echo "$as_me:$LINENO: result: unsupported" >&5
$as_echo "unsupported" >&6; } ;;
*)
CC="$CC $ac_cv_prog_cc_c89"
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+ { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5
$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
esac
-if test "x$ac_cv_prog_cc_c89" != xno; then :
-
-fi
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC understands -c and -o together" >&5
-$as_echo_n "checking whether $CC understands -c and -o together... " >&6; }
-if ${am_cv_prog_cc_c_o+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-int
-main ()
-{
- ;
- return 0;
-}
-_ACEOF
- # Make sure it works both with $CC and with simple cc.
- # Following AC_PROG_CC_C_O, we do the test twice because some
- # compilers refuse to overwrite an existing .o file with -o,
- # though they will create one.
- am_cv_prog_cc_c_o=yes
- for am_i in 1 2; do
- if { echo "$as_me:$LINENO: $CC -c conftest.$ac_ext -o conftest2.$ac_objext" >&5
- ($CC -c conftest.$ac_ext -o conftest2.$ac_objext) >&5 2>&5
- ac_status=$?
- echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } \
- && test -f conftest2.$ac_objext; then
- : OK
- else
- am_cv_prog_cc_c_o=no
- break
- fi
- done
- rm -f core conftest*
- unset am_i
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_prog_cc_c_o" >&5
-$as_echo "$am_cv_prog_cc_c_o" >&6; }
-if test "$am_cv_prog_cc_c_o" != yes; then
- # Losing compiler, so override with the script.
- # FIXME: It is wrong to rewrite CC.
- # But if we don't then we get into trouble of one sort or another.
- # A longer-term fix would be to have automake use am__CC in this case,
- # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
- CC="$am_aux_dir/compile $CC"
-fi
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
depcc="$CC" am_compiler_list=
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
$as_echo_n "checking dependency style of $depcc... " >&6; }
-if ${am_cv_CC_dependencies_compiler_type+:} false; then :
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
# We make a subdir and do the tests there. Otherwise we can end up
# making bogus files that we don't know about and never remove. For
# instance it was reported that on HP-UX the gcc test will end up
- # making a dummy file named 'D' -- because '-MD' means "put the output
- # in D".
- rm -rf conftest.dir
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
mkdir conftest.dir
# Copy depcomp to subdir because otherwise we won't find it if we're
# using a relative directory.
@@ -4262,16 +3971,16 @@ else
: > sub/conftest.c
for i in 1 2 3 4 5 6; do
echo '#include "conftst'$i'.h"' >> sub/conftest.c
- # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
- # Solaris 10 /bin/sh.
- echo '/* dummy */' > sub/conftst$i.h
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
done
echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
- # We check with '-c' and '-o' for the sake of the "dashmstdout"
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
# mode. It turns out that the SunPro C++ compiler does not properly
- # handle '-M -o', and we need to detect this. Also, some Intel
- # versions had trouble with output in subdirs.
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
am__obj=sub/conftest.${OBJEXT-o}
am__minus_obj="-o $am__obj"
case $depmode in
@@ -4280,16 +3989,16 @@ else
test "$am__universal" = false || continue
;;
nosideeffect)
- # After this tag, mechanisms are not by side-effect, so they'll
- # only be used when explicitly requested.
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
if test "x$enable_dependency_tracking" = xyes; then
continue
else
break
fi
;;
- msvc7 | msvc7msys | msvisualcpp | msvcmsys)
- # This compiler won't grok '-c -o', but also, the minuso test has
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
# not run yet. These depmodes are late enough in the game, and
# so weak that their functioning should not be impacted.
am__obj=conftest.${OBJEXT-o}
@@ -4328,7 +4037,7 @@ else
fi
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5
$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
@@ -4343,6 +4052,137 @@ else
fi
+if test "x$CC" != xcc; then
+ { $as_echo "$as_me:$LINENO: checking whether $CC and cc understand -c and -o together" >&5
+$as_echo_n "checking whether $CC and cc understand -c and -o together... " >&6; }
+else
+ { $as_echo "$as_me:$LINENO: checking whether cc understands -c and -o together" >&5
+$as_echo_n "checking whether cc understands -c and -o together... " >&6; }
+fi
+set dummy $CC; ac_cc=`$as_echo "$2" |
+ sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
+if { as_var=ac_cv_prog_cc_${ac_cc}_c_o; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+# Make sure it works both with $CC and with simple cc.
+# We do the test twice because some compilers refuse to overwrite an
+# existing .o file with -o, though they will create one.
+ac_try='$CC -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
+rm -f conftest2.*
+if { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ test -f conftest2.$ac_objext && { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); };
+then
+ eval ac_cv_prog_cc_${ac_cc}_c_o=yes
+ if test "x$CC" != xcc; then
+ # Test first that cc exists at all.
+ if { ac_try='cc -c conftest.$ac_ext >&5'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_try='cc -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
+ rm -f conftest2.*
+ if { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ test -f conftest2.$ac_objext && { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); };
+ then
+ # cc works too.
+ :
+ else
+ # cc exists but doesn't like -o.
+ eval ac_cv_prog_cc_${ac_cc}_c_o=no
+ fi
+ fi
+ fi
+else
+ eval ac_cv_prog_cc_${ac_cc}_c_o=no
+fi
+rm -f core conftest*
+
+fi
+if eval test \$ac_cv_prog_cc_${ac_cc}_c_o = yes; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+
+cat >>confdefs.h <<\_ACEOF
+#define NO_MINUS_C_MINUS_O 1
+_ACEOF
+
+fi
+
+# FIXME: we rely on the cache variable name because
+# there is no other way.
+set dummy $CC
+am_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+
ax_cxx_compile_cxx11_required=true
@@ -4352,12 +4192,16 @@ ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
ac_success=no
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++11 features by default" >&5
+ { $as_echo "$as_me:$LINENO: checking whether $CXX supports C++11 features by default" >&5
$as_echo_n "checking whether $CXX supports C++11 features by default... " >&6; }
-if ${ax_cv_cxx_compile_cxx11+:} false; then :
+if test "${ax_cv_cxx_compile_cxx11+set}" = set; then
$as_echo_n "(cached) " >&6
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
@@ -4646,14 +4490,35 @@ namespace cxx11
_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ax_cv_cxx_compile_cxx11=yes
else
- ax_cv_cxx_compile_cxx11=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ax_cv_cxx_compile_cxx11=no
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_cxx_compile_cxx11" >&5
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cxx_compile_cxx11" >&5
$as_echo "$ax_cv_cxx_compile_cxx11" >&6; }
if test x$ax_cv_cxx_compile_cxx11 = xyes; then
ac_success=yes
@@ -4662,14 +4527,18 @@ $as_echo "$ax_cv_cxx_compile_cxx11" >&6; }
if test x$ac_success = xno; then
for switch in -std=gnu++11 -std=gnu++0x; do
cachevar=`$as_echo "ax_cv_cxx_compile_cxx11_$switch" | $as_tr_sh`
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++11 features with $switch" >&5
+ { $as_echo "$as_me:$LINENO: checking whether $CXX supports C++11 features with $switch" >&5
$as_echo_n "checking whether $CXX supports C++11 features with $switch... " >&6; }
-if eval \${$cachevar+:} false; then :
+if { as_var=$cachevar; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ac_save_CXX="$CXX"
CXX="$CXX $switch"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
@@ -4958,16 +4827,38 @@ namespace cxx11
_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
eval $cachevar=yes
else
- eval $cachevar=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval $cachevar=no
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CXX="$ac_save_CXX"
fi
-eval ac_res=\$$cachevar
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+ac_res=`eval 'as_val=${'$cachevar'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
$as_echo "$ac_res" >&6; }
if eval test x\$$cachevar = xyes; then
CXX="$CXX $switch"
@@ -4983,14 +4874,18 @@ $as_echo "$ac_res" >&6; }
if test x$ac_success = xno; then
for switch in -std=c++11 -std=c++0x +std=c++11 "-h std=c++11"; do
cachevar=`$as_echo "ax_cv_cxx_compile_cxx11_$switch" | $as_tr_sh`
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++11 features with $switch" >&5
+ { $as_echo "$as_me:$LINENO: checking whether $CXX supports C++11 features with $switch" >&5
$as_echo_n "checking whether $CXX supports C++11 features with $switch... " >&6; }
-if eval \${$cachevar+:} false; then :
+if { as_var=$cachevar; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ac_save_CXX="$CXX"
CXX="$CXX $switch"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
@@ -5279,16 +5174,38 @@ namespace cxx11
_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
eval $cachevar=yes
else
- eval $cachevar=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval $cachevar=no
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CXX="$ac_save_CXX"
fi
-eval ac_res=\$$cachevar
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+ac_res=`eval 'as_val=${'$cachevar'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
$as_echo "$ac_res" >&6; }
if eval test x\$$cachevar = xyes; then
CXX="$CXX $switch"
@@ -5308,17 +5225,21 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
if test x$ax_cxx_compile_cxx11_required = xtrue; then
if test x$ac_success = xno; then
- as_fn_error $? "*** A compiler with support for C++11 language features is required." "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: *** A compiler with support for C++11 language features is required." >&5
+$as_echo "$as_me: error: *** A compiler with support for C++11 language features is required." >&2;}
+ { (exit 1); exit 1; }; }
fi
fi
if test x$ac_success = xno; then
HAVE_CXX11=0
- { $as_echo "$as_me:${as_lineno-$LINENO}: No compiler with C++11 support was found" >&5
+ { $as_echo "$as_me:$LINENO: No compiler with C++11 support was found" >&5
$as_echo "$as_me: No compiler with C++11 support was found" >&6;}
else
HAVE_CXX11=1
-$as_echo "#define HAVE_CXX11 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_CXX11 1
+_ACEOF
fi
@@ -5326,14 +5247,19 @@ $as_echo "#define HAVE_CXX11 1" >>confdefs.h
# Checks for libraries.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for omp_set_num_threads in -lgomp" >&5
+
+{ $as_echo "$as_me:$LINENO: checking for omp_set_num_threads in -lgomp" >&5
$as_echo_n "checking for omp_set_num_threads in -lgomp... " >&6; }
-if ${ac_cv_lib_gomp_omp_set_num_threads+:} false; then :
+if test "${ac_cv_lib_gomp_omp_set_num_threads+set}" = set; then
$as_echo_n "(cached) " >&6
else
ac_check_lib_save_LIBS=$LIBS
LIBS="-lgomp $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
/* Override any GCC internal prototype to avoid an error.
@@ -5351,18 +5277,43 @@ return omp_set_num_threads ();
return 0;
}
_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
ac_cv_lib_gomp_omp_set_num_threads=yes
else
- ac_cv_lib_gomp_omp_set_num_threads=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_gomp_omp_set_num_threads=no
fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_gomp_omp_set_num_threads" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_gomp_omp_set_num_threads" >&5
$as_echo "$ac_cv_lib_gomp_omp_set_num_threads" >&6; }
-if test "x$ac_cv_lib_gomp_omp_set_num_threads" = xyes; then :
+if test "x$ac_cv_lib_gomp_omp_set_num_threads" = x""yes; then
cat >>confdefs.h <<_ACEOF
#define HAVE_LIBGOMP 1
_ACEOF
@@ -5370,18 +5321,23 @@ _ACEOF
LIBS="-lgomp $LIBS"
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Unable to locate OpenMP library, you should probably specify '--disable-openmp'." >&5
+ { $as_echo "$as_me:$LINENO: WARNING: Unable to locate OpenMP library, you should probably specify '--disable-openmp'." >&5
$as_echo "$as_me: WARNING: Unable to locate OpenMP library, you should probably specify '--disable-openmp'." >&2;}
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for gzread in -lz" >&5
+
+{ $as_echo "$as_me:$LINENO: checking for gzread in -lz" >&5
$as_echo_n "checking for gzread in -lz... " >&6; }
-if ${ac_cv_lib_z_gzread+:} false; then :
+if test "${ac_cv_lib_z_gzread+set}" = set; then
$as_echo_n "(cached) " >&6
else
ac_check_lib_save_LIBS=$LIBS
LIBS="-lz $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
/* Override any GCC internal prototype to avoid an error.
@@ -5399,18 +5355,43 @@ return gzread ();
return 0;
}
_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
ac_cv_lib_z_gzread=yes
else
- ac_cv_lib_z_gzread=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_z_gzread=no
fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
LIBS=$ac_check_lib_save_LIBS
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_z_gzread" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_z_gzread" >&5
$as_echo "$ac_cv_lib_z_gzread" >&6; }
-if test "x$ac_cv_lib_z_gzread" = xyes; then :
+if test "x$ac_cv_lib_z_gzread" = x""yes; then
cat >>confdefs.h <<_ACEOF
#define HAVE_LIBZ 1
_ACEOF
@@ -5418,20 +5399,31 @@ _ACEOF
LIBS="-lz $LIBS"
else
- as_fn_error $? "Zlib not found, reading gzipped files will not be possible." "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: Zlib not found, reading gzipped files will not be possible." >&5
+$as_echo "$as_me: error: Zlib not found, reading gzipped files will not be possible." >&2;}
+ { (exit 1); exit 1; }; }
fi
# Checks for header files.
+
+
+
+
+
ac_header_dirent=no
for ac_hdr in dirent.h sys/ndir.h sys/dir.h ndir.h; do
as_ac_Header=`$as_echo "ac_cv_header_dirent_$ac_hdr" | $as_tr_sh`
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_hdr that defines DIR" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_hdr that defines DIR" >&5
$as_echo_n "checking for $ac_hdr that defines DIR... " >&6; }
-if eval \${$as_ac_Header+:} false; then :
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <sys/types.h>
#include <$ac_hdr>
@@ -5445,17 +5437,41 @@ return 0;
return 0;
}
_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
eval "$as_ac_Header=yes"
else
- eval "$as_ac_Header=no"
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_Header=no"
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
-eval ac_res=\$$as_ac_Header
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
$as_echo "$ac_res" >&6; }
-if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+as_val=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
cat >>confdefs.h <<_ACEOF
#define `$as_echo "HAVE_$ac_hdr" | $as_tr_cpp` 1
_ACEOF
@@ -5466,13 +5482,17 @@ fi
done
# Two versions of opendir et al. are in -ldir and -lx on SCO Xenix.
if test $ac_header_dirent = dirent.h; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing opendir" >&5
+ { $as_echo "$as_me:$LINENO: checking for library containing opendir" >&5
$as_echo_n "checking for library containing opendir... " >&6; }
-if ${ac_cv_search_opendir+:} false; then :
+if test "${ac_cv_search_opendir+set}" = set; then
$as_echo_n "(cached) " >&6
else
ac_func_search_save_LIBS=$LIBS
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
/* Override any GCC internal prototype to avoid an error.
@@ -5497,39 +5517,70 @@ for ac_lib in '' dir; do
ac_res=-l$ac_lib
LIBS="-l$ac_lib $ac_func_search_save_LIBS"
fi
- if ac_fn_c_try_link "$LINENO"; then :
+ rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
ac_cv_search_opendir=$ac_res
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext
- if ${ac_cv_search_opendir+:} false; then :
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext
+ if test "${ac_cv_search_opendir+set}" = set; then
break
fi
done
-if ${ac_cv_search_opendir+:} false; then :
-
+if test "${ac_cv_search_opendir+set}" = set; then
+ :
else
ac_cv_search_opendir=no
fi
rm conftest.$ac_ext
LIBS=$ac_func_search_save_LIBS
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_opendir" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_search_opendir" >&5
$as_echo "$ac_cv_search_opendir" >&6; }
ac_res=$ac_cv_search_opendir
-if test "$ac_res" != no; then :
+if test "$ac_res" != no; then
test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
fi
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing opendir" >&5
+ { $as_echo "$as_me:$LINENO: checking for library containing opendir" >&5
$as_echo_n "checking for library containing opendir... " >&6; }
-if ${ac_cv_search_opendir+:} false; then :
+if test "${ac_cv_search_opendir+set}" = set; then
$as_echo_n "(cached) " >&6
else
ac_func_search_save_LIBS=$LIBS
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
/* Override any GCC internal prototype to avoid an error.
@@ -5554,27 +5605,54 @@ for ac_lib in '' x; do
ac_res=-l$ac_lib
LIBS="-l$ac_lib $ac_func_search_save_LIBS"
fi
- if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_search_opendir=$ac_res
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext
- if ${ac_cv_search_opendir+:} false; then :
- break
-fi
-done
-if ${ac_cv_search_opendir+:} false; then :
+ rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_search_opendir=$ac_res
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext
+ if test "${ac_cv_search_opendir+set}" = set; then
+ break
+fi
+done
+if test "${ac_cv_search_opendir+set}" = set; then
+ :
else
ac_cv_search_opendir=no
fi
rm conftest.$ac_ext
LIBS=$ac_func_search_save_LIBS
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_opendir" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_search_opendir" >&5
$as_echo "$ac_cv_search_opendir" >&6; }
ac_res=$ac_cv_search_opendir
-if test "$ac_res" != no; then :
+if test "$ac_res" != no; then
test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
fi
@@ -5586,14 +5664,14 @@ ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5
+{ $as_echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5
$as_echo_n "checking how to run the C preprocessor... " >&6; }
# On Suns, sometimes $CPP names a directory.
if test -n "$CPP" && test -d "$CPP"; then
CPP=
fi
if test -z "$CPP"; then
- if ${ac_cv_prog_CPP+:} false; then :
+ if test "${ac_cv_prog_CPP+set}" = set; then
$as_echo_n "(cached) " >&6
else
# Double quotes because CPP needs to be expanded
@@ -5608,7 +5686,11 @@ do
# <limits.h> exists even on freestanding compilers.
# On the NeXT, cc -E runs the code through the compiler's parser,
# not just through cpp. "Syntax error" is here to catch this case.
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#ifdef __STDC__
# include <limits.h>
@@ -5617,34 +5699,78 @@ do
#endif
Syntax error
_ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
-
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
# Broken: fails on valid input.
continue
fi
-rm -f conftest.err conftest.i conftest.$ac_ext
+
+rm -f conftest.err conftest.$ac_ext
# OK, works on sane cases. Now check whether nonexistent headers
# can be detected and how.
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <ac_nonexistent.h>
_ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
# Broken: success on invalid input.
continue
else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
# Passes both tests.
ac_preproc_ok=:
break
fi
-rm -f conftest.err conftest.i conftest.$ac_ext
+
+rm -f conftest.err conftest.$ac_ext
done
# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
-rm -f conftest.i conftest.err conftest.$ac_ext
-if $ac_preproc_ok; then :
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
break
fi
@@ -5656,7 +5782,7 @@ fi
else
ac_cv_prog_CPP=$CPP
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5
+{ $as_echo "$as_me:$LINENO: result: $CPP" >&5
$as_echo "$CPP" >&6; }
ac_preproc_ok=false
for ac_c_preproc_warn_flag in '' yes
@@ -5667,7 +5793,11 @@ do
# <limits.h> exists even on freestanding compilers.
# On the NeXT, cc -E runs the code through the compiler's parser,
# not just through cpp. "Syntax error" is here to catch this case.
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#ifdef __STDC__
# include <limits.h>
@@ -5676,40 +5806,87 @@ do
#endif
Syntax error
_ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
-
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
# Broken: fails on valid input.
continue
fi
-rm -f conftest.err conftest.i conftest.$ac_ext
+
+rm -f conftest.err conftest.$ac_ext
# OK, works on sane cases. Now check whether nonexistent headers
# can be detected and how.
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <ac_nonexistent.h>
_ACEOF
-if ac_fn_c_try_cpp "$LINENO"; then :
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
# Broken: success on invalid input.
continue
else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
# Passes both tests.
ac_preproc_ok=:
break
fi
-rm -f conftest.err conftest.i conftest.$ac_ext
+
+rm -f conftest.err conftest.$ac_ext
done
# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
-rm -f conftest.i conftest.err conftest.$ac_ext
-if $ac_preproc_ok; then :
-
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+ :
else
- { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error $? "C preprocessor \"$CPP\" fails sanity check
-See \`config.log' for more details" "$LINENO" 5; }
+{ { $as_echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
fi
ac_ext=c
@@ -5719,9 +5896,9 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
+{ $as_echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5
$as_echo_n "checking for grep that handles long lines and -e... " >&6; }
-if ${ac_cv_path_GREP+:} false; then :
+if test "${ac_cv_path_GREP+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -z "$GREP"; then
@@ -5732,10 +5909,10 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_prog in grep ggrep; do
+ for ac_prog in grep ggrep; do
for ac_exec_ext in '' $ac_executable_extensions; do
ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
- as_fn_executable_p "$ac_path_GREP" || continue
+ { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
# Check for GNU ac_path_GREP and select it if it is found.
# Check for GNU $ac_path_GREP
case `"$ac_path_GREP" --version 2>&1` in
@@ -5752,7 +5929,7 @@ case `"$ac_path_GREP" --version 2>&1` in
$as_echo 'GREP' >> "conftest.nl"
"$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
- as_fn_arith $ac_count + 1 && ac_count=$as_val
+ ac_count=`expr $ac_count + 1`
if test $ac_count -gt ${ac_path_GREP_max-0}; then
# Best one so far, save it but keep looking for a better one
ac_cv_path_GREP="$ac_path_GREP"
@@ -5767,24 +5944,26 @@ esac
$ac_path_GREP_found && break 3
done
done
- done
+done
IFS=$as_save_IFS
if test -z "$ac_cv_path_GREP"; then
- as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
+$as_echo "$as_me: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
+ { (exit 1); exit 1; }; }
fi
else
ac_cv_path_GREP=$GREP
fi
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5
$as_echo "$ac_cv_path_GREP" >&6; }
GREP="$ac_cv_path_GREP"
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
+{ $as_echo "$as_me:$LINENO: checking for egrep" >&5
$as_echo_n "checking for egrep... " >&6; }
-if ${ac_cv_path_EGREP+:} false; then :
+if test "${ac_cv_path_EGREP+set}" = set; then
$as_echo_n "(cached) " >&6
else
if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
@@ -5798,10 +5977,10 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_prog in egrep; do
+ for ac_prog in egrep; do
for ac_exec_ext in '' $ac_executable_extensions; do
ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
- as_fn_executable_p "$ac_path_EGREP" || continue
+ { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
# Check for GNU ac_path_EGREP and select it if it is found.
# Check for GNU $ac_path_EGREP
case `"$ac_path_EGREP" --version 2>&1` in
@@ -5818,7 +5997,7 @@ case `"$ac_path_EGREP" --version 2>&1` in
$as_echo 'EGREP' >> "conftest.nl"
"$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
- as_fn_arith $ac_count + 1 && ac_count=$as_val
+ ac_count=`expr $ac_count + 1`
if test $ac_count -gt ${ac_path_EGREP_max-0}; then
# Best one so far, save it but keep looking for a better one
ac_cv_path_EGREP="$ac_path_EGREP"
@@ -5833,10 +6012,12 @@ esac
$ac_path_EGREP_found && break 3
done
done
- done
+done
IFS=$as_save_IFS
if test -z "$ac_cv_path_EGREP"; then
- as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
+$as_echo "$as_me: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
+ { (exit 1); exit 1; }; }
fi
else
ac_cv_path_EGREP=$EGREP
@@ -5844,17 +6025,21 @@ fi
fi
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5
$as_echo "$ac_cv_path_EGREP" >&6; }
EGREP="$ac_cv_path_EGREP"
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
+{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5
$as_echo_n "checking for ANSI C header files... " >&6; }
-if ${ac_cv_header_stdc+:} false; then :
+if test "${ac_cv_header_stdc+set}" = set; then
$as_echo_n "(cached) " >&6
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <stdlib.h>
#include <stdarg.h>
@@ -5869,23 +6054,48 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_cv_header_stdc=yes
else
- ac_cv_header_stdc=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_header_stdc=no
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
if test $ac_cv_header_stdc = yes; then
# SunOS 4.x string.h does not declare mem*, contrary to ANSI.
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <string.h>
_ACEOF
if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
- $EGREP "memchr" >/dev/null 2>&1; then :
-
+ $EGREP "memchr" >/dev/null 2>&1; then
+ :
else
ac_cv_header_stdc=no
fi
@@ -5895,14 +6105,18 @@ fi
if test $ac_cv_header_stdc = yes; then
# ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <stdlib.h>
_ACEOF
if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
- $EGREP "free" >/dev/null 2>&1; then :
-
+ $EGREP "free" >/dev/null 2>&1; then
+ :
else
ac_cv_header_stdc=no
fi
@@ -5912,10 +6126,14 @@ fi
if test $ac_cv_header_stdc = yes; then
# /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
- if test "$cross_compiling" = yes; then :
+ if test "$cross_compiling" = yes; then
:
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <ctype.h>
#include <stdlib.h>
@@ -5942,33 +6160,118 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_c_try_run "$LINENO"; then :
-
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ :
else
- ac_cv_header_stdc=no
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_header_stdc=no
fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
- conftest.$ac_objext conftest.beam conftest.$ac_ext
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
+
fi
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5
$as_echo "$ac_cv_header_stdc" >&6; }
if test $ac_cv_header_stdc = yes; then
-$as_echo "#define STDC_HEADERS 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define STDC_HEADERS 1
+_ACEOF
fi
# On IRIX 5.3, sys/types and inttypes.h are conflicting.
+
+
+
+
+
+
+
+
+
for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
inttypes.h stdint.h unistd.h
-do :
- as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
-"
-if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ eval "$as_ac_Header=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_Header=no"
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
cat >>confdefs.h <<_ACEOF
#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
_ACEOF
@@ -5978,11 +6281,147 @@ fi
done
+
+
+
+
for ac_header in float.h limits.h stdlib.h string.h
-do :
- as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
-if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5
+$as_echo_n "checking $ac_header usability... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_header_compiler=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5
+$as_echo_n "checking $ac_header presence... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <$ac_header>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ ac_header_preproc=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+ yes:no: )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+ ac_header_preproc=yes
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ eval "$as_ac_Header=\$ac_header_preproc"
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+
+fi
+as_val=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
cat >>confdefs.h <<_ACEOF
#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
_ACEOF
@@ -5996,18 +6435,17 @@ done
OPENMP_CFLAGS=
# Check whether --enable-openmp was given.
-if test "${enable_openmp+set}" = set; then :
+if test "${enable_openmp+set}" = set; then
enableval=$enable_openmp;
fi
if test "$enable_openmp" != no; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to support OpenMP" >&5
+ { $as_echo "$as_me:$LINENO: checking for $CC option to support OpenMP" >&5
$as_echo_n "checking for $CC option to support OpenMP... " >&6; }
-if ${ac_cv_prog_c_openmp+:} false; then :
+if test "${ac_cv_prog_c_openmp+set}" = set; then
$as_echo_n "(cached) " >&6
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
+ cat >conftest.$ac_ext <<_ACEOF
#ifndef _OPENMP
choke me
@@ -6016,16 +6454,37 @@ else
int main () { return omp_get_num_threads (); }
_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
ac_cv_prog_c_openmp='none needed'
else
- ac_cv_prog_c_openmp='unsupported'
- for ac_option in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp -homp \
- -Popenmp --openmp; do
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_prog_c_openmp='unsupported'
+ for ac_option in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
ac_save_CFLAGS=$CFLAGS
CFLAGS="$CFLAGS $ac_option"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
+ cat >conftest.$ac_ext <<_ACEOF
#ifndef _OPENMP
choke me
@@ -6034,111 +6493,276 @@ else
int main () { return omp_get_num_threads (); }
_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
ac_cv_prog_c_openmp=$ac_option
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
CFLAGS=$ac_save_CFLAGS
if test "$ac_cv_prog_c_openmp" != unsupported; then
break
fi
done
fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_c_openmp" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_c_openmp" >&5
$as_echo "$ac_cv_prog_c_openmp" >&6; }
case $ac_cv_prog_c_openmp in #(
"none needed" | unsupported)
- ;; #(
+ ;; #(
*)
- OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;;
+ OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;;
esac
fi
# Checks for typedefs, structures, and compiler characteristics.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for stdbool.h that conforms to C99" >&5
+{ $as_echo "$as_me:$LINENO: checking for stdbool.h that conforms to C99" >&5
$as_echo_n "checking for stdbool.h that conforms to C99... " >&6; }
-if ${ac_cv_header_stdbool_h+:} false; then :
+if test "${ac_cv_header_stdbool_h+set}" = set; then
$as_echo_n "(cached) " >&6
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
- #include <stdbool.h>
- #ifndef bool
- "error: bool is not defined"
- #endif
- #ifndef false
- "error: false is not defined"
- #endif
- #if false
- "error: false is not 0"
- #endif
- #ifndef true
- "error: true is not defined"
- #endif
- #if true != 1
- "error: true is not 1"
- #endif
- #ifndef __bool_true_false_are_defined
- "error: __bool_true_false_are_defined is not defined"
- #endif
-
- struct s { _Bool s: 1; _Bool t; } s;
-
- char a[true == 1 ? 1 : -1];
- char b[false == 0 ? 1 : -1];
- char c[__bool_true_false_are_defined == 1 ? 1 : -1];
- char d[(bool) 0.5 == true ? 1 : -1];
- /* See body of main program for 'e'. */
- char f[(_Bool) 0.0 == false ? 1 : -1];
- char g[true];
- char h[sizeof (_Bool)];
- char i[sizeof s.t];
- enum { j = false, k = true, l = false * true, m = true * 256 };
- /* The following fails for
- HP aC++/ANSI C B3910B A.05.55 [Dec 04 2003]. */
- _Bool n[m];
- char o[sizeof n == m * sizeof n[0] ? 1 : -1];
- char p[-1 - (_Bool) 0 < 0 && -1 - (bool) 0 < 0 ? 1 : -1];
- /* Catch a bug in an HP-UX C compiler. See
- http://gcc.gnu.org/ml/gcc-patches/2003-12/msg02303.html
- http://lists.gnu.org/archive/html/bug-coreutils/2005-11/msg00161.html
- */
- _Bool q = true;
- _Bool *pq = &q;
+#include <stdbool.h>
+#ifndef bool
+ "error: bool is not defined"
+#endif
+#ifndef false
+ "error: false is not defined"
+#endif
+#if false
+ "error: false is not 0"
+#endif
+#ifndef true
+ "error: true is not defined"
+#endif
+#if true != 1
+ "error: true is not 1"
+#endif
+#ifndef __bool_true_false_are_defined
+ "error: __bool_true_false_are_defined is not defined"
+#endif
+
+ struct s { _Bool s: 1; _Bool t; } s;
+
+ char a[true == 1 ? 1 : -1];
+ char b[false == 0 ? 1 : -1];
+ char c[__bool_true_false_are_defined == 1 ? 1 : -1];
+ char d[(bool) 0.5 == true ? 1 : -1];
+ bool e = &s;
+ char f[(_Bool) 0.0 == false ? 1 : -1];
+ char g[true];
+ char h[sizeof (_Bool)];
+ char i[sizeof s.t];
+ enum { j = false, k = true, l = false * true, m = true * 256 };
+ /* The following fails for
+ HP aC++/ANSI C B3910B A.05.55 [Dec 04 2003]. */
+ _Bool n[m];
+ char o[sizeof n == m * sizeof n[0] ? 1 : -1];
+ char p[-1 - (_Bool) 0 < 0 && -1 - (bool) 0 < 0 ? 1 : -1];
+# if defined __xlc__ || defined __GNUC__
+ /* Catch a bug in IBM AIX xlc compiler version 6.0.0.0
+ reported by James Lemley on 2005-10-05; see
+ http://lists.gnu.org/archive/html/bug-coreutils/2005-10/msg00086.html
+ This test is not quite right, since xlc is allowed to
+ reject this program, as the initializer for xlcbug is
+ not one of the forms that C requires support for.
+ However, doing the test right would require a runtime
+ test, and that would make cross-compilation harder.
+ Let us hope that IBM fixes the xlc bug, and also adds
+ support for this kind of constant expression. In the
+ meantime, this test will reject xlc, which is OK, since
+ our stdbool.h substitute should suffice. We also test
+ this with GCC, where it should work, to detect more
+ quickly whether someone messes up the test in the
+ future. */
+ char digs[] = "0123456789";
+ int xlcbug = 1 / (&(digs + 5)[-2 + (bool) 1] == &digs[4] ? 1 : -1);
+# endif
+ /* Catch a bug in an HP-UX C compiler. See
+ http://gcc.gnu.org/ml/gcc-patches/2003-12/msg02303.html
+ http://lists.gnu.org/archive/html/bug-coreutils/2005-11/msg00161.html
+ */
+ _Bool q = true;
+ _Bool *pq = &q;
int
main ()
{
- bool e = &s;
- *pq |= q;
- *pq |= ! q;
- /* Refer to every declared value, to avoid compiler optimizations. */
- return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
- + !m + !n + !o + !p + !q + !pq);
+ *pq |= q;
+ *pq |= ! q;
+ /* Refer to every declared value, to avoid compiler optimizations. */
+ return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
+ + !m + !n + !o + !p + !q + !pq);
;
return 0;
}
_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_cv_header_stdbool_h=yes
else
- ac_cv_header_stdbool_h=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_header_stdbool_h=no
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdbool_h" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdbool_h" >&5
$as_echo "$ac_cv_header_stdbool_h" >&6; }
- ac_fn_c_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
-if test "x$ac_cv_type__Bool" = xyes; then :
+{ $as_echo "$as_me:$LINENO: checking for _Bool" >&5
+$as_echo_n "checking for _Bool... " >&6; }
+if test "${ac_cv_type__Bool+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_type__Bool=no
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof (_Bool))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof ((_Bool)))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_type__Bool=yes
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_type__Bool" >&5
+$as_echo "$ac_cv_type__Bool" >&6; }
+if test "x$ac_cv_type__Bool" = x""yes; then
cat >>confdefs.h <<_ACEOF
#define HAVE__BOOL 1
@@ -6147,29 +6771,34 @@ _ACEOF
fi
-
if test $ac_cv_header_stdbool_h = yes; then
-$as_echo "#define HAVE_STDBOOL_H 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_STDBOOL_H 1
+_ACEOF
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5
+{ $as_echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5
$as_echo_n "checking for an ANSI C-conforming const... " >&6; }
-if ${ac_cv_c_const+:} false; then :
+if test "${ac_cv_c_const+set}" = set; then
$as_echo_n "(cached) " >&6
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
int
main ()
{
-
+/* FIXME: Include the comments suggested by Paul. */
#ifndef __cplusplus
- /* Ultrix mips cc rejects this sort of thing. */
+ /* Ultrix mips cc rejects this. */
typedef int charset[2];
- const charset cs = { 0, 0 };
+ const charset cs;
/* SunOS 4.1.1 cc rejects this. */
char const *const *pcpcc;
char **ppc;
@@ -6186,9 +6815,8 @@ main ()
++pcpcc;
ppc = (char**) pcpcc;
pcpcc = (char const *const *) ppc;
- { /* SCO 3.2v4 cc rejects this sort of thing. */
- char tx;
- char *t = &tx;
+ { /* SCO 3.2v4 cc rejects this. */
+ char *t;
char const *s = 0 ? (char *) 0 : (char const *) 0;
*t++ = 0;
@@ -6204,10 +6832,10 @@ main ()
iptr p = 0;
++p;
}
- { /* AIX XL C 1.02.0.0 rejects this sort of thing, saying
+ { /* AIX XL C 1.02.0.0 rejects this saying
"k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */
- struct s { int j; const int *ap[3]; } bx;
- struct s *b = &bx; b->j = 5;
+ struct s { int j; const int *ap[3]; };
+ struct s *b; b->j = 5;
}
{ /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */
const int foo = 10;
@@ -6220,24 +6848,140 @@ main ()
return 0;
}
_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
ac_cv_c_const=yes
else
- ac_cv_c_const=no
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_c_const=no
fi
+
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5
$as_echo "$ac_cv_c_const" >&6; }
if test $ac_cv_c_const = no; then
-$as_echo "#define const /**/" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define const /**/
+_ACEOF
fi
-ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default"
-if test "x$ac_cv_type_size_t" = xyes; then :
+{ $as_echo "$as_me:$LINENO: checking for size_t" >&5
+$as_echo_n "checking for size_t... " >&6; }
+if test "${ac_cv_type_size_t+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_type_size_t=no
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof (size_t))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof ((size_t)))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_type_size_t=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5
+$as_echo "$ac_cv_type_size_t" >&6; }
+if test "x$ac_cv_type_size_t" = x""yes; then
+ :
else
cat >>confdefs.h <<_ACEOF
@@ -6248,15 +6992,19 @@ fi
# Checks for library functions.
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether closedir returns void" >&5
+{ $as_echo "$as_me:$LINENO: checking whether closedir returns void" >&5
$as_echo_n "checking whether closedir returns void... " >&6; }
-if ${ac_cv_func_closedir_void+:} false; then :
+if test "${ac_cv_func_closedir_void+set}" = set; then
$as_echo_n "(cached) " >&6
else
- if test "$cross_compiling" = yes; then :
+ if test "$cross_compiling" = yes; then
ac_cv_func_closedir_void=yes
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
$ac_includes_default
#include <$ac_header_dirent>
@@ -6272,45 +7020,212 @@ return closedir (opendir (".")) != 0;
return 0;
}
_ACEOF
-if ac_fn_c_try_run "$LINENO"; then :
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
ac_cv_func_closedir_void=no
else
- ac_cv_func_closedir_void=yes
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_func_closedir_void=yes
fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
- conftest.$ac_objext conftest.beam conftest.$ac_ext
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
+
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_closedir_void" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_func_closedir_void" >&5
$as_echo "$ac_cv_func_closedir_void" >&6; }
if test $ac_cv_func_closedir_void = yes; then
-$as_echo "#define CLOSEDIR_VOID 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define CLOSEDIR_VOID 1
+_ACEOF
fi
+
for ac_header in stdlib.h
-do :
- ac_fn_c_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
-if test "x$ac_cv_header_stdlib_h" = xyes; then :
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5
+$as_echo_n "checking $ac_header usability... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_header_compiler=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5
+$as_echo_n "checking $ac_header presence... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <$ac_header>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ ac_header_preproc=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+ yes:no: )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+ ac_header_preproc=yes
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ eval "$as_ac_Header=\$ac_header_preproc"
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+
+fi
+as_val=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
cat >>confdefs.h <<_ACEOF
-#define HAVE_STDLIB_H 1
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
_ACEOF
fi
done
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible malloc" >&5
+{ $as_echo "$as_me:$LINENO: checking for GNU libc compatible malloc" >&5
$as_echo_n "checking for GNU libc compatible malloc... " >&6; }
-if ${ac_cv_func_malloc_0_nonnull+:} false; then :
+if test "${ac_cv_func_malloc_0_nonnull+set}" = set; then
$as_echo_n "(cached) " >&6
else
- if test "$cross_compiling" = yes; then :
+ if test "$cross_compiling" = yes; then
ac_cv_func_malloc_0_nonnull=no
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#if defined STDC_HEADERS || defined HAVE_STDLIB_H
# include <stdlib.h>
@@ -6326,24 +7241,55 @@ return ! malloc (0);
return 0;
}
_ACEOF
-if ac_fn_c_try_run "$LINENO"; then :
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
ac_cv_func_malloc_0_nonnull=yes
else
- ac_cv_func_malloc_0_nonnull=no
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_func_malloc_0_nonnull=no
fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
- conftest.$ac_objext conftest.beam conftest.$ac_ext
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
+
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_malloc_0_nonnull" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_func_malloc_0_nonnull" >&5
$as_echo "$ac_cv_func_malloc_0_nonnull" >&6; }
-if test $ac_cv_func_malloc_0_nonnull = yes; then :
+if test $ac_cv_func_malloc_0_nonnull = yes; then
-$as_echo "#define HAVE_MALLOC 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_MALLOC 1
+_ACEOF
else
- $as_echo "#define HAVE_MALLOC 0" >>confdefs.h
+ cat >>confdefs.h <<\_ACEOF
+#define HAVE_MALLOC 0
+_ACEOF
case " $LIBOBJS " in
*" malloc.$ac_objext "* ) ;;
@@ -6352,32 +7298,173 @@ else
esac
-$as_echo "#define malloc rpl_malloc" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define malloc rpl_malloc
+_ACEOF
fi
+
+
for ac_header in stdlib.h
-do :
- ac_fn_c_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
-if test "x$ac_cv_header_stdlib_h" = xyes; then :
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5
+$as_echo_n "checking $ac_header usability... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_header_compiler=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5
+$as_echo_n "checking $ac_header presence... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <$ac_header>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ ac_header_preproc=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+ yes:no: )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+ ac_header_preproc=yes
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ eval "$as_ac_Header=\$ac_header_preproc"
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+
+fi
+as_val=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
cat >>confdefs.h <<_ACEOF
-#define HAVE_STDLIB_H 1
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
_ACEOF
fi
done
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible realloc" >&5
+{ $as_echo "$as_me:$LINENO: checking for GNU libc compatible realloc" >&5
$as_echo_n "checking for GNU libc compatible realloc... " >&6; }
-if ${ac_cv_func_realloc_0_nonnull+:} false; then :
+if test "${ac_cv_func_realloc_0_nonnull+set}" = set; then
$as_echo_n "(cached) " >&6
else
- if test "$cross_compiling" = yes; then :
+ if test "$cross_compiling" = yes; then
ac_cv_func_realloc_0_nonnull=no
else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#if defined STDC_HEADERS || defined HAVE_STDLIB_H
# include <stdlib.h>
@@ -6393,24 +7480,55 @@ return ! realloc (0, 0);
return 0;
}
_ACEOF
-if ac_fn_c_try_run "$LINENO"; then :
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
ac_cv_func_realloc_0_nonnull=yes
else
- ac_cv_func_realloc_0_nonnull=no
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_func_realloc_0_nonnull=no
fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
- conftest.$ac_objext conftest.beam conftest.$ac_ext
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
+
fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_realloc_0_nonnull" >&5
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_func_realloc_0_nonnull" >&5
$as_echo "$ac_cv_func_realloc_0_nonnull" >&6; }
-if test $ac_cv_func_realloc_0_nonnull = yes; then :
+if test $ac_cv_func_realloc_0_nonnull = yes; then
-$as_echo "#define HAVE_REALLOC 1" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_REALLOC 1
+_ACEOF
else
- $as_echo "#define HAVE_REALLOC 0" >>confdefs.h
+ cat >>confdefs.h <<\_ACEOF
+#define HAVE_REALLOC 0
+_ACEOF
case " $LIBOBJS " in
*" realloc.$ac_objext "* ) ;;
@@ -6419,22 +7537,208 @@ else
esac
-$as_echo "#define realloc rpl_realloc" >>confdefs.h
+cat >>confdefs.h <<\_ACEOF
+#define realloc rpl_realloc
+_ACEOF
+
+fi
+
+
+
+
+
+
+
+for ac_func in floor memset pow sqrt
+do
+as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5
+$as_echo_n "checking for $ac_func... " >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
+int
+main ()
+{
+return $ac_func ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ eval "$as_ac_var=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_var=no"
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+
+#
+# Test if regular expressions are functional. Early regex implementations have nonfunctional stubs,
+# so the check for C++11 succeeds, but the compiled code will throw an exception.
+#
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+
+
+{ $as_echo "$as_me:$LINENO: checking for functional regular expressions" >&5
+$as_echo_n "checking for functional regular expressions... " >&6; }
+if test "${stacks_cv_header_regex_func+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+stacks_cv_header_regex_func=no
+if test "$cross_compiling" = yes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Requires g++ 4.9.0 or greater." >&5
+$as_echo "$as_me: WARNING: Requires g++ 4.9.0 or greater." >&2;}
+
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+#include <regex>
+int main() {
+ const std::regex regex(".*");
+ const std::string string = "This should match!";
+ const auto result = std::regex_search(string, regex);
+ return result ? 0 : 1;
+}
+
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ stacks_cv_header_regex_func=yes
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+{ { $as_echo "$as_me:$LINENO: error: Regular expressions are not functional, you need g++ 4.9.0 or greater." >&5
+$as_echo "$as_me: error: Regular expressions are not functional, you need g++ 4.9.0 or greater." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
fi
+{ $as_echo "$as_me:$LINENO: result: $stacks_cv_header_regex_func" >&5
+$as_echo "$stacks_cv_header_regex_func" >&6; }
+if test "$stacks_cv_header_regex_func" = yes; then
-
-for ac_func in floor memset pow sqrt
-do :
- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
- cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+cat >>confdefs.h <<\_ACEOF
+#define REGEX_FUNCTIONAL 1
_ACEOF
fi
-done
# For test harness
@@ -6442,9 +7746,9 @@ for ac_prog in gawk mawk nawk awk
do
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_prog_AWK+:} false; then :
+if test "${ac_cv_prog_AWK+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test -n "$AWK"; then
@@ -6455,24 +7759,24 @@ for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_AWK="$ac_prog"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
- done
+done
IFS=$as_save_IFS
fi
fi
AWK=$ac_cv_prog_AWK
if test -n "$AWK"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
+ { $as_echo "$as_me:$LINENO: result: $AWK" >&5
$as_echo "$AWK" >&6; }
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
@@ -6510,13 +7814,13 @@ _ACEOF
case $ac_val in #(
*${as_nl}*)
case $ac_var in #(
- *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+ *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5
$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
esac
case $ac_var in #(
_ | IFS | as_nl) ;; #(
BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
- *) { eval $ac_var=; unset $ac_var;} ;;
+ *) $as_unset $ac_var ;;
esac ;;
esac
done
@@ -6524,8 +7828,8 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
(set) 2>&1 |
case $as_nl`(ac_space=' '; set) 2>&1` in #(
*${as_nl}ac_space=\ *)
- # `set' does not quote correctly, so add quotes: double-quote
- # substitution turns \\\\ into \\, and sed turns \\ into \.
+ # `set' does not quote correctly, so add quotes (double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \).
sed -n \
"s/'/'\\\\''/g;
s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
@@ -6547,23 +7851,12 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
:end' >>confcache
if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
if test -w "$cache_file"; then
- if test "x$cache_file" != "x/dev/null"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+ test "x$cache_file" != "x/dev/null" &&
+ { $as_echo "$as_me:$LINENO: updating cache $cache_file" >&5
$as_echo "$as_me: updating cache $cache_file" >&6;}
- if test ! -f "$cache_file" || test -h "$cache_file"; then
- cat confcache >"$cache_file"
- else
- case $cache_file in #(
- */* | ?:*)
- mv -f confcache "$cache_file"$$ &&
- mv -f "$cache_file"$$ "$cache_file" ;; #(
- *)
- mv -f confcache "$cache_file" ;;
- esac
- fi
- fi
+ cat confcache >$cache_file
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+ { $as_echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5
$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
fi
fi
@@ -6577,29 +7870,20 @@ DEFS=-DHAVE_CONFIG_H
ac_libobjs=
ac_ltlibobjs=
-U=
for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
# 1. Remove the extension, and $U if already installed.
ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
# 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
# will be set to the directory where LIBOBJS objects are built.
- as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
- as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+ ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo'
done
LIBOBJS=$ac_libobjs
LTLIBOBJS=$ac_ltlibobjs
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking that generated files are newer than configure" >&5
-$as_echo_n "checking that generated files are newer than configure... " >&6; }
- if test -n "$am_sleep_pid"; then
- # Hide warnings about reused PIDs.
- wait $am_sleep_pid 2>/dev/null
- fi
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: done" >&5
-$as_echo "done" >&6; }
if test -n "$EXEEXT"; then
am__EXEEXT_TRUE=
am__EXEEXT_FALSE='#'
@@ -6609,26 +7893,34 @@ else
fi
if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
- as_fn_error $? "conditional \"AMDEP\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
fi
if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
- as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
fi
if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
- as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
fi
-: "${CONFIG_STATUS=./config.status}"
+: ${CONFIG_STATUS=./config.status}
ac_write_fail=0
ac_clean_files_save=$ac_clean_files
ac_clean_files="$ac_clean_files $CONFIG_STATUS"
-{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+{ $as_echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5
$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
-as_write_fail=0
-cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+cat >$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
#! $SHELL
# Generated by $as_me.
# Run this file to recreate the current configuration.
@@ -6638,18 +7930,17 @@ cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
debug=false
ac_cs_recheck=false
ac_cs_silent=false
-
SHELL=\${CONFIG_SHELL-$SHELL}
-export SHELL
-_ASEOF
-cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
-## -------------------- ##
-## M4sh Initialization. ##
-## -------------------- ##
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+## --------------------- ##
+## M4sh Initialization. ##
+## --------------------- ##
# Be more Bourne compatible
DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
emulate sh
NULLCMD=:
# Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
@@ -6657,15 +7948,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
alias -g '${1+"$@"}'='"$@"'
setopt NO_GLOB_SUBST
else
- case `(set -o) 2>/dev/null` in #(
- *posix*) :
- set -o posix ;; #(
- *) :
- ;;
+ case `(set -o) 2>/dev/null` in
+ *posix*) set -o posix ;;
esac
+
fi
+
+
+# PATH needs CR
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
as_nl='
'
export as_nl
@@ -6673,13 +7972,7 @@ export as_nl
as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-# Prefer a ksh shell builtin over an external printf program on Solaris,
-# but without wasting forks for bash or zsh.
-if test -z "$BASH_VERSION$ZSH_VERSION" \
- && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
- as_echo='print -r --'
- as_echo_n='print -rn --'
-elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
as_echo='printf %s\n'
as_echo_n='printf %s'
else
@@ -6690,7 +7983,7 @@ else
as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
as_echo_n_body='eval
arg=$1;
- case $arg in #(
+ case $arg in
*"$as_nl"*)
expr "X$arg" : "X\\(.*\\)$as_nl";
arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
@@ -6713,6 +8006,13 @@ if test "${PATH_SEPARATOR+set}" != set; then
}
fi
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ as_unset=unset
+else
+ as_unset=false
+fi
+
# IFS
# We need space, tab and new line, in precisely that order. Quoting is
@@ -6722,16 +8022,15 @@ fi
IFS=" "" $as_nl"
# Find who we are. Look in the path if we contain no directory separator.
-as_myself=
-case $0 in #((
+case $0 in
*[\\/]* ) as_myself=$0 ;;
*) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
- done
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+done
IFS=$as_save_IFS
;;
@@ -6743,16 +8042,12 @@ if test "x$as_myself" = x; then
fi
if test ! -f "$as_myself"; then
$as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
- exit 1
+ { (exit 1); exit 1; }
fi
-# Unset variables that we do not need and which cause bugs (e.g. in
-# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
-# suppresses any "Segmentation fault" message there. '((' could
-# trigger a bug in pdksh 5.2.14.
-for as_var in BASH_ENV ENV MAIL MAILPATH
-do eval test x\${$as_var+set} = xset \
- && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+# Work around bugs in pre-3.0 UWIN ksh.
+for as_var in ENV MAIL MAILPATH
+do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
done
PS1='$ '
PS2='> '
@@ -6764,89 +8059,7 @@ export LC_ALL
LANGUAGE=C
export LANGUAGE
-# CDPATH.
-(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-
-
-# as_fn_error STATUS ERROR [LINENO LOG_FD]
-# ----------------------------------------
-# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
-# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with STATUS, using 1 if that was 0.
-as_fn_error ()
-{
- as_status=$1; test $as_status -eq 0 && as_status=1
- if test "$4"; then
- as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
- fi
- $as_echo "$as_me: error: $2" >&2
- as_fn_exit $as_status
-} # as_fn_error
-
-
-# as_fn_set_status STATUS
-# -----------------------
-# Set $? to STATUS, without forking.
-as_fn_set_status ()
-{
- return $1
-} # as_fn_set_status
-
-# as_fn_exit STATUS
-# -----------------
-# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
-as_fn_exit ()
-{
- set +e
- as_fn_set_status $1
- exit $1
-} # as_fn_exit
-
-# as_fn_unset VAR
-# ---------------
-# Portably unset VAR.
-as_fn_unset ()
-{
- { eval $1=; unset $1;}
-}
-as_unset=as_fn_unset
-# as_fn_append VAR VALUE
-# ----------------------
-# Append the text in VALUE to the end of the definition contained in VAR. Take
-# advantage of any shell optimizations that allow amortized linear growth over
-# repeated appends, instead of the typical quadratic growth present in naive
-# implementations.
-if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
- eval 'as_fn_append ()
- {
- eval $1+=\$2
- }'
-else
- as_fn_append ()
- {
- eval $1=\$$1\$2
- }
-fi # as_fn_append
-
-# as_fn_arith ARG...
-# ------------------
-# Perform arithmetic evaluation on the ARGs, and store the result in the
-# global $as_val. Take advantage of shells that can avoid forks. The arguments
-# must be portable across $(()) and expr.
-if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
- eval 'as_fn_arith ()
- {
- as_val=$(( $* ))
- }'
-else
- as_fn_arith ()
- {
- as_val=`expr "$@" || test $? -eq 1`
- }
-fi # as_fn_arith
-
-
+# Required to use basename.
if expr a : '\(a\)' >/dev/null 2>&1 &&
test "X`expr 00001 : '.*\(...\)'`" = X001; then
as_expr=expr
@@ -6860,12 +8073,8 @@ else
as_basename=false
fi
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
- as_dirname=dirname
-else
- as_dirname=false
-fi
+# Name of the executable.
as_me=`$as_basename -- "$0" ||
$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
X"$0" : 'X\(//\)$' \| \
@@ -6885,25 +8094,76 @@ $as_echo X/"$0" |
}
s/.*/./; q'`
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
+# CDPATH.
+$as_unset CDPATH
+
+
+
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
+
+ # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
+ # uniformly replaced by the line number. The first 'sed' inserts a
+ # line-number line after each line using $LINENO; the second 'sed'
+ # does the real work. The second script uses 'N' to pair each
+ # line-number line with the line containing $LINENO, and appends
+ # trailing '-' during substitution so that $LINENO is not a special
+ # case at line end.
+ # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+ # scripts with optimization help from Paolo Bonzini. Blame Lee
+ # E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
+ { (exit 1); exit 1; }; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
ECHO_C= ECHO_N= ECHO_T=
-case `echo -n x` in #(((((
+case `echo -n x` in
-n*)
- case `echo 'xy\c'` in
+ case `echo 'x\c'` in
*c*) ECHO_T=' ';; # ECHO_T is single tab character.
- xy) ECHO_C='\c';;
- *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
- ECHO_T=' ';;
+ *) ECHO_C='\c';;
esac;;
*)
ECHO_N='-n';;
esac
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
rm -f conf$$ conf$$.exe conf$$.file
if test -d conf$$.dir; then
@@ -6918,85 +8178,49 @@ if (echo >conf$$.file) 2>/dev/null; then
# ... but there are two gotchas:
# 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
# 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
- # In both cases, we have to default to `cp -pR'.
+ # In both cases, we have to default to `cp -p'.
ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
- as_ln_s='cp -pR'
+ as_ln_s='cp -p'
elif ln conf$$.file conf$$ 2>/dev/null; then
as_ln_s=ln
else
- as_ln_s='cp -pR'
+ as_ln_s='cp -p'
fi
else
- as_ln_s='cp -pR'
+ as_ln_s='cp -p'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null
-
-# as_fn_mkdir_p
-# -------------
-# Create "$as_dir" as a directory, including parents if necessary.
-as_fn_mkdir_p ()
-{
-
- case $as_dir in #(
- -*) as_dir=./$as_dir;;
- esac
- test -d "$as_dir" || eval $as_mkdir_p || {
- as_dirs=
- while :; do
- case $as_dir in #(
- *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
- *) as_qdir=$as_dir;;
- esac
- as_dirs="'$as_qdir' $as_dirs"
- as_dir=`$as_dirname -- "$as_dir" ||
-$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$as_dir" : 'X\(//\)[^/]' \| \
- X"$as_dir" : 'X\(//\)$' \| \
- X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$as_dir" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
- test -d "$as_dir" && break
- done
- test -z "$as_dirs" || eval "mkdir $as_dirs"
- } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
-
-
-} # as_fn_mkdir_p
if mkdir -p . 2>/dev/null; then
- as_mkdir_p='mkdir -p "$as_dir"'
+ as_mkdir_p=:
else
test -d ./-p && rmdir ./-p
as_mkdir_p=false
fi
-
-# as_fn_executable_p FILE
-# -----------------------
-# Test if FILE is an executable regular file.
-as_fn_executable_p ()
-{
- test -f "$1" && test -x "$1"
-} # as_fn_executable_p
-as_test_x='test -x'
-as_executable_p=as_fn_executable_p
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
# Sed expression to map a string onto a valid CPP name.
as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
@@ -7006,19 +8230,13 @@ as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
exec 6>&1
-## ----------------------------------- ##
-## Main body of $CONFIG_STATUS script. ##
-## ----------------------------------- ##
-_ASEOF
-test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
-cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-# Save the log message, to keep $0 and so on meaningful, and to
+# Save the log message, to keep $[0] and so on meaningful, and to
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by Stacks $as_me 1.44, which was
-generated by GNU Autoconf 2.69. Invocation command line was
+This file was extended by Stacks $as_me 1.46, which was
+generated by GNU Autoconf 2.63. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
CONFIG_HEADERS = $CONFIG_HEADERS
@@ -7050,15 +8268,13 @@ _ACEOF
cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
ac_cs_usage="\
-\`$as_me' instantiates files and other configuration actions
-from templates according to the current configuration. Unless the files
-and actions are specified as TAGs, all are instantiated by default.
+\`$as_me' instantiates files from templates according to the
+current configuration.
-Usage: $0 [OPTION]... [TAG]...
+Usage: $0 [OPTION]... [FILE]...
-h, --help print this help, then exit
-V, --version print version number and configuration settings, then exit
- --config print configuration, then exit
-q, --quiet, --silent
do not print progress messages
-d, --debug don't remove temporary files
@@ -7077,17 +8293,16 @@ $config_headers
Configuration commands:
$config_commands
-Report bugs to the package provider."
+Report bugs to <bug-autoconf at gnu.org>."
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-Stacks config.status 1.44
-configured by $0, generated by GNU Autoconf 2.69,
- with options \\"\$ac_cs_config\\"
+Stacks config.status 1.46
+configured by $0, generated by GNU Autoconf 2.63,
+ with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
-Copyright (C) 2012 Free Software Foundation, Inc.
+Copyright (C) 2008 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."
@@ -7105,16 +8320,11 @@ ac_need_defaults=:
while test $# != 0
do
case $1 in
- --*=?*)
+ --*=*)
ac_option=`expr "X$1" : 'X\([^=]*\)='`
ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
ac_shift=:
;;
- --*=)
- ac_option=`expr "X$1" : 'X\([^=]*\)='`
- ac_optarg=
- ac_shift=:
- ;;
*)
ac_option=$1
ac_optarg=$2
@@ -7128,29 +8338,27 @@ do
ac_cs_recheck=: ;;
--version | --versio | --versi | --vers | --ver | --ve | --v | -V )
$as_echo "$ac_cs_version"; exit ;;
- --config | --confi | --conf | --con | --co | --c )
- $as_echo "$ac_cs_config"; exit ;;
--debug | --debu | --deb | --de | --d | -d )
debug=: ;;
--file | --fil | --fi | --f )
$ac_shift
case $ac_optarg in
*\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
- '') as_fn_error $? "missing file argument" ;;
esac
- as_fn_append CONFIG_FILES " '$ac_optarg'"
+ CONFIG_FILES="$CONFIG_FILES '$ac_optarg'"
ac_need_defaults=false;;
--header | --heade | --head | --hea )
$ac_shift
case $ac_optarg in
*\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
esac
- as_fn_append CONFIG_HEADERS " '$ac_optarg'"
+ CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'"
ac_need_defaults=false;;
--he | --h)
# Conflict between --help and --header
- as_fn_error $? "ambiguous option: \`$1'
-Try \`$0 --help' for more information.";;
+ { $as_echo "$as_me: error: ambiguous option: $1
+Try \`$0 --help' for more information." >&2
+ { (exit 1); exit 1; }; };;
--help | --hel | -h )
$as_echo "$ac_cs_usage"; exit ;;
-q | -quiet | --quiet | --quie | --qui | --qu | --q \
@@ -7158,10 +8366,11 @@ Try \`$0 --help' for more information.";;
ac_cs_silent=: ;;
# This is an error.
- -*) as_fn_error $? "unrecognized option: \`$1'
-Try \`$0 --help' for more information." ;;
+ -*) { $as_echo "$as_me: error: unrecognized option: $1
+Try \`$0 --help' for more information." >&2
+ { (exit 1); exit 1; }; } ;;
- *) as_fn_append ac_config_targets " $1"
+ *) ac_config_targets="$ac_config_targets $1"
ac_need_defaults=false ;;
esac
@@ -7178,7 +8387,7 @@ fi
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
if \$ac_cs_recheck; then
- set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
shift
\$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
CONFIG_SHELL='$SHELL'
@@ -7216,7 +8425,9 @@ do
"depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
"Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
- *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+ *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
+$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
+ { (exit 1); exit 1; }; };;
esac
done
@@ -7239,24 +8450,26 @@ fi
# after its creation but before its name has been assigned to `$tmp'.
$debug ||
{
- tmp= ac_tmp=
+ tmp=
trap 'exit_status=$?
- : "${ac_tmp:=$tmp}"
- { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
+ { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
' 0
- trap 'as_fn_exit 1' 1 2 13 15
+ trap '{ (exit 1); exit 1; }' 1 2 13 15
}
# Create a (secure) tmp directory for tmp files.
{
tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
- test -d "$tmp"
+ test -n "$tmp" && test -d "$tmp"
} ||
{
tmp=./conf$$-$RANDOM
(umask 077 && mkdir "$tmp")
-} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
-ac_tmp=$tmp
+} ||
+{
+ $as_echo "$as_me: cannot create a temporary directory in ." >&2
+ { (exit 1); exit 1; }
+}
# Set up the scripts for CONFIG_FILES section.
# No need to generate them if there are no CONFIG_FILES.
@@ -7264,13 +8477,7 @@ ac_tmp=$tmp
if test -n "$CONFIG_FILES"; then
-ac_cr=`echo X | tr X '\015'`
-# On cygwin, bash can eat \r inside `` if the user requested igncr.
-# But we know of no other shell where ac_cr would be empty at this
-# point, so we can use a bashism as a fallback.
-if test "x$ac_cr" = x; then
- eval ac_cr=\$\'\\r\'
-fi
+ac_cr='
'
ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
ac_cs_awk_cr='\\r'
@@ -7278,7 +8485,7 @@ else
ac_cs_awk_cr=$ac_cr
fi
-echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
+echo 'BEGIN {' >"$tmp/subs1.awk" &&
_ACEOF
@@ -7287,18 +8494,24 @@ _ACEOF
echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
echo "_ACEOF"
} >conf$$subs.sh ||
- as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
-ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+ { (exit 1); exit 1; }; }
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'`
ac_delim='%!_!# '
for ac_last_try in false false false false false :; do
. ./conf$$subs.sh ||
- as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+ { (exit 1); exit 1; }; }
ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
if test $ac_delim_n = $ac_delim_num; then
break
elif $ac_last_try; then
- as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+ { (exit 1); exit 1; }; }
else
ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
fi
@@ -7306,7 +8519,7 @@ done
rm -f conf$$subs.sh
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
+cat >>"\$tmp/subs1.awk" <<\\_ACAWK &&
_ACEOF
sed -n '
h
@@ -7320,7 +8533,7 @@ s/'"$ac_delim"'$//
t delim
:nl
h
-s/\(.\{148\}\)..*/\1/
+s/\(.\{148\}\).*/\1/
t more1
s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
p
@@ -7334,7 +8547,7 @@ s/.\{148\}//
t nl
:delim
h
-s/\(.\{148\}\)..*/\1/
+s/\(.\{148\}\).*/\1/
t more2
s/["\\]/\\&/g; s/^/"/; s/$/"/
p
@@ -7354,7 +8567,7 @@ t delim
rm -f conf$$subs.awk
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
_ACAWK
-cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
+cat >>"\$tmp/subs1.awk" <<_ACAWK &&
for (key in S) S_is_set[key] = 1
FS = ""
@@ -7386,29 +8599,23 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
else
cat
-fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
- || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
+ || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5
+$as_echo "$as_me: error: could not setup config files machinery" >&2;}
+ { (exit 1); exit 1; }; }
_ACEOF
-# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
-# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# VPATH may cause trouble with some makes, so we remove $(srcdir),
+# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and
# trailing colons and then remove the whole line if VPATH becomes empty
# (actually we leave an empty line to preserve line numbers).
if test "x$srcdir" = x.; then
- ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
-h
-s///
-s/^/:/
-s/[ ]*$/:/
-s/:\$(srcdir):/:/g
-s/:\${srcdir}:/:/g
-s/:@srcdir@:/:/g
-s/^:*//
+ ac_vpsub='/^[ ]*VPATH[ ]*=/{
+s/:*\$(srcdir):*/:/
+s/:*\${srcdir}:*/:/
+s/:*@srcdir@:*/:/
+s/^\([^=]*=[ ]*\):*/\1/
s/:*$//
-x
-s/\(=[ ]*\).*/\1/
-G
-s/\n//
s/^[^=]*=[ ]*$//
}'
fi
@@ -7420,7 +8627,7 @@ fi # test -n "$CONFIG_FILES"
# No need to generate them if there are no CONFIG_HEADERS.
# This happens for instance with `./config.status Makefile'.
if test -n "$CONFIG_HEADERS"; then
-cat >"$ac_tmp/defines.awk" <<\_ACAWK ||
+cat >"$tmp/defines.awk" <<\_ACAWK ||
BEGIN {
_ACEOF
@@ -7432,11 +8639,13 @@ _ACEOF
# handling of long lines.
ac_delim='%!_!# '
for ac_last_try in false false :; do
- ac_tt=`sed -n "/$ac_delim/p" confdefs.h`
- if test -z "$ac_tt"; then
+ ac_t=`sed -n "/$ac_delim/p" confdefs.h`
+ if test -z "$ac_t"; then
break
elif $ac_last_try; then
- as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_HEADERS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_HEADERS" >&2;}
+ { (exit 1); exit 1; }; }
else
ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
fi
@@ -7521,7 +8730,9 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
_ACAWK
_ACEOF
cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
- as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5
+$as_echo "$as_me: error: could not setup config headers machinery" >&2;}
+ { (exit 1); exit 1; }; }
fi # test -n "$CONFIG_HEADERS"
@@ -7534,7 +8745,9 @@ do
esac
case $ac_mode$ac_tag in
:[FHL]*:*);;
- :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
+ :L* | :C*:*) { { $as_echo "$as_me:$LINENO: error: invalid tag $ac_tag" >&5
+$as_echo "$as_me: error: invalid tag $ac_tag" >&2;}
+ { (exit 1); exit 1; }; };;
:[FH]-) ac_tag=-:-;;
:[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
esac
@@ -7553,7 +8766,7 @@ do
for ac_f
do
case $ac_f in
- -) ac_f="$ac_tmp/stdin";;
+ -) ac_f="$tmp/stdin";;
*) # Look for the file first in the build tree, then in the source tree
# (if the path is not absolute). The absolute path cannot be DOS-style,
# because $ac_f cannot contain `:'.
@@ -7562,10 +8775,12 @@ do
[\\/$]*) false;;
*) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
esac ||
- as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+ { { $as_echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5
+$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;}
+ { (exit 1); exit 1; }; };;
esac
case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
- as_fn_append ac_file_inputs " '$ac_f'"
+ ac_file_inputs="$ac_file_inputs '$ac_f'"
done
# Let's still pretend it is `configure' which instantiates (i.e., don't
@@ -7576,7 +8791,7 @@ do
`' by configure.'
if test x"$ac_file" != x-; then
configure_input="$ac_file. $configure_input"
- { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+ { $as_echo "$as_me:$LINENO: creating $ac_file" >&5
$as_echo "$as_me: creating $ac_file" >&6;}
fi
# Neutralize special characters interpreted by sed in replacement strings.
@@ -7588,8 +8803,10 @@ $as_echo "$as_me: creating $ac_file" >&6;}
esac
case $ac_tag in
- *:-:* | *:-) cat >"$ac_tmp/stdin" \
- || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ *:-:* | *:-) cat >"$tmp/stdin" \
+ || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+ { (exit 1); exit 1; }; } ;;
esac
;;
esac
@@ -7617,7 +8834,47 @@ $as_echo X"$ac_file" |
q
}
s/.*/./; q'`
- as_dir="$ac_dir"; as_fn_mkdir_p
+ { as_dir="$ac_dir"
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
+$as_echo "$as_me: error: cannot create directory $as_dir" >&2;}
+ { (exit 1); exit 1; }; }; }
ac_builddir=.
case "$ac_dir" in
@@ -7674,6 +8931,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# If the template does not know about datarootdir, expand it.
# FIXME: This hack should be removed a few years after 2.60.
ac_datarootdir_hack=; ac_datarootdir_seen=
+
ac_sed_dataroot='
/datarootdir/ {
p
@@ -7683,11 +8941,12 @@ ac_sed_dataroot='
/@docdir@/p
/@infodir@/p
/@localedir@/p
-/@mandir@/p'
+/@mandir@/p
+'
case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
*datarootdir*) ac_datarootdir_seen=yes;;
*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
@@ -7697,7 +8956,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
s&@infodir@&$infodir&g
s&@localedir@&$localedir&g
s&@mandir@&$mandir&g
- s&\\\${datarootdir}&$datarootdir&g' ;;
+ s&\\\${datarootdir}&$datarootdir&g' ;;
esac
_ACEOF
@@ -7725,24 +8984,27 @@ s&@INSTALL@&$ac_INSTALL&;t t
s&@MKDIR_P@&$ac_MKDIR_P&;t t
$ac_datarootdir_hack
"
-eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
- >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \
+ || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+ { (exit 1); exit 1; }; }
test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
- { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
- { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \
- "$ac_tmp/out"`; test -z "$ac_out"; } &&
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined. Please make sure it is defined" >&5
+ { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined." >&5
$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined. Please make sure it is defined" >&2;}
+which seems to be undefined. Please make sure it is defined." >&2;}
- rm -f "$ac_tmp/stdin"
+ rm -f "$tmp/stdin"
case $ac_file in
- -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
- *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
+ -) cat "$tmp/out" && rm -f "$tmp/out";;
+ *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
esac \
- || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+ { (exit 1); exit 1; }; }
;;
:H)
#
@@ -7751,21 +9013,27 @@ which seems to be undefined. Please make sure it is defined" >&2;}
if test x"$ac_file" != x-; then
{
$as_echo "/* $configure_input */" \
- && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs"
- } >"$ac_tmp/config.h" \
- || as_fn_error $? "could not create $ac_file" "$LINENO" 5
- if diff "$ac_file" "$ac_tmp/config.h" >/dev/null 2>&1; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
+ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
+ } >"$tmp/config.h" \
+ || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+ { (exit 1); exit 1; }; }
+ if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
+ { $as_echo "$as_me:$LINENO: $ac_file is unchanged" >&5
$as_echo "$as_me: $ac_file is unchanged" >&6;}
else
rm -f "$ac_file"
- mv "$ac_tmp/config.h" "$ac_file" \
- || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ mv "$tmp/config.h" "$ac_file" \
+ || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+ { (exit 1); exit 1; }; }
fi
else
$as_echo "/* $configure_input */" \
- && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" \
- || as_fn_error $? "could not create -" "$LINENO" 5
+ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
+ || { { $as_echo "$as_me:$LINENO: error: could not create -" >&5
+$as_echo "$as_me: error: could not create -" >&2;}
+ { (exit 1); exit 1; }; }
fi
# Compute "$ac_file"'s index in $config_headers.
_am_arg="$ac_file"
@@ -7803,7 +9071,7 @@ $as_echo X"$_am_arg" |
s/.*/./; q'`/stamp-h$_am_stamp_count
;;
- :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+ :C) { $as_echo "$as_me:$LINENO: executing $ac_file commands" >&5
$as_echo "$as_me: executing $ac_file commands" >&6;}
;;
esac
@@ -7811,7 +9079,7 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
case $ac_file$ac_mode in
"depfiles":C) test x"$AMDEP_TRUE" != x"" || {
- # Older Autoconf quotes --file arguments for eval, but not when files
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
# are listed without --file. Let's play safe and only enable the eval
# if we detect the quoting.
case $CONFIG_FILES in
@@ -7824,7 +9092,7 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
# Strip MF so we end up with the name of the file.
mf=`echo "$mf" | sed -e 's/:.*$//'`
# Check whether this is an Automake generated Makefile or not.
- # We used to match only the files named 'Makefile.in', but
+ # We used to match only the files named `Makefile.in', but
# some people rename them; so instead we look at the file content.
# Grep'ing the first line is not enough: some people post-process
# each Makefile.in and add a new line on top of each file to say so.
@@ -7858,19 +9126,21 @@ $as_echo X"$mf" |
continue
fi
# Extract the definition of DEPDIR, am__include, and am__quote
- # from the Makefile without running 'make'.
+ # from the Makefile without running `make'.
DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
test -z "$DEPDIR" && continue
am__include=`sed -n 's/^am__include = //p' < "$mf"`
- test -z "$am__include" && continue
+ test -z "am__include" && continue
am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
# Find all dependency output files, they are included files with
# $(DEPDIR) in their names. We invoke sed twice because it is the
# simplest approach to changing $(DEPDIR) to its actual value in the
# expansion.
for file in `sed -n "
s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
- sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
# Make sure the directory exists.
test -f "$dirpart/$file" && continue
fdir=`$as_dirname -- "$file" ||
@@ -7896,7 +9166,47 @@ $as_echo X"$file" |
q
}
s/.*/./; q'`
- as_dir=$dirpart/$fdir; as_fn_mkdir_p
+ { as_dir=$dirpart/$fdir
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
+$as_echo "$as_me: error: cannot create directory $as_dir" >&2;}
+ { (exit 1); exit 1; }; }; }
# echo "creating $dirpart/$file"
echo '# dummy' > "$dirpart/$file"
done
@@ -7908,12 +9218,15 @@ $as_echo X"$file" |
done # for ac_tag
-as_fn_exit 0
+{ (exit 0); exit 0; }
_ACEOF
+chmod +x $CONFIG_STATUS
ac_clean_files=$ac_clean_files_save
test $ac_write_fail = 0 ||
- as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+ { { $as_echo "$as_me:$LINENO: error: write failure creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: write failure creating $CONFIG_STATUS" >&2;}
+ { (exit 1); exit 1; }; }
# configure is writing to config.log, and then calls config.status.
@@ -7934,10 +9247,10 @@ if test "$no_create" != yes; then
exec 5>>config.log
# Use ||, not &&, to avoid exiting from the if with $? = 1, which
# would make configure fail if this is the last instruction.
- $ac_cs_success || as_fn_exit 1
+ $ac_cs_success || { (exit 1); exit 1; }
fi
if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+ { $as_echo "$as_me:$LINENO: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
fi
diff --git a/configure.ac b/configure.ac
index ca61f7a..418ea25 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
-AC_INIT([Stacks], [1.44])
+AC_INIT([Stacks], [1.46])
AC_CONFIG_AUX_DIR([config])
AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
AC_CONFIG_SRCDIR([src/ustacks.cc])
@@ -70,6 +70,35 @@ AC_FUNC_MALLOC
AC_FUNC_REALLOC
AC_CHECK_FUNCS([floor memset pow sqrt])
+#
+# Test if regular expressions are functional. Early regex implementations have nonfunctional stubs,
+# so the check for C++11 succeeds, but the compiled code will throw an exception.
+#
+AC_LANG(C++)
+AC_DEFUN([AC_REGEX_FUNC], [
+AC_CACHE_CHECK([for functional regular expressions], [stacks_cv_header_regex_func],
+[
+stacks_cv_header_regex_func=no
+AC_RUN_IFELSE([AC_LANG_SOURCE([[
+#include <regex>
+int main() {
+ const std::regex regex(".*");
+ const std::string string = "This should match!";
+ const auto result = std::regex_search(string, regex);
+ return result ? 0 : 1;
+}
+]])],
+ [stacks_cv_header_regex_func=yes],
+ [AC_MSG_ERROR([Regular expressions are not functional, you need g++ 4.9.0 or greater.])],
+ [AC_MSG_WARN([Requires g++ 4.9.0 or greater.])]
+)])
+if test "$stacks_cv_header_regex_func" = yes; then
+ AC_DEFINE([REGEX_FUNCTIONAL], [1], [Regular expressions are defined and implemented])
+fi
+])
+
+AC_REGEX_FUNC
+
# For test harness
AC_PROG_AWK
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diff --git a/htslib/._plugin.c b/htslib/._plugin.c
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diff --git a/htslib/._tabix.c b/htslib/._tabix.c
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diff --git a/scripts/count_fixed_catalog_snps.py b/scripts/count_fixed_catalog_snps.py
new file mode 100755
index 0000000..4a4b6e7
--- /dev/null
+++ b/scripts/count_fixed_catalog_snps.py
@@ -0,0 +1,323 @@
+#!/usr/bin/env python
+
+import optparse
+import sys
+import os
+import gzip
+import re
+
+#
+# Global configuration variables.
+#
+path = ""
+aln_path = ""
+out_path = ""
+batch_id = -1
+
+def parse_command_line():
+ global path
+ global batch_id
+
+ p = optparse.OptionParser()
+
+ #
+ # Add options.
+ #
+ p.add_option("-p", action="store", dest="path",
+ help="path to Stacks directory.")
+ p.add_option("-b", action="store", dest="batch_id",
+ help="Stacks batch ID.")
+
+ #
+ # Parse the command line
+ #
+ (opts, args) = p.parse_args()
+
+ if opts.path != None:
+ path = opts.path
+ if opts.batch_id != None:
+ batch_id = int(opts.batch_id)
+
+ if len(path) == 0 or os.path.exists(path) == False:
+ print >> sys.stderr, "You must specify a valid path to Stacks input files."
+ p.print_help()
+ sys.exit()
+
+ if batch_id < 0:
+ pritn >> sys.stderr, "You must specify the batch ID that was supplied to Stacks."
+ p.print_help()
+ sys.exit()
+
+ if path.endswith("/") == False:
+ path += "/"
+
+
+def find_stacks_files(path, files):
+ try:
+ entries = os.listdir(path)
+
+ for entry in entries:
+ pos = entry.find(".matches.tsv.gz")
+ if (pos == -1):
+ pos = entry.find(".matches.tsv")
+ if (pos != -1):
+ files.append(entry[0:pos])
+ print >> sys.stderr, "Found", len(files), "Stacks samples."
+
+ except:
+ print >> sys.stderr, "Unable to read files from Stacks directory, '" + path + "'"
+
+
+def parse_cigar(cigar, components):
+ #
+ # Parse a cigar string, e.g. 48M1D47M or 43M3D52M3D.
+ #
+ start = 0
+ end = 0
+ dist = ""
+ for c in cigar:
+ if c.isalpha():
+ dist = int(cigar[start:end])
+ op = c.upper();
+ end += 1
+ start = end
+ components.append((op, dist))
+ else:
+ end += 1
+
+
+def adjust_snps(cigar, sample_snps):
+ #
+ # Adjust SNP positions according to how this sample was aligned to the catalog
+ # (which is described by the CIGAR string).
+ #
+ if len(sample_snps) == 0:
+ return
+
+ comp = []
+ parse_cigar(cigar, comp)
+
+ index = 0
+ offset = 0
+ bp = 0
+ for (op, dist) in comp:
+ if op == 'M' or op == 'I':
+ bp += dist
+ while index < len(sample_snps) and sample_snps[index] < bp:
+ sample_snps[index] += offset
+ index += 1
+ if op == 'D':
+ offset += dist
+
+
+def count_sample_snps(path, file, sample_snps):
+ matches = {}
+ cigars = {}
+ #
+ # Open the matches file and load the matches to the catalog.
+ #
+ p = path + file + ".matches.tsv.gz"
+ if os.path.exists(p):
+ gzipped = True;
+ fh = gzip.open(p, 'rb')
+ else:
+ gzipped = False;
+ fh = open(path + file + ".matches.tsv", "r")
+
+ for line in fh:
+ line = line.strip("\n")
+
+ if len(line) == 0 or line[0] == "#":
+ continue
+
+ parts = line.split("\t")
+
+ cat_locus = int(parts[2])
+ sample_locus = int(parts[4])
+ if len(parts) == 9:
+ cigar = parts[8] if len(parts[8]) > 0 else ""
+ else:
+ cigar = ""
+
+ if sample_locus not in matches:
+ matches[sample_locus] = cat_locus
+ else:
+ if cat_locus != matches[sample_locus]:
+ print >> sys.stderr, "Error: sample locus", sample_locus, "matches more than one catalog locus."
+
+ if len(cigar) > 0:
+ if sample_locus not in cigars:
+ cigars[sample_locus] = cigar
+ else:
+ if cigar != cigars[sample_locus]:
+ print >> sys.stderr, "Error: sample locus", sample_locus, "has multiple cigar alignments."
+
+ fh.close()
+
+ #
+ # Open the SNPs file and record all the SNP positions found in this sample.
+ #
+ if gzipped:
+ fh = gzip.open(path + file + ".snps.tsv.gz", "rb")
+ else:
+ fh = open(path + file + ".snps.tsv", "r")
+
+ snps = {}
+
+ for line in fh:
+ if line[0] == "#":
+ continue
+
+ if len(line) == 0:
+ continue
+
+ parts = line.split("\t")
+ sample_locus = int(parts[2])
+ col = int(parts[3])
+ model = parts[4]
+
+ if model != "E":
+ continue
+
+ if sample_locus not in matches:
+ continue
+
+ if sample_locus not in snps:
+ snps[sample_locus] = []
+ snps[sample_locus].append(col)
+
+ fh.close()
+
+ #
+ # Adjust SNP positions according to the gapped alignments recorded in the CIGAR string.
+ #
+ for sample_locus in snps:
+ if sample_locus in cigars:
+ adjust_snps(cigars[sample_locus], snps[sample_locus])
+
+ snp_cnt = 0
+
+ #
+ # Transfer this sample's SNPs to the catalog level dictionary.
+ #
+ for sample_locus in snps:
+ cat_locus = matches[sample_locus]
+
+ for col in snps[sample_locus]:
+ if cat_locus in sample_snps:
+ if col in sample_snps[cat_locus]:
+ sample_snps[cat_locus][col] += 1
+ # print >> sys.stderr, "CatLocus:", cat_locus, "; col:", col
+ else:
+ sample_snps[cat_locus][col] = 1
+ snp_cnt += 1
+ else:
+ sample_snps[cat_locus] = {}
+ sample_snps[cat_locus][col] = 1
+ snp_cnt += 1
+
+ return snp_cnt
+
+
+def count_catalog_snps(path, batch_id, catalog_snps):
+ #
+ # Open the tags file and rewrite it with the alignment coordinates.
+ #
+ p = path + "batch_" + str(batch_id) + ".catalog.snps.tsv.gz"
+ if os.path.exists(p):
+ gzipped = True;
+ fh = gzip.open(path + "batch_" + str(batch_id) + ".catalog.snps.tsv.gz", "rb")
+ else:
+ gzipped = False;
+ fh = open(path + "batch_" + str(batch_id) + ".catalog.snps.tsv", "r")
+
+ out_fh = open(out_path + "batch_" + str(batch_id) + ".catalog.snps.tsv", "w")
+
+ snp_cnt = 0
+
+ for line in fh:
+ if line[0] == "#":
+ continue
+
+ if len(line) == 0:
+ continue
+
+ parts = line.split("\t")
+ cat_locus = int(parts[2])
+ col = int(parts[3])
+ model = parts[4]
+
+ if model != "E":
+ continue
+
+ snp_cnt += 1
+
+ if cat_locus not in catalog_snps:
+ catalog_snps[cat_locus] = []
+
+ catalog_snps[cat_locus].append(col)
+
+ fh.close()
+
+ return snp_cnt
+
+# # # #
+# # ------------------------------------------------------------------------------------------- # #
+# # # #
+
+parse_command_line()
+
+files = []
+catalog_snps = {}
+sample_snps = {}
+
+#
+# Find all the sample files by looking for the matches files in the Stacks directory.
+#
+find_stacks_files(path, files)
+
+#
+# Count all the SNPs identified in the samples.
+#
+i = 1
+for file in files:
+ print >> sys.stderr, "Processing file", str(i), "of", len(files), "['" + file + "']"
+ cnt = count_sample_snps(path, file, sample_snps)
+ print >> sys.stderr, " Found", cnt, "heterozygous SNPs in sample."
+ i += 1
+
+total_snps = 0
+for locus in sample_snps:
+ for col in sample_snps[locus]:
+ total_snps += 1
+print >> sys.stderr, "Found", total_snps, "variable sites across the population."
+
+#
+# Count all the SNPs found in the catalog.
+#
+print >> sys.stderr, "Processing the catalog"
+cnt = count_catalog_snps(path, batch_id, catalog_snps)
+print >> sys.stderr, " Found", cnt, "heterozygous SNPs in the catalog."
+
+#
+# Count all the SNPs in the catalog but not in any sample: these are the fixed differences cstacks identified.
+#
+total_snps = 0
+fixed_snps = 0
+
+for locus in catalog_snps:
+ if locus not in sample_snps:
+ continue
+ c = {}
+ for col in catalog_snps[locus]:
+ c[col] = 1
+ total_snps += 1
+ if col not in sample_snps[locus]:
+ # print >> sys.stderr, "Locus:", locus, "Catalog SNPs:", catalog_snps[locus], "Sample SNPs:", sample_snps[locus]
+ fixed_snps += 1
+ for col in sample_snps[locus]:
+ if col not in c:
+ print "Locus:", locus, "col:", col, "Catalog SNPs:", catalog_snps[locus], "Sample SNPs:", sample_snps[locus]
+
+print >> sys.stderr, "Found", total_snps, "SNPs across all samples and in the catalog."
+print >> sys.stderr, "Found", fixed_snps, "fixed SNPs only in the catalog."
diff --git a/scripts/denovo_map.pl b/scripts/denovo_map.pl
index cd5f0c1..d326cb9 100755
--- a/scripts/denovo_map.pl
+++ b/scripts/denovo_map.pl
@@ -134,11 +134,11 @@ sub execute_stacks {
$path = $sample->{'path'} . $sample->{'file'} . "." . $sample->{'suffix'};
if ($sample->{'type'} eq "sample") {
- $cmd = $exe_path . "ustacks -t $sample->{'fmt'} -f $path -o $out_path -i $sample_id -r $minc " . join(" ", @_ustacks) . " 2>&1";
+ $cmd = $exe_path . "ustacks -t $sample->{'fmt'} -f $path -o $out_path -i $sample_id $minc " . join(" ", @_ustacks) . " 2>&1";
} elsif ($sample->{'type'} eq "parent") {
- $cmd = $exe_path . "ustacks -t $sample->{'fmt'} -f $path -o $out_path -i $sample_id -r $minc " . join(" ", @_ustacks) . " 2>&1";
+ $cmd = $exe_path . "ustacks -t $sample->{'fmt'} -f $path -o $out_path -i $sample_id $minc " . join(" ", @_ustacks) . " 2>&1";
} elsif ($sample->{'type'} eq "progeny") {
- $cmd = $exe_path . "ustacks -t $sample->{'fmt'} -f $path -o $out_path -i $sample_id -r $minrc " . join(" ", @_ustacks) . " 2>&1";
+ $cmd = $exe_path . "ustacks -t $sample->{'fmt'} -f $path -o $out_path -i $sample_id $minrc " . join(" ", @_ustacks) . " 2>&1";
}
print STDERR " $cmd\n";
print $log_fh "$cmd\n";
@@ -891,6 +891,11 @@ sub parse_command_line {
usage();
}
+ if (scalar(@parents) == 0 && scalar(@samples) == 0 && length($popmap_path) > 0 && length($sample_path) == 0) {
+ print STDERR "If you are using a population map to specify samples, you must specify the path to the directory containing the samples (--samples).\n";
+ usage();
+ }
+
if (length($sample_path) > 0) {
$sample_path .= "/" if (substr($sample_path, -1) ne "/");
}
diff --git a/scripts/integrate_alignments.py b/scripts/integrate_alignments.py
index f8a88ee..7e5c1f9 100755
--- a/scripts/integrate_alignments.py
+++ b/scripts/integrate_alignments.py
@@ -297,6 +297,7 @@ def convert_sample(path, file, out_path, alns):
if sample_locus in alns_written:
if read_type == "consensus":
+ cat_locus = matches[sample_locus]
(chr, bp, strand) = alns[cat_locus]
buf = "\t".join(parts[0:3]) + "\t" + chr + "\t" + str(bp) + "\t" + strand + "\t" + "\t".join(parts[6:])
out_fh.write(buf)
diff --git a/scripts/ref_map.pl b/scripts/ref_map.pl
index acc2aab..49118d6 100755
--- a/scripts/ref_map.pl
+++ b/scripts/ref_map.pl
@@ -148,8 +148,8 @@ sub execute_stacks {
#
# Pull the depth of coverage from pstacks.
#
- my @lines = grep(/Mean coverage depth is/, @results);
- my ($depth) = ($lines[0] =~ /^ Mean coverage depth is (\d+\.?\d*); Std Dev: .+; Max: .+$/);
+ my @lines = grep(/mean coverage/, @results);
+ my ($depth) = ($lines[-1] =~ /^Kept \d+ loci; mean coverage is ([\d.]+) \(stdev: [\d.]+, max: [\d.]+\).$/);
push(@depths_of_cov, [$sample->{'file'}, $depth]);
}
write_results(\@results, $log_fh);
@@ -850,6 +850,11 @@ sub parse_command_line {
usage();
}
+ if (scalar(@parents) == 0 && scalar(@samples) == 0 && length($popmap_path) > 0 && length($sample_path) == 0) {
+ print STDERR "If you are using a population map to specify samples, you must specify the path to the directory containing the samples (--samples).\n";
+ usage();
+ }
+
if (length($sample_path) > 0) {
$sample_path .= "/" if (substr($sample_path, -1) ne "/");
}
diff --git a/src/BamI.h b/src/BamI.h
index 92f4ff4..2e4c798 100644
--- a/src/BamI.h
+++ b/src/BamI.h
@@ -28,10 +28,18 @@
#ifdef HAVE_BAM
+#include <algorithm>
+
+#include "sam.h" //htslib
+
+#include "stacks.h"
#include "input.h"
-#include "sam.h"
+
+int bam_find_start_bp(int, strand_type, const vector<pair<char, uint> > &);
+int bam_edit_gaps(vector<pair<char, uint> > &, char *);
class Bam: public Input {
+private:
htsFile *bam_fh;
bam_hdr_t *bamh;
bam1_t *aln;
@@ -39,11 +47,7 @@ class Bam: public Input {
map<uint, string> chrs;
int parse_header();
- int parse_cigar(const char *, vector<pair<char, uint> > &, bool);
- int parse_bam_cigar(vector<pair<char, uint> > &, bool);
- int find_start_bp_pos(int, vector<pair<char, uint> > &);
- int find_start_bp_neg(int, vector<pair<char, uint> > &);
- int edit_gaps(vector<pair<char, uint> > &, char *);
+ void parse_cigar(vector<pair<char, uint> > &);
public:
Bam(const char *path) : Input() {
@@ -92,67 +96,33 @@ Bam::next_seq()
int
Bam::next_seq(Seq& s)
{
- int bytes_read = 0;
- int sflag = 0;
- int flag = 0;
//
// Read a record from the file, skipping unmapped reads, and place it in a Seq object.
//
- do {
- bytes_read = sam_read1(this->bam_fh, this->bamh, this->aln);
-
- if (bytes_read <= 0)
- return 0;
-
- flag = ((this->aln->core.flag & BAM_FUNMAP) != 0);
-
- } while (flag == 1);
-
- //
- // Check which strand this is aligned to:
- // SAM reference: FLAG bit 0x10 - sequence is reverse complemented
- //
- sflag = ((this->aln->core.flag & BAM_FREVERSE) != 0);
-
- //
- // If the read was aligned on the reverse strand (and is therefore reverse complemented)
- // alter the start point of the alignment to reflect the right-side of the read, at the
- // end of the RAD cut site.
- //
- // To accomplish this, we must parse the alignment CIGAR string
- //
- vector<pair<char, uint> > cigar;
- this->parse_bam_cigar(cigar, sflag);
+ if (sam_read1(bam_fh, bamh, aln) < 0)
+ return false;
- uint bp = sflag ?
- this->find_start_bp_neg(this->aln->core.pos, cigar) :
- this->find_start_bp_pos(this->aln->core.pos, cigar);
-
- //
- // Check if this is the primary or secondary alignment.
//
- alnt aln_type = pri_aln;
- flag = ((this->aln->core.flag & BAM_FSECONDARY) != 0);
- if (flag)
- aln_type = sec_aln;
+ // Parse the type of the record.
//
- // Check if this is a supplemenatry (chimeric) alignment (not yet defined in Bam.h).
- //
- flag = ((this->aln->core.flag & 2048) != 0);
- if (flag)
- aln_type = sup_aln;
+ AlnT aln_type;
+ if (aln->core.flag & BAM_FUNMAP)
+ aln_type = AlnT::null;
+ else if (aln->core.flag & BAM_FSECONDARY)
+ aln_type = AlnT::secondary;
+ else if (aln->core.flag & BAM_FSUPPLEMENTARY)
+ aln_type = AlnT::supplementary;
+ else
+ aln_type = AlnT::primary;
//
// Fetch the sequence.
//
string seq;
- uint8_t j;
-
- seq.reserve(this->aln->core.l_qseq);
-
- for (int i = 0; i < this->aln->core.l_qseq; i++) {
- j = bam_seqi(bam_get_seq(this->aln), i);
+ seq.reserve(aln->core.l_qseq);
+ for (int i = 0; i < aln->core.l_qseq; i++) {
+ uint8_t j = bam_seqi(bam_get_seq(aln), i);
switch(j) {
case 1:
seq += 'A';
@@ -169,6 +139,9 @@ Bam::next_seq(Seq& s)
case 15:
seq += 'N';
break;
+ default:
+ // assert(false);
+ break;
}
}
@@ -176,48 +149,62 @@ Bam::next_seq(Seq& s)
// Fetch the quality score.
//
string qual;
- uint8_t *q = bam_get_qual(this->aln);
+ uint8_t *q = bam_get_qual(aln);
for (int i = 0; i < this->aln->core.l_qseq; i++) {
qual += char(int(q[i]) + 33);
}
- string chr = this->chrs[this->aln->core.tid];
+ if (aln_type == AlnT::null) {
+ s = Seq(bam_get_qname(aln), seq.c_str(), qual.c_str());
+ } else {
+ // Fetch the chromosome.
+ string chr = chrs[aln->core.tid];
- //
- // Calculate the percentage of the sequence that was aligned to the reference.
- //
- double len = 0.0;
- for (uint i = 0; i < cigar.size(); i++)
- switch (cigar[i].first) {
- case 'M':
- case 'I':
- case '=':
- case 'X':
- len += cigar[i].second;
- break;
- case 'D':
- case 'S':
- case 'H':
- case 'N':
- break;
- default:
- cerr << "Error parsing CIGAR string '" << cigar[i].second << cigar[i].first << "'.\n";
- break;
- }
- double pct_aln = len / double(seq.length());
+ //
+ // Check which strand this is aligned to:
+ // SAM reference: FLAG bit 0x10 - sequence is reverse complemented
+ //
+ strand_type strand = aln->core.flag & BAM_FREVERSE ? strand_minus : strand_plus;
+
+ //
+ // Parse the alignment CIGAR string.
+ // If aligned to the negative strand, sequence has been reverse complemented and
+ // CIGAR string should be interpreted in reverse.
+ //
+ vector<pair<char, uint> > cigar;
+ parse_cigar(cigar);
+ if (strand == strand_minus)
+ std::reverse(cigar.begin(), cigar.end());
- s = Seq((const char *) bam_get_qname(this->aln), seq.c_str(), qual.c_str(),
- chr.c_str(), bp, sflag ? strand_minus : strand_plus,
- aln_type, pct_aln);
+ //
+ // If the read was aligned on the reverse strand (and is therefore reverse complemented)
+ // alter the start point of the alignment to reflect the right-side of the read, at the
+ // end of the RAD cut site.
+ //
- if (cigar.size() > 0)
- this->edit_gaps(cigar, s.seq);
+ uint bp = bam_find_start_bp(aln->core.pos, strand, cigar);
+
+ //
+ // Calculate the percentage of the sequence that was aligned to the reference.
+ //
+ uint clipped = 0;
+ for (auto& op : cigar)
+ if (op.first == 'S')
+ clipped += op.second;
+ double pct_clipped = (double) clipped / seq.length();
- return 1;
+ s = Seq(bam_get_qname(aln), seq.c_str(), qual.c_str(),
+ chr.c_str(), bp, strand, aln_type, pct_clipped, aln->core.qual);
+
+ if (cigar.size() > 0)
+ bam_edit_gaps(cigar, s.seq);
+ }
+
+ return true;
}
-int
-Bam::parse_bam_cigar(vector<pair<char, uint> > &cigar, bool orientation)
+void
+Bam::parse_cigar(vector<pair<char, uint> > &cigar)
{
int op, len;
char c;
@@ -243,12 +230,12 @@ Bam::parse_bam_cigar(vector<pair<char, uint> > &cigar, bool orientation)
case BAM_CDEL:
c = 'D';
break;
- case BAM_CREF_SKIP:
- c = 'N';
- break;
case BAM_CSOFT_CLIP:
c = 'S';
break;
+ case BAM_CREF_SKIP:
+ c = 'N';
+ break;
case BAM_CHARD_CLIP:
c = 'H';
break;
@@ -256,109 +243,53 @@ Bam::parse_bam_cigar(vector<pair<char, uint> > &cigar, bool orientation)
c = 'P';
break;
default:
- cerr << "Unknown operation present in CIGAR string.\n";
+ cerr << "Warning: Unknown CIGAR operation (current read name is '" << bam_get_qname(aln) << "').\n";
break;
}
- //
- // If aligned to the negative strand, sequence has been reverse complemented and
- // CIGAR string should be interpreted in reverse.
- //
- if (orientation == strand_plus)
- cigar.push_back(make_pair(c, len));
- else
- cigar.insert(cigar.begin(), make_pair(c, len));
- }
-
- return 0;
-}
-
-int
-Bam::parse_cigar(const char *cigar_str, vector<pair<char, uint> > &cigar, bool orientation)
-{
- char buf[id_len];
- int dist;
- const char *p, *q;
-
- p = cigar_str;
-
- if (*p == '*') return 0;
-
- while (*p != '\0') {
- q = p + 1;
-
- while (*q != '\0' && isdigit(*q))
- q++;
- strncpy(buf, p, q - p);
- buf[q-p] = '\0';
- dist = atoi(buf);
-
- //
- // If aligned to the negative strand, sequence has been reverse complemented and
- // CIGAR string should be interpreted in reverse.
- //
- if (orientation == strand_plus)
- cigar.push_back(make_pair(*q, dist));
- else
- cigar.insert(cigar.begin(), make_pair(*q, dist));
-
- p = q + 1;
+ cigar.push_back(make_pair(c, len));
}
-
- return 0;
}
int
-Bam::find_start_bp_neg(int aln_bp, vector<pair<char, uint> > &cigar)
+bam_find_start_bp(int aln_bp, strand_type strand, const vector<pair<char, uint> > &cigar)
{
- uint size = cigar.size();
- char op;
- uint dist;
-
- for (uint i = 0; i < size; i++) {
- op = cigar[i].first;
- dist = cigar[i].second;
-
- switch(op) {
- case 'I':
- case 'H':
- break;
- case 'S':
- if (i < size - 1)
+ if (strand == strand_plus) {
+ if (cigar.at(0).first == 'S')
+ aln_bp -= cigar.at(0).second;
+ } else {
+ // assert(strand == strand_minus);
+ for (uint i = 0; i < cigar.size(); i++) {
+ char op = cigar[i].first;
+ uint dist = cigar[i].second;
+
+ switch(op) {
+ case 'I':
+ case 'H':
+ break;
+ case 'S':
+ if (i < cigar.size() - 1)
+ aln_bp += dist;
+ break;
+ case 'M':
+ case '=':
+ case 'X':
+ case 'D':
+ case 'N':
aln_bp += dist;
- break;
- case 'M':
- case '=':
- case 'X':
- case 'D':
- case 'N':
- aln_bp += dist;
- break;
- default:
- break;
+ break;
+ default:
+ break;
+ }
}
+ aln_bp -= 1;
}
- return aln_bp - 1;
-}
-
-int
-Bam::find_start_bp_pos(int aln_bp, vector<pair<char, uint> > &cigar)
-{
- char op;
- uint dist;
-
- op = cigar[0].first;
- dist = cigar[0].second;
-
- if (op == 'S')
- aln_bp -= dist;
-
return aln_bp;
}
int
-Bam::edit_gaps(vector<pair<char, uint> > &cigar, char *seq)
+bam_edit_gaps(vector<pair<char, uint> > &cigar, char *seq)
{
char *buf;
uint size = cigar.size();
diff --git a/src/MetaPopInfo.cc b/src/MetaPopInfo.cc
index 0ec5799..4bccc04 100644
--- a/src/MetaPopInfo.cc
+++ b/src/MetaPopInfo.cc
@@ -11,9 +11,7 @@
#include "MetaPopInfo.h"
-using std::ifstream;
-using std::cerr;
-using std::exception;
+using namespace std;
const string MetaPopInfo::Pop::default_name = "defaultpop";
const string MetaPopInfo::Group::default_name = "defaultgrp";
@@ -36,11 +34,13 @@ void MetaPopInfo::reset_group_map() {
group_indexes_.insert( {groups_[i].name, i} );
}
-bool MetaPopInfo::init_popmap(const string& pmap_path) {
+void MetaPopInfo::init_popmap(const string& pmap_path) {
ifstream fh(pmap_path.c_str(), ifstream::in);
- if (fh.fail())
- return false;
+ if (fh.fail()) {
+ cerr << "Error: Failed to open population map file '" << pmap_path << "'.\n";
+ throw exception();
+ }
size_t p = 0; // pop index counter
size_t g = 0; // group index counter
@@ -72,7 +72,7 @@ bool MetaPopInfo::init_popmap(const string& pmap_path) {
|| parts.size() > 3
|| parts[0].empty()
|| parts[1].empty()) {
- cerr << "Error: Malformed population map -- expected 'SAMPLE\\tPOP[\\tGROUP]'. In file '" << pmap_path << "', line :\n" << line << "\n";
+ cerr << "Error: Malformed population map -- expected 'SAMPLE \\t POP [\\t GROUP]'. In file '" << pmap_path << "', line :\n" << line << "\n";
throw exception();
}
@@ -125,9 +125,10 @@ bool MetaPopInfo::init_popmap(const string& pmap_path) {
}
}
}
- if (samples_.empty())
- // Empty population map.
- return false;
+ if (samples_.empty()) {
+ cerr << "Error: Population map '" << pmap_path << "' appears to be empty.\n";
+ throw exception();
+ }
//
// Check that all the populations are in a group. Put
@@ -177,13 +178,13 @@ bool MetaPopInfo::init_popmap(const string& pmap_path) {
}
}
pops_[curr_pop].last_sample = samples_.size()-1;
-
- return true;
}
-bool MetaPopInfo::init_names(const vector<string>& sample_names) {
- if(sample_names.empty())
- return false;
+void MetaPopInfo::init_names(const vector<string>& sample_names) {
+ if(sample_names.empty()) {
+ cerr << "Error: No samples.\n";
+ throw exception();
+ }
// Create the samples
for (vector<string>::const_iterator s=sample_names.begin(); s!= sample_names.end(); ++s) {
@@ -206,11 +207,9 @@ bool MetaPopInfo::init_names(const vector<string>& sample_names) {
reset_sample_map();
reset_pop_map();
reset_group_map();
-
- return true;
}
-bool MetaPopInfo::init_directory(const string& dir_path) {
+void MetaPopInfo::init_directory(const string& dir_path) {
//
// Find all sample names.
@@ -238,11 +237,15 @@ bool MetaPopInfo::init_directory(const string& dir_path) {
}
closedir(dir);
+ if (sample_names.empty()) {
+ cerr << "Error: Failed to find sample files in directory '" << dir_path << "'.\n";
+ throw exception();
+ }
+
//
// Initialize the MetaPopInfo
//
-
- return init_names(sample_names);
+ init_names(sample_names);
}
void MetaPopInfo::delete_samples(const vector<size_t>& rm_samples) {
diff --git a/src/MetaPopInfo.h b/src/MetaPopInfo.h
index 57d6f6f..952ba1d 100644
--- a/src/MetaPopInfo.h
+++ b/src/MetaPopInfo.h
@@ -63,9 +63,9 @@ public:
// -- from a population map file.
// -- from just a vector of sample names.
// -- or by looking for "*.tags.tsv(.gz)" files in a directory.
- bool init_popmap(const string& popmap_path);
- bool init_names(const vector<string>& sample_names);
- bool init_directory(const string& dir_path);
+ void init_popmap(const string& popmap_path);
+ void init_names(const vector<string>& sample_names);
+ void init_directory(const string& dir_path);
// Delete samples from the metapopulation.
// (As samples, populations or groups may be deleted, the indexes of
diff --git a/src/PopMap.h b/src/PopMap.h
index 1b699f2..817be1a 100644
--- a/src/PopMap.h
+++ b/src/PopMap.h
@@ -59,7 +59,6 @@ public:
char *cigar; // CIGAR string describing how the datum aligns to the catalog locus.
double lnl; // Log likelihood of this locus.
vector<char *> obshap; // Observed Haplotypes
- vector<SNP *> snps; // All calls for this sample for this locus. size() is [len].
Datum() {
this->id = -1;
this->corrected = false;
@@ -75,8 +74,6 @@ public:
~Datum() {
for (uint i = 0; i < this->obshap.size(); i++)
delete [] this->obshap[i];
- for (uint i = 0; i < this->snps.size(); i++)
- delete this->snps[i];
delete [] this->gtype;
delete [] this->trans_gtype;
delete [] this->model;
@@ -165,6 +162,12 @@ PopMap<LocusT>::PopMap(const MetaPopInfo& mpopi, int num_loci)
template<class LocusT>
PopMap<LocusT>::~PopMap() {
+
+ typename std::map<string, vector<LocusT *> >::iterator it;
+ for (it = this->ordered_loci.begin(); it != this->ordered_loci.end(); it++)
+ it->second.clear();
+ this->ordered_loci.clear();
+
for (int i = 0; i < this->num_loci; i++) {
for (int j = 0; j < metapopinfo.samples().size(); j++)
delete this->data[i][j];
diff --git a/src/SamI.h b/src/SamI.h
index b347cfc..74c9de7 100644
--- a/src/SamI.h
+++ b/src/SamI.h
@@ -29,22 +29,31 @@
//
// One record per line.
//
-
+#include "stacks.h"
#include "input.h"
+# include "aln_utils.h"
+#include "BamI.h"
class Sam: public Input {
- int parse_cigar(const char *, vector<pair<char, uint> > &, bool);
- int find_start_bp_neg(int, vector<pair<char, uint> > &);
- int find_start_bp_pos(int, vector<pair<char, uint> > &);
- int edit_gaps(vector<pair<char, uint> > &, char *);
- public:
- Sam(const char *path) : Input(path) {}
+public:
+ Sam(const char *path);
~Sam() {}
Seq *next_seq();
int next_seq(Seq& s);
+
+private:
+ static const size_t n_mandatory_fields = 11;
};
+Sam::Sam(const char *path)
+: Input(path)
+{
+ while(fh.peek() == '@') {
+ fh.getline(line, max_len);
+ }
+}
+
Seq* Sam::next_seq() {
Seq* s = new Seq();
if(next_seq(*s) != 1) {
@@ -57,291 +66,84 @@ Seq* Sam::next_seq() {
int Sam::next_seq(Seq& s) {
vector<string> parts;
int flag = 0;
- int sflag = 0;
- int aflag = 0;
- uint len;
-
- //
- // Read a record from the file and place it in a Seq object, skipping header
- // definitions and unaligned sequences.
- //
- do {
- this->fh.getline(this->line, max_len);
-
- if (!this->fh.good())
- return 0;
- len = strlen(this->line);
- if (this->line[len - 1] == '\r') this->line[len - 1] = '\0';
+ if(!fh.getline(line, max_len))
+ return false;
- parse_tsv(this->line, parts);
+ int len = strlen(line);
+ if (line[len - 1] == '\r')
+ line[len - 1] = '\0';
- //
- // According to SAM spec FLAGs are the second field,
- // if FLAG bit 0x4 is set, sequence is not mapped.
- //
- flag = atoi(parts[1].c_str());
- flag = flag & 4;
- flag = flag >> 2;
-
- } while (parts[0][0] == '@' || flag == 1);
-
- //
- // Check which strand this is aligned to:
- // SAM reference: FLAG bit 0x10 - sequence is reverse complemented
- //
- flag = atoi(parts[1].c_str());
- sflag = flag & 16;
- sflag = sflag >> 4;
-
- //
- // Check if this is the primary or secondary alignment.
- //
- alnt aln_type = pri_aln;
- aflag = flag & 256;
- aflag = aflag >> 8;
- if (aflag)
- aln_type = sec_aln;
-
- //
- // Check if this is a supplemenatry (chimeric) alignment (not yet defined in Bam.h).
- //
- aflag = flag & 2048;
- aflag = aflag >> 11;
- if (aflag)
- aln_type = sup_aln;
-
- //
- // If the read was aligned on the reverse strand (and is therefore reverse complemented)
- // alter the start point of the alignment to reflect the right-side of the read, at the
- // end of the RAD cut site.
- //
- // To accomplish this, we must parse the alignment CIGAR string
- //
- vector<pair<char, uint> > cigar;
- this->parse_cigar(parts[5].c_str(), cigar, sflag);
-
- int bp = sflag ?
- this->find_start_bp_neg(atoi(parts[3].c_str()), cigar) :
- this->find_start_bp_pos(atoi(parts[3].c_str()), cigar);
+ parse_tsv(line, parts);
+ if (parts.size() < n_mandatory_fields) {
+ cerr << "Error: Malformed SAM record:\n" << line << "\n";
+ throw std::exception();
+ }
//
- // Sam format has a 1-based offset for chrmosome/basepair positions, adjust it to match
- // the Stacks, 0-based offset.
+ // According to SAM spec FLAGs are the second field,
+ // if FLAG bit 0x4 is set, sequence is not mapped.
//
- bp--;
+ flag = atoi(parts[1].c_str());
//
- // Calculate the percentage of the sequence that was aligned to the reference.
+ // Parse the type of the record.
//
- len = 0;
- for (uint i = 0; i < cigar.size(); i++)
- switch (cigar[i].first) {
- case 'M':
- case 'I':
- case '=':
- case 'X':
- len += cigar[i].second;
- break;
- case 'D':
- case 'S':
- case 'H':
- case 'N':
- break;
- default:
- cerr << "Error parsing CIGAR string '" << cigar[i].second << cigar[i].first << "'.\n";
- break;
- }
- double pct_aln = double(len) / double(parts[9].length());
-
- s = Seq(parts[0].c_str(), parts[9].c_str(), parts[10].c_str(), // Read ID, Sequence, Quality
- parts[2].c_str(), bp, sflag ? strand_minus : strand_plus, // Chr, BasePair, Strand
- aln_type, pct_aln); // Alignment type (primary or secondary), percent of read aligned
-
- if (cigar.size() > 0)
- this->edit_gaps(cigar, s.seq);
-
- return 1;
-}
-
-int
-Sam::parse_cigar(const char *cigar_str, vector<pair<char, uint> > &cigar, bool orientation)
-{
- char buf[id_len];
- int dist;
- const char *p, *q;
-
- p = cigar_str;
-
- if (*p == '*') return 0;
-
- while (*p != '\0') {
- q = p + 1;
-
- while (*q != '\0' && isdigit(*q))
- q++;
- strncpy(buf, p, q - p);
- buf[q-p] = '\0';
- dist = atoi(buf);
-
+ AlnT aln_type;
+ if (flag & BAM_FUNMAP)
+ aln_type = AlnT::null;
+ else if (flag & BAM_FSECONDARY)
+ aln_type = AlnT::secondary;
+ else if (flag & BAM_FSUPPLEMENTARY)
+ aln_type = AlnT::supplementary;
+ else
+ aln_type = AlnT::primary;
+
+ if (aln_type == AlnT::null) {
+ s = Seq(parts[0].c_str(), parts[9].c_str(), parts[10].c_str()); // Read ID, Sequence, Quality
+ } else {
//
- // If aligned to the negative strand, sequence has been reverse complemented and
- // CIGAR string should be interpreted in reverse.
+ // Check which strand this is aligned to:
//
- if (orientation == strand_plus)
- cigar.push_back(make_pair(*q, dist));
- else
- cigar.insert(cigar.begin(), make_pair(*q, dist));
-
- p = q + 1;
- }
-
- return 0;
-}
-
-int
-Sam::find_start_bp_neg(int aln_bp, vector<pair<char, uint> > &cigar)
-{
- uint size = cigar.size();
- char op;
- uint dist;
-
- for (uint i = 0; i < size; i++) {
- op = cigar[i].first;
- dist = cigar[i].second;
-
- switch(op) {
- case 'I':
- case 'H':
- break;
- case 'S':
- if (i < size - 1)
- aln_bp += dist;
- break;
- case 'M':
- case '=':
- case 'X':
- case 'D':
- case 'N':
- aln_bp += dist;
- break;
- default:
- break;
- }
- }
-
- return aln_bp - 1;
-}
-
-int
-Sam::find_start_bp_pos(int aln_bp, vector<pair<char, uint> > &cigar)
-{
- char op;
- uint dist;
-
- op = cigar[0].first;
- dist = cigar[0].second;
-
- if (op == 'S')
- aln_bp -= dist;
-
- return aln_bp;
-}
-
-int
-Sam::edit_gaps(vector<pair<char, uint> > &cigar, char *seq)
-{
- char *buf;
- uint size = cigar.size();
- char op;
- uint dist, bp, len, buf_len, buf_size, j, k, stop;
-
- len = strlen(seq);
- bp = 0;
-
- buf = new char[len + 1];
- buf_size = len + 1;
-
- for (uint i = 0; i < size; i++) {
- op = cigar[i].first;
- dist = cigar[i].second;
-
- switch(op) {
- case 'S':
- stop = bp + dist;
- stop = stop > len ? len : stop;
- while (bp < stop) {
- seq[bp] = 'N';
- bp++;
- }
- break;
- case 'D':
- //
- // A deletion has occured in the read relative to the reference genome.
- // Pad the read with sufficent Ns to match the deletion, shifting the existing
- // sequence down. Trim the final length to keep the read length consistent.
- //
- k = bp >= len ? len : bp;
-
- strncpy(buf, seq + k, buf_size - 1);
- buf[buf_size - 1] = '\0';
- buf_len = strlen(buf);
-
- stop = bp + dist;
- stop = stop > len ? len : stop;
- while (bp < stop) {
- seq[bp] = 'N';
- bp++;
- }
+ strand_type strand = flag & BAM_FREVERSE ? strand_minus : strand_plus;
- j = bp;
- k = 0;
- while (j < len && k < buf_len) {
- seq[j] = buf[k];
- k++;
- j++;
- }
- break;
- case 'I':
- //
- // An insertion has occurred in the read relative to the reference genome. Delete the
- // inserted bases and pad the end of the read with Ns.
- //
- if (bp >= len) break;
-
- k = bp + dist > len ? len : bp + dist;
- strncpy(buf, seq + k, buf_size - 1);
- buf[buf_size - 1] = '\0';
- buf_len = strlen(buf);
+ //
+ // Parse the alignment CIGAR string.
+ //
+ vector<pair<char, uint> > cigar;
+ parse_cigar(parts[5].c_str(), cigar, true);
+ if (strand == strand_minus)
+ std::reverse(cigar.begin(), cigar.end());
- j = bp;
- k = 0;
- while (j < len && k < buf_len) {
- seq[j] = buf[k];
- k++;
- j++;
- }
+ //
+ // If the read was aligned on the reverse strand (and is therefore reverse complemented)
+ // alter the start point of the alignment to reflect the right-side of the read, at the
+ // end of the RAD cut site.
+ //
+ int bp = bam_find_start_bp(atoi(parts[3].c_str()), strand, cigar);
+ bp--; // SAM uses 1-based genome positions.
- stop = j + dist;
- stop = stop > len ? len : stop;
- while (j < stop) {
- seq[j] = 'N';
- j++;
- }
- break;
- case 'M':
- case '=':
- case 'X':
- bp += dist;
- break;
- default:
- break;
- }
+ //
+ // Calculate the percentage of the sequence that was aligned to the reference.
+ //
+ uint clipped = 0;
+ for (auto& op : cigar)
+ if (op.first == 'S')
+ clipped += op.second;
+ double pct_clipped = (double) clipped / parts[9].length();
+
+ int map_qual = is_integer(parts[4].c_str());
+ if (map_qual == -1)
+ // Ignore malformed quality.
+ map_qual = 255;
+
+ s = Seq(parts[0].c_str(), parts[9].c_str(), parts[10].c_str(), // Read ID, Sequence, Quality
+ parts[2].c_str(), bp, strand, aln_type, pct_clipped, map_qual); // Chromosome, etc.
+
+ if (cigar.size() > 0)
+ bam_edit_gaps(cigar, s.seq);
}
-
- delete [] buf;
-
- return 0;
+ return true;
}
#endif // __SAMI_H__
diff --git a/src/Vcf.cc b/src/Vcf.cc
index 44a3025..2033b66 100644
--- a/src/Vcf.cc
+++ b/src/Vcf.cc
@@ -14,6 +14,8 @@ const map<string, VcfMeta> VcfMeta::predefined = {
{"FORMAT/DP", VcfMeta("FORMAT","<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">")},
{"FORMAT/AD", VcfMeta("FORMAT","<ID=AD,Number=1,Type=Integer,Description=\"Allele Depth\">")},
{"FORMAT/GL", VcfMeta("FORMAT","<ID=GL,Number=.,Type=Float,Description=\"Genotype Likelihood\">")},
+ // Custom fields.
+ {"INFO/locori", VcfMeta("INFO","<ID=locori,Number=1,Type=Character,Description=\"Orientation the corresponding Stacks locus aligns in\">")},
};
void VcfHeader::init_meta(const string& fileformat) {
diff --git a/src/aln_utils.cc b/src/aln_utils.cc
index 9e3d19b..5d59708 100644
--- a/src/aln_utils.cc
+++ b/src/aln_utils.cc
@@ -38,31 +38,42 @@ invert_cigar(string cigar)
}
int
-parse_cigar(const char *cigar_str, vector<pair<char, uint> > &cigar)
+parse_cigar(const char *cigar_str, vector<pair<char, uint> > &cigar, bool check_correctness)
{
- char buf[id_len];
- int dist;
- const char *p, *q;
-
- uint seqlen = 0;
-
cigar.clear();
+ const char* p = cigar_str;
+ uint seqlen = 0;
+
+ while(*p != '\0') {
+ char* q;
+ uint len = strtol(p, &q, 10);
+ char c = *q;
+
+ if (check_correctness) {
+ if (q == p || c == '\0') {
+ // No number or no qualifier, respectively.
+ cerr << "Error: Malformed CIGAR string '" << cigar_str << "'.\n";
+ throw std::exception();
+ }
+ switch (c) {
+ case 'M':
+ case '=':
+ case 'X':
+ case 'I':
+ case 'D':
+ case 'S':
+ case 'N':
+ case 'H':
+ case 'P':
+ break;
+ default:
+ cerr << "Warning: Unknown CIGAR operation '" << c << "' in '" << cigar_str << "'.\n";
+ break;
+ }
+ }
- p = cigar_str;
-
- while (*p != '\0') {
- q = p + 1;
-
- while (*q != '\0' && isdigit(*q))
- q++;
- strncpy(buf, p, q - p);
- buf[q-p] = '\0';
- dist = is_integer(buf);
-
- cigar.push_back(make_pair(*q, dist));
-
- seqlen += dist;
-
+ cigar.push_back({c, len});
+ seqlen += len;
p = q + 1;
}
diff --git a/src/aln_utils.h b/src/aln_utils.h
index c19b76e..321fd2a 100644
--- a/src/aln_utils.h
+++ b/src/aln_utils.h
@@ -34,7 +34,7 @@ using std::vector;
#include "utils.h"
string invert_cigar(string);
-int parse_cigar(const char *, vector<pair<char, uint> > &);
+int parse_cigar(const char *, vector<pair<char, uint> > &, bool check_correctness = false);
string apply_cigar_to_seq(const char *, vector<pair<char, uint> > &);
string remove_cigar_from_seq(const char *, vector<pair<char, uint> > &);
string apply_cigar_to_model_seq(const char *, vector<pair<char, uint> > &);
diff --git a/src/bootstrap.h b/src/bootstrap.h
index 333e769..37c2c80 100644
--- a/src/bootstrap.h
+++ b/src/bootstrap.h
@@ -312,19 +312,10 @@ template<class StatT>
double
Bootstrap<StatT>::pval(double stat, vector<double> &dist)
{
- vector<double>::iterator up;
- double pos;
-
- up = upper_bound(dist.begin(), dist.end(), stat);
-
- if (up == dist.begin())
- pos = 1;
- else if (up == dist.end())
- pos = dist.size();
- else
- pos = up - dist.begin() + 1;
-
- double res = 1.0 - (pos / (double) dist.size());
+ // Rank `stat` relative to the bootstrapped distribution.
+ // `first_greater` is between 0 (if `stat` is smaller than all values in the
+ // distribution) and `dist.size()` (if `stat` is greater than all of them).
+ size_t first_greater = upper_bound(dist.begin(), dist.end(), stat) - dist.begin();
// cerr << "Generated Smoothed Fst Distribution:\n";
// for (uint n = 0; n < dist.size(); n++)
@@ -334,7 +325,7 @@ Bootstrap<StatT>::pval(double stat, vector<double> &dist)
// << " at position " << (up - dist.begin()) << " out of "
// << dist.size() << " positions (converted position: " << pos << "); pvalue: " << res << ".\n";
- return res;
+ return 1.0 - (double) first_greater / dist.size();
}
diff --git a/src/catalog_utils.cc b/src/catalog_utils.cc
index 1d99926..9908557 100644
--- a/src/catalog_utils.cc
+++ b/src/catalog_utils.cc
@@ -25,8 +25,30 @@
// jcatchen at uoregon.edu
// University of Oregon
//
+#include <regex>
+
+#include "utils.h"
+
#include "catalog_utils.h"
+using namespace std;
+
+const regex catalog_tags_regex ("^batch_([0-9]+).catalog.tags.tsv(.gz)?$");
+
+vector<int> find_catalogs(const string& dir_path) {
+ vector<int> ids;
+
+ for (DirIterator e (dir_path); e; ++e) {
+ smatch m;
+ string name (e.name());
+ regex_match(name, m, catalog_tags_regex);
+ if (!m.empty())
+ ids.push_back(stoi(m[1].str()));
+ }
+
+ return ids;
+}
+
int
reduce_catalog(map<int, CSLocus *> &catalog, set<int> &whitelist, set<int> &blacklist)
{
diff --git a/src/catalog_utils.h b/src/catalog_utils.h
index a68f0ee..bc9b352 100644
--- a/src/catalog_utils.h
+++ b/src/catalog_utils.h
@@ -21,6 +21,8 @@
#ifndef __CATALOG_UTILS_H__
#define __CATALOG_UTILS_H__
+#include <vector>
+#include <string>
#include <map>
using std::map;
#include <set>
@@ -33,6 +35,10 @@ using std::set;
#include "PopSum.h"
#include "Vcf.h"
+// find_catalogs()
+// Looks for catalog files in the given directory and returns the associated ID(s).
+std::vector<int> find_catalogs(const std::string& dir_path);
+
int check_whitelist_integrity(map<int, CSLocus *> &, map<int, set<int> > &);
int reduce_catalog(map<int, CSLocus *> &, set<int> &, set<int> &);
int reduce_catalog(map<int, CSLocus *> &, map<int, set<int> > &, set<int> &);
diff --git a/src/clone_filter.cc b/src/clone_filter.cc
index 05d4b76..51c3d51 100644
--- a/src/clone_filter.cc
+++ b/src/clone_filter.cc
@@ -60,6 +60,7 @@ uint max_bc_size_2;
double win_size;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
@@ -185,6 +186,7 @@ int main (int argc, char* argv[]) {
<< counters["dis_reads"] << " pairs of reads, " << buf << " clone reads.\n";
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int
diff --git a/src/constants.cc b/src/constants.cc
new file mode 100644
index 0000000..e89d2df
--- /dev/null
+++ b/src/constants.cc
@@ -0,0 +1,88 @@
+#include <regex>
+#include <cassert>
+#include <map>
+
+#include "constants.h"
+
+using namespace std;
+
+const
+map<string, FileT> known_extensions = {
+ {".fa", FileT::fasta},
+ {".fasta", FileT::fasta},
+ {".fa.gz", FileT::gzfasta},
+ {".fasta.gz", FileT::gzfasta},
+ {".fq", FileT::fastq},
+ {".fastq", FileT::fastq},
+ {".fq.gz", FileT::gzfastq},
+ {".fastq.gz", FileT::gzfastq},
+ {".sam", FileT::sam},
+ {".bam", FileT::bam}
+};
+
+string remove_suffix(FileT type, const string& orig) {
+ string file (orig);
+
+ int pos = file.find_last_of(".");
+
+ if ((type == FileT::gzfastq || type == FileT::gzfasta) && file.substr(pos) == ".gz")
+ file = file.substr(0, pos);
+
+ pos = file.find_last_of(".");
+
+ if (type == FileT::gzfastq || type == FileT::fastq) {
+
+ if (file.substr(pos) == ".fastq" || file.substr(pos) == ".fq")
+ file = file.substr(0, pos);
+
+ } else if (type == FileT::gzfasta || type == FileT::fasta) {
+
+ if (file.substr(pos) == ".fasta" || file.substr(pos) == ".fa")
+ file = file.substr(0, pos);
+ }
+
+ return file;
+}
+
+regex init_file_ext_regex () {
+ string s = "(";
+
+ auto i = known_extensions.begin();
+ assert(!known_extensions.empty());
+ string ext = i->first;
+ escape_char('.', ext);
+ s += ext;
+ ++i;
+ while(i != known_extensions.end()) {
+ ext = i->first;
+ escape_char('.', ext);
+ s += "|" + ext;
+ ++i;
+ }
+
+ s += ")$";
+ return regex(s);
+}
+
+FileT guess_file_type (const string& path) {
+
+ static const regex reg = init_file_ext_regex();
+
+ smatch m;
+ regex_search(path, m, reg);
+
+ if (m.empty())
+ return FileT::unknown;
+ else
+ return known_extensions.at(m.str());
+}
+
+void escape_char(char c, string& s) {
+ vector<size_t> dots;
+ size_t i = -1;
+ while ((i = s.find(c, i+1)) != string::npos)
+ dots.push_back(i);
+
+ for(auto j=dots.rbegin(); j!=dots.rend(); ++j)
+ s.insert(*j, 1, '\\');
+}
diff --git a/src/constants.h b/src/constants.h
index de1358a..dc248f8 100644
--- a/src/constants.h
+++ b/src/constants.h
@@ -28,12 +28,76 @@
#include "config.h"
#endif
-typedef unsigned int uint;
+#include <cstdlib>
+#include <cstddef>
+#include <cstring>
+#include <cmath>
+#include <cassert>
+#include <vector>
+#include <string>
+#include <set>
+#include <map>
+#include <unordered_set>
+#include <unordered_map>
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <iomanip>
+#include <utility>
+#include <algorithm>
+#include <functional>
-//
-//
-//
-const unsigned int fieldw = 4;
+// OpenMP
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+// Debugging-related macros.
+#ifdef DEBUG
+#define IF_NDEBUG_TRY
+#define IF_NDEBUG_CATCH_ALL_EXCEPTIONS
+
+#else
+#define NDEBUG
+#define IF_NDEBUG_TRY \
+ try {
+#define IF_NDEBUG_CATCH_ALL_EXCEPTIONS \
+ } catch (const std::exception& e) { \
+ std::cerr << "Aborted."; \
+ if (e.what() != std::exception().what()) \
+ std::cerr << " (" << e.what() << ")"; \
+ std::cerr << "\n"; \
+ return 13; \
+ }
+
+#endif
+
+using std::vector;
+using std::string;
+using std::set;
+using std::map;
+using std::unordered_set;
+using std::unordered_map;
+using std::ostream;
+using std::istream;
+using std::streambuf;
+using std::cout;
+using std::cerr;
+using std::cin;
+using std::flush;
+using std::endl;
+using std::ifstream;
+using std::ofstream;
+using std::stringstream;
+using std::pair;
+using std::make_pair;
+using std::stoi;
+using std::getline;
+using std::exception;
+using std::move;
+
+typedef unsigned int uint;
+typedef unsigned char uchar;
//
// Maximum line length for parsing input files.
@@ -51,6 +115,11 @@ const int id_len = 255;
const int libz_buffer_size = 1048576;
//
+// Number of digits to use when writing numbers in scientific notation.
+//
+const unsigned int fieldw = 4;
+
+//
// Supported file types
//
enum class FileT {unknown,
@@ -60,4 +129,10 @@ enum class FileT {unknown,
bowtie, sam, bam, tsv,
bustard, phase, fastphase, beagle};
+std::string remove_suffix(FileT, const string&);
+
+FileT guess_file_type(const string&);
+
+void escape_char(char c, string& s);
+
#endif
diff --git a/src/cstacks.cc b/src/cstacks.cc
index fd0fca1..8316edb 100644
--- a/src/cstacks.cc
+++ b/src/cstacks.cc
@@ -22,6 +22,8 @@
// cstacks -- Create a catalog of Stacks.
//
+#include "MetaPopInfo.h"
+
#include "cstacks.h"
// Global variables to hold command-line options.
@@ -29,7 +31,7 @@ queue<pair<int, string> > samples;
string out_path;
string catalog_path;
FileT in_file_type = FileT::sql;
-int batch_id = 0;
+int batch_id = -1;
int ctag_dist = 1;
bool set_kmer_len = true;
int kmer_len = 0;
@@ -42,18 +44,22 @@ bool gapped_alignments = false;
double min_match_len = 0.80;
double max_gaps = 2.0;
+using namespace std;
+
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
uint sample_cnt = samples.size();
- cerr << "cstacks paramters selected:\n"
- << " Loci matched based on " << (search_type == sequence ? "sequence identity" : "genomic location") << ".\n";
+ cerr << "cstacks parameters selected:\n"
+ << " Database/Batch ID: " << batch_id << "\n"
+ << " Loci matched based on " << (search_type == sequence ? "sequence identity" : "aligned genomic location") << ".\n";
if (search_type == sequence)
- cerr << " Number of mismatches allowed between stacks: " << ctag_dist << "\n";
- cerr << " Gapped alignments: " << (gapped_alignments ? "enabled" : "disabled") << "\n"
- << "Constructing catalog from " << sample_cnt << " samples.\n";
+ cerr << " Number of mismatches allowed between stacks: " << ctag_dist << "\n"
+ << " Gapped alignments: " << (gapped_alignments ? "enabled" : "disabled") << "\n";
+ cerr << "Constructing catalog from " << sample_cnt << " samples.\n";
//
// Set the number of OpenMP parallel threads to execute.
@@ -69,8 +75,10 @@ int main (int argc, char* argv[]) {
bool compressed = false;
int i;
+ set<int> seen_sample_ids; // For checking sample ID unicity.
+
if (catalog_path.length() > 0) {
- cerr << "Initializing existing catalog...\n";
+ cerr << "\nInitializing existing catalog...\n";
if (!initialize_existing_catalog(catalog_path, catalog)) {
cerr << "Failed to initialize the catalog.\n";
return 1;
@@ -81,12 +89,13 @@ int main (int argc, char* argv[]) {
s = samples.front();
samples.pop();
- cerr << "Initializing new catalog...\n";
+ cerr << "\nInitializing new catalog...\n";
if (!initialize_new_catalog(s, catalog)) {
cerr << "Failed to initialize the catalog.\n";
return 1;
}
i = 2;
+ seen_sample_ids.insert(catalog.begin()->second->sample_id);
}
//
@@ -101,11 +110,11 @@ int main (int argc, char* argv[]) {
while (!samples.empty()) {
map<int, QLocus *> sample;
- cerr << "Processing sample " << s.second << " [" << i << " of " << sample_cnt << "]\n";
-
s = samples.front();
samples.pop();
+ cerr << "\nProcessing sample " << s.second << " [" << i << " of " << sample_cnt << "]\n";
+
if (!load_loci(s.second, sample, false, false, compressed)) {
cerr << "Failed to load sample " << i << "\n";
continue;
@@ -115,6 +124,13 @@ int main (int argc, char* argv[]) {
//
s.first = sample.begin()->second->sample_id;
+ // Check for unique sample IDs.
+ if (!seen_sample_ids.insert(s.first).second) {
+ // Insert failed.
+ cerr << "Error: Sample ID '" << s.first << "' occurs more than once. Sample IDs must be unique." << endl;
+ return -1;
+ }
+
//dump_loci(sample);
if (search_type == sequence) {
@@ -161,9 +177,9 @@ int main (int argc, char* argv[]) {
sample.clear();
}
- cerr << "Writing catalog to '" << out_path << "...";
+ cerr << "\nWriting catalog in directory '" << out_path << "'.\n";
write_catalog(catalog);
- cerr << " done.\n";
+ cerr << "cstacks is done.\n";
//
// Free memory associated with the catalog.
@@ -173,6 +189,7 @@ int main (int argc, char* argv[]) {
catalog.clear();
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int update_catalog_index(map<int, CLocus *> &catalog, map<string, int> &cat_index) {
@@ -1738,6 +1755,7 @@ initialize_existing_catalog(string catalog_path, map<int, CLocus *> &catalog)
//
// Parse the input files.
//
+ catalog_path += ".catalog";
if (!load_loci(catalog_path, catalog, false, false, compressed))
return 0;
@@ -1781,15 +1799,15 @@ initialize_existing_catalog(string catalog_path, map<int, CLocus *> &catalog)
}
int parse_command_line(int argc, char* argv[]) {
- int c;
- string sstr;
+ string in_dir;
+ string popmap_path;
while (1) {
static struct option long_options[] = {
{"help", no_argument, NULL, 'h'},
- {"version", no_argument, NULL, 'v'},
+ {"version", no_argument, NULL, 1000},
{"mmatches", no_argument, NULL, 'm'},
- {"genomic_loc", no_argument, NULL, 'g'},
+ {"aligned", no_argument, NULL, 'g'},
{"uniq_haplotypes", no_argument, NULL, 'u'},
{"report_mmatches", no_argument, NULL, 'R'},
{"gapped", no_argument, NULL, 'G'},
@@ -1805,10 +1823,8 @@ int parse_command_line(int argc, char* argv[]) {
{0, 0, 0, 0}
};
- // getopt_long stores the option index here.
int option_index = 0;
-
- c = getopt_long(argc, argv, "hgvuRmGX:x:o:s:c:b:p:n:k:", long_options, &option_index);
+ int c = getopt_long(argc, argv, "hgvuRmGX:x:o:s:c:b:p:n:k:P:M:", long_options, &option_index);
// Detect the end of the options.
if (c == -1)
@@ -1820,10 +1836,6 @@ int parse_command_line(int argc, char* argv[]) {
break;
case 'b':
batch_id = is_integer(optarg);
- if (batch_id < 0) {
- cerr << "Batch ID (-b) must be an integer, e.g. 1, 2, 3\n";
- help();
- }
break;
case 'n':
ctag_dist = is_integer(optarg);
@@ -1842,8 +1854,7 @@ int parse_command_line(int argc, char* argv[]) {
search_type = genomic_loc;
break;
case 's':
- sstr = optarg;
- samples.push(make_pair(0, sstr));
+ samples.push(make_pair(0, optarg));
break;
case 'c':
catalog_path = optarg;
@@ -1863,12 +1874,18 @@ int parse_command_line(int argc, char* argv[]) {
case 'x':
min_match_len = is_double(optarg);
break;
- case 'v':
+ case 1000:
version();
break;
case 'p':
num_threads = is_integer(optarg);
break;
+ case 'P':
+ in_dir = optarg;
+ break;
+ case 'M':
+ popmap_path = optarg;
+ break;
case '?':
// getopt_long already printed an error message.
help();
@@ -1879,51 +1896,92 @@ int parse_command_line(int argc, char* argv[]) {
}
}
- if (set_kmer_len == false && (kmer_len < 5 || kmer_len > 31)) {
- cerr << "Kmer length must be between 5 and 31bp.\n";
+ if (optind < argc) {
+ cerr << "Error: Failed to parse command line: '" << argv[optind] << "' is seen as a positional argument. Expected no positional arguments.\n";
help();
}
- if (samples.size() == 0) {
- cerr << "You must specify at least one sample file.\n";
+ if (in_dir.empty() && samples.empty()) {
+ cerr << "Error: You must specify one of -P or -s.\n";
+ help();
+ } else if ((!in_dir.empty() || !popmap_path.empty())
+ && (!samples.empty() || !out_path.empty())) {
+ cerr << "Error: Please use options -P/-M or -s/-o, not both.\n";
help();
}
- if (out_path.length() == 0)
- out_path = ".";
+ if (!in_dir.empty()) {
+ if (popmap_path.empty()) {
+ cerr << "Error: Please specify a population map (-M).\n";
+ help();
+ }
+
+ if (in_dir.back() != '/')
+ in_dir += "/";
+
+ // Set `samples`.
+ MetaPopInfo popmap;
+ popmap.init_popmap(popmap_path);
+ for (const MetaPopInfo::Sample& s : popmap.samples())
+ samples.push({0, in_dir + s.name});
+
+ // Set `out_path`.
+ out_path = in_dir;
- if (out_path.at(out_path.length() - 1) != '/')
- out_path += "/";
+ if (batch_id < 0)
+ batch_id = 1;
+
+ } else if (!samples.empty()) {
+ if (out_path.empty())
+ out_path = ".";
+
+ if (out_path.back() != '/')
+ out_path += "/";
+
+ if (batch_id < 0)
+ batch_id = 1;
+ }
+
+ if (set_kmer_len == false && (kmer_len < 5 || kmer_len > 31)) {
+ cerr << "Kmer length must be between 5 and 31bp.\n";
+ help();
+ }
return 0;
}
void version() {
- std::cerr << "cstacks " << VERSION << "\n\n";
+ std::cerr << "cstacks " << VERSION << "\n";
exit(0);
}
void help() {
std::cerr << "cstacks " << VERSION << "\n"
- << "cstacks -b batch_id -s sample_file [-s sample_file_2 ...] [-o path] [-g] [-n num] [-p num_threads] [--catalog path] [-h]" << "\n"
- << " b: MySQL ID of this batch." << "\n"
- << " s: filename prefix from which to load loci into the catalog." << "\n"
+ << "cstacks -P in_dir -M popmap [-n num_mismatches] [--gapped] [-p num_threads] [-b batch_id]" << "\n"
+ << "cstacks --aligned -P in_dir -M popmap [-p num_threads] [-b batch_id]" << "\n"
+ << "cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [--gapped] [-p num_threads] [-b batch_id]" << "\n"
+ << "cstacks --aligned -s sample1_path [-s sample2_path ...] -o path [-p num_threads] [-b batch_id]" << "\n"
+ << "\n"
+ << " b: database/batch ID for this catalog (default 1)." << "\n"
+ << " P: path to the directory containing Stacks files.\n"
+ << " M: path to a population map file.\n"
+ << " g,--aligned: base catalog construction on alignment position, not sequence identity." << "\n"
+ << " n: number of mismatches allowed between sample loci when build the catalog (default 1)." << "\n"
+ << " p: enable parallel execution with num_threads threads.\n"
+ << " s: sample prefix from which to load loci into the catalog." << "\n"
<< " o: output path to write results." << "\n"
- << " g: base catalog matching on genomic location, not sequence identity." << "\n"
+ << " --catalog <path>: add to an existing catalog.\n"
+ << "\n"
+ << "Gapped assembly options:\n"
+ << " --gapped: preform gapped alignments between stacks.\n"
+ << " --max_gaps: number of gaps allowed between stacks before merging (default: 2).\n"
+ << " --min_aln_len: minimum length of aligned sequence in a gapped alignment (default: 0.80).\n"
+ << "\n"
+ << "Advanced options:\n"
<< " m: include tags in the catalog that match to more than one entry (default false)." << "\n"
- << " n: number of mismatches allowed between sample tags when generating the catalog (default 1)." << "\n"
- << " p: enable parallel execution with num_threads threads.\n"
- << " h: display this help messsage." << "\n\n"
- << " Catalog editing:\n"
- << " --catalog <path>: provide the path to an existing catalog. cstacks will add data to this existing catalog.\n\n"
- << " Gapped assembly options:\n"
- << " --gapped: preform gapped alignments between stacks.\n"
- << " --max_gaps: number of gaps allowed between stacks before merging (default: 2).\n"
- << " --min_aln_len: minimum length of aligned sequence in a gapped alignment (default: 0.80).\n\n"
- << " Advanced options:\n"
- << " --k_len <len>: specify k-mer size for matching between between catalog loci (automatically calculated by default).\n"
- << " --report_mmatches: report query loci that match more than one catalog locus.\n";
+ << " --k_len <len>: specify k-mer size for matching between between catalog loci (automatically calculated by default).\n"
+ << " --report_mmatches: report query loci that match more than one catalog locus.\n";
exit(0);
}
diff --git a/src/estacks.cc b/src/estacks.cc
index 1ef5cf3..a02a719 100644
--- a/src/estacks.cc
+++ b/src/estacks.cc
@@ -47,6 +47,7 @@ double heterozygote_limit = -3.84;
double homozygote_limit = 3.84;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
@@ -82,6 +83,7 @@ int main (int argc, char* argv[]) {
write_sql(merged, unique);
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int call_alleles(MergedStack *mtag, vector<DNANSeq *> &reads) {
@@ -199,7 +201,7 @@ int call_consensus(map<int, MergedStack *> &merged, map<int, PStack *> &unique,
if (invoke_model) {
call_alleles(mtag, reads);
- if (model_type == fixed) {
+ if (model_type == ::fixed) {
//
// Mask nucleotides that are not fixed.
//
@@ -499,6 +501,9 @@ int load_radtags(string in_file, HashMap &radtags) {
while ((c = fh->next_seq()) != NULL) {
if (i % 10000 == 0) cerr << "Loading aligned sequence " << i << " \r";
+ if (c->aln_type == AlnT::null)
+ continue;
+
radtags[c->seq].push_back(c);
i++;
}
@@ -660,7 +665,7 @@ int parse_command_line(int argc, char* argv[]) {
if (out_path.at(out_path.length() - 1) != '/')
out_path += "/";
- if (model_type == fixed && barcode_err_freq == 0) {
+ if (model_type == ::fixed && barcode_err_freq == 0) {
cerr << "You must specify the barcode error frequency.\n";
help();
}
diff --git a/src/export_formats.cc b/src/export_formats.cc
index 51bdbe4..2bbf20e 100644
--- a/src/export_formats.cc
+++ b/src/export_formats.cc
@@ -264,15 +264,6 @@ write_vcf_ordered(map<int, CSLocus *> &catalog,
exit(-1);
}
- bool gl = false; // Whether to include the GL genotype subfield.
- if (input_mode == InputMode::stacks
- && !debug_flags.count("VCFCOMP")) {
- gl=true;
- // Load SNP data so that model likelihoods can be output to VCF file.
- cerr << "In preparation for VCF export, loading SNP data for " << mpopi.samples().size() << " samples.\n";
- populate_snp_calls(catalog, pmap, merge_map);
- }
-
//
// Obtain the current date.
//
@@ -337,8 +328,6 @@ write_vcf_ordered(map<int, CSLocus *> &catalog,
rec.format.push_back("GT");
rec.format.push_back("DP");
rec.format.push_back("AD");
- if (gl)
- rec.format.push_back("GL");
for (int j = 0; j < pmap->sample_cnt(); j++) {
stringstream sample;
@@ -346,13 +335,9 @@ write_vcf_ordered(map<int, CSLocus *> &catalog,
if (d[j] == NULL || col >= d[j]->len) {
// Data does not exist.
sample << "./.:0:.,.";
- if (gl)
- sample << ":.,.,.";
} else if (d[j]->model[col] == 'U') {
// Data exists, but the model call was uncertain.
sample << "./.:" << d[j]->tot_depth << ":.,.";
- if (gl)
- sample << ":.,.,.";
} else {
char allele1, allele2;
tally_observed_haplotypes(d[j]->obshap, snp_index, allele1, allele2);
@@ -360,34 +345,23 @@ write_vcf_ordered(map<int, CSLocus *> &catalog,
if (allele1 == 0) {
// More than two alleles in this sample
sample << "./.:" << d[j]->tot_depth << ":.,.";
- if (gl)
- sample << ":.,.,.";
} else {
// Write the genotype.
int dp1, dp2;
find_datum_allele_depths(d[j], snp_index, allele1, allele2, dp1, dp2);
- if(gl && col >= d[j]->snps.size())
- cerr << "Warning, unable to locate SNP call in column " << col << " for catalog locus " << loc->id << ", tag ID " << d[j]->id << "\n";
-
if (allele2 == 0) {
// homozygote
if (allele1 == ref) {
sample << "0/0:" << d[j]->tot_depth << ":" << dp1 << "," << dp2;
- if (gl)
- sample << ":" << - d[j]->snps[col]->lratio << ",.,.";
} else {
sample << "1/1:" << d[j]->tot_depth << ":" << dp2 << "," << dp1;
- if (gl)
- sample << ":.,.," << - d[j]->snps[col]->lratio;
}
} else {
// heterozygote
sample << "0/1:" << d[j]->tot_depth
<< ":" << (allele1 == ref ? dp1 : dp2) << "," << (allele1 == ref ? dp2 : dp1);
- if (gl)
- sample << ":.," << - d[j]->snps[col]->lratio << ",.";
}
}
}
@@ -417,15 +391,6 @@ write_vcf(map<int, CSLocus *> &catalog,
exit(-1);
}
- bool gl = false; // Whether to include the GL genotype subfield.
- if (input_mode == InputMode::stacks
- && !debug_flags.count("VCFCOMP")) {
- gl=true;
- // Load SNP data so that model likelihoods can be output to VCF file.
- cerr << "In preparation for VCF export, loading SNP data for " << mpopi.samples().size() << " samples.\n";
- populate_snp_calls(catalog, pmap, merge_map);
- }
-
//
// Output the header.
//
@@ -446,6 +411,7 @@ write_vcf(map<int, CSLocus *> &catalog,
header.add_meta(VcfMeta::predefined.at("FORMAT/DP"));
header.add_meta(VcfMeta::predefined.at("FORMAT/AD"));
header.add_meta(VcfMeta::predefined.at("FORMAT/GL"));
+ header.add_meta(VcfMeta::predefined.at("INFO/locori"));
for(auto& s : mpopi.samples()) {
header.add_sample(s.name);
}
@@ -499,11 +465,10 @@ write_vcf(map<int, CSLocus *> &catalog,
rec.filter.push_back("PASS");
rec.info.push_back({"NS",to_string(t->nucs[col].num_indv)});
rec.info.push_back({"AF",freq_alt});
+ rec.info.push_back({"locori", loc->loc.strand == strand_plus ? "p" : "m"});
rec.format.push_back("GT");
rec.format.push_back("DP");
rec.format.push_back("AD");
- if (gl)
- rec.format.push_back("GL");
for (int j = 0; j < pmap->sample_cnt(); j++) {
stringstream sample;
@@ -511,13 +476,9 @@ write_vcf(map<int, CSLocus *> &catalog,
if (d[j] == NULL || col >= uint(d[j]->len)) {
// Data does not exist.
sample << "./.:0:.,.";
- if (gl)
- sample << ":.,.,.";
} else if (d[j]->model[col] == 'U') {
// Data exists, but the model call was uncertain.
sample << "./.:" << d[j]->tot_depth << ":.,.";
- if (gl)
- sample << ":.,.,.";
} else {
char allele1, allele2;
tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, allele1, allele2);
@@ -525,8 +486,6 @@ write_vcf(map<int, CSLocus *> &catalog,
if (allele1 == 0) {
// More than two alleles in this sample
sample << "./.:" << d[j]->tot_depth << ":.,.";
- if (gl)
- sample << ":.,.,.";
} else {
// Write the genotype.
@@ -537,19 +496,13 @@ write_vcf(map<int, CSLocus *> &catalog,
// homozygote
if (allele1 == ref) {
sample << "0/0:" << d[j]->tot_depth << ":" << dp1 << "," << dp2;
- if (gl)
- sample << ":" << - d[j]->snps[col]->lratio << ",.,.";
} else {
sample << "1/1:" << d[j]->tot_depth << ":" << dp2 << "," << dp1;
- if (gl)
- sample << ":.,.," << - d[j]->snps[col]->lratio;
}
} else {
// heterozygote
sample << "0/1:" << d[j]->tot_depth
<< ":" << (allele1 == ref ? dp1 : dp2) << "," << (allele1 == ref ? dp2 : dp1);
- if (gl)
- sample << ":.," << - d[j]->snps[col]->lratio << ",.";
}
}
}
@@ -596,6 +549,7 @@ write_vcf_haplotypes(map<int, CSLocus *> &catalog,
header.add_meta(VcfMeta::predefined.at("INFO/AF"));
header.add_meta(VcfMeta::predefined.at("FORMAT/GT"));
header.add_meta(VcfMeta::predefined.at("FORMAT/DP"));
+ header.add_meta(VcfMeta::predefined.at("INFO/locori"));
for(auto& s : mpopi.samples()) {
header.add_sample(s.name);
}
@@ -630,6 +584,7 @@ write_vcf_haplotypes(map<int, CSLocus *> &catalog,
rec.chrom = loc->loc.chr;
rec.pos = loc->sort_bp() + 1;
rec.id = to_string(loc->id);
+ rec.info.push_back({"locori", loc->loc.strand == strand_plus ? "p" : "m"});
//alleles
vector<pair<string, double> > ordered_hap (hap_freq.begin(), hap_freq.end());
@@ -637,7 +592,7 @@ write_vcf_haplotypes(map<int, CSLocus *> &catalog,
map<string, int> hap_index;
for (size_t i = 0; i < ordered_hap.size(); i++) {
string h = ordered_hap[i].first;
- rec.alleles.push_back(loc->loc.strand == strand_plus ? h : string(rev_comp(h.c_str())));
+ rec.alleles.push_back(loc->loc.strand == strand_plus ? h : rev_comp(h));
hap_index[h] = i;
}
@@ -3062,57 +3017,6 @@ write_fullseq_phylip(map<int, CSLocus *> &catalog,
return 0;
}
-int
-populate_snp_calls(map<int, CSLocus *> &catalog,
- PopMap<CSLocus> *pmap,
- map<int, pair<merget, int> > &merge_map)
-{
- map<int, CSLocus *>::iterator cit;
- map<int, SNPRes *>::iterator sit;
- CSLocus *loc;
- Datum *datum;
- SNPRes *snpr;
- SNP *snp;
-
- for (uint i = 0; i < mpopi.samples().size(); i++) {
- map<int, SNPRes *> snpres;
- load_snp_calls(in_path + mpopi.samples()[i].name, snpres);
-
- for (cit = catalog.begin(); cit != catalog.end(); cit++) {
- loc = cit->second;
- datum = pmap->datum(loc->id, mpopi.samples()[i].id);
-
- if (datum != NULL && snpres.count(datum->id)) {
-
- if (merge_sites && merge_map.count(loc->id)) {
- datum_adjust_snp_positions(merge_map, loc, datum, snpres);
- } else {
- //
- // Deep copy the SNP objects.
- //
- snpr = snpres[datum->id];
- for (uint j = 0; j < snpr->snps.size(); j++) {
- snp = new SNP;
- snp->col = snpr->snps[j]->col;
- snp->lratio = snpr->snps[j]->lratio;
- snp->rank_1 = snpr->snps[j]->rank_1;
- snp->rank_2 = snpr->snps[j]->rank_2;
- snp->rank_3 = snpr->snps[j]->rank_3;
- snp->rank_4 = snpr->snps[j]->rank_4;
-
- datum->snps.push_back(snp);
- }
- }
- }
- }
-
- for (sit = snpres.begin(); sit != snpres.end(); sit++)
- delete sit->second;
- }
-
- return 0;
-}
-
/*
* Calculate the SNP-wise allelic depths by adding up the haplotype depths.
*/
@@ -3268,66 +3172,3 @@ int tally_haplotype_freq(CSLocus *locus, PopMap<CSLocus> *pmap,
return 0;
}
-
-int
-datum_adjust_snp_positions(map<int, pair<merget, int> > &merge_map,
- CSLocus *loc, Datum *datum,
- map<int, SNPRes *> &snpres)
-{
- //
- // We will start with the 'sink' locus, which was originally on the negative strand:
- // 1. If the locus was shorter than the catalog locus, pad the difference.
- // 2. Convert to positive strand: Reverse the order, complement the alleles,
- // alter the internal column position.
- //
- SNP *snp;
- SNPRes *snpr = snpres[datum->id];
- int index = 0;
- int stop_pos = renz_olap[enz] - 1;
-
- //
- // We know the catalog was padded since we already padded hte model call string
- // if it was necessary when originally merging.
- //
- while (datum->model[index] == 'N') {
- snp = new SNP;
- snp->col = index;
- snp->lratio = 0.0;
- snp->rank_1 = 'N';
- snp->type = snp_type_unk;
- datum->snps.push_back(snp);
- index++;
- }
-
- for (int j = snpr->snps.size() - 1; j > stop_pos; j--) {
- snp = new SNP;
- snp->col = index;
- snp->lratio = snpr->snps[j]->lratio;
- snp->rank_1 = reverse(snpr->snps[j]->rank_1);
- snp->rank_2 = reverse(snpr->snps[j]->rank_2);
- snp->rank_3 = reverse(snpr->snps[j]->rank_3);
- snp->rank_4 = reverse(snpr->snps[j]->rank_4);
- datum->snps.push_back(snp);
- index++;
- }
-
- //
- // Now we fetch the former locus, the 'src', which was originally on the positive strand.
- // All we have to do is adjust the column position of each SNP.
- //
- snpr = snpres[datum->merge_partner];
-
- for (uint j = 0; j < snpres[datum->id]->snps.size(); j++) {
- snp = new SNP;
- snp->col = index;
- snp->lratio = snpr->snps[j]->lratio;
- snp->rank_1 = snpr->snps[j]->rank_1;
- snp->rank_2 = snpr->snps[j]->rank_2;
- snp->rank_3 = snpr->snps[j]->rank_3;
- snp->rank_4 = snpr->snps[j]->rank_4;
- datum->snps.push_back(snp);
- index++;
- }
-
- return 0;
-}
diff --git a/src/export_formats.h b/src/export_formats.h
index c867c68..dd085a7 100644
--- a/src/export_formats.h
+++ b/src/export_formats.h
@@ -61,10 +61,8 @@ int write_treemix(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
int write_phylip(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
int write_fullseq_phylip(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
-int populate_snp_calls(map<int, CSLocus *> &, PopMap<CSLocus> *, map<int, pair<merget, int> > &);
int find_datum_allele_depths(Datum *, int, char, char, int &, int &);
int tally_observed_haplotypes(vector<char *> &, int, char &, char &);
int tally_haplotype_freq(CSLocus *, PopMap<CSLocus> *, int &, double &, string &);
-int datum_adjust_snp_positions(map<int, pair<merget, int> > &, CSLocus *, Datum *, map<int, SNPRes *> &);
#endif // EXPORT_FORMATS_H
diff --git a/src/file_io.cc b/src/file_io.cc
index d54f997..584cfb8 100644
--- a/src/file_io.cc
+++ b/src/file_io.cc
@@ -974,27 +974,3 @@ build_file_list(vector<pair<string, string> > &files)
return 0;
}
-
-string
-remove_suffix(FileT type, string file)
-{
- int pos = file.find_last_of(".");
-
- if ((type == FileT::gzfastq || type == FileT::gzfasta) && file.substr(pos) == ".gz")
- file = file.substr(0, pos);
-
- pos = file.find_last_of(".");
-
- if (type == FileT::gzfastq || type == FileT::fastq) {
-
- if (file.substr(pos) == ".fastq" || file.substr(pos) == ".fq")
- file = file.substr(0, pos);
-
- } else if (type == FileT::gzfasta || type == FileT::fasta) {
-
- if (file.substr(pos) == ".fasta" || file.substr(pos) == ".fa")
- file = file.substr(0, pos);
- }
-
- return file;
-}
diff --git a/src/file_io.h b/src/file_io.h
index 95518a6..dc18033 100644
--- a/src/file_io.h
+++ b/src/file_io.h
@@ -92,6 +92,5 @@ int open_files(vector<pair<string, string> > &,
map<string, map<string, long> > &);
int close_file_handles(map<BarcodePair, ofstream *> &);
int close_file_handles(map<BarcodePair, gzFile *> &);
-string remove_suffix(FileT, string);
#endif // __FILE_IO_H__
diff --git a/src/genotypes.cc b/src/genotypes.cc
index b1e06cf..c2871d6 100644
--- a/src/genotypes.cc
+++ b/src/genotypes.cc
@@ -72,6 +72,7 @@ map<string, int> renz_len;
map<string, map<string, string> > global_dictionary;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
initialize_renz(renz, renz_cnt, renz_len);
@@ -88,10 +89,6 @@ int main (int argc, char* argv[]) {
MetaPopInfo mpopi;
mpopi.init_directory(in_path);
- if (mpopi.samples().empty()) {
- cerr << "Error: Failed to find sample files in directory '" << in_path << "'.\n";
- return -1;
- }
if (wl_file.length() > 0) {
load_marker_list(wl_file, whitelist);
@@ -296,7 +293,9 @@ int main (int argc, char* argv[]) {
if (out_type == genomic)
write_genomic(catalog, pmap);
+ cerr << "genotypes is done.\n";
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int
@@ -2828,6 +2827,7 @@ int parse_command_line(int argc, char* argv[]) {
break;
case 'e':
enz = optarg;
+ enz.at(0) = tolower(enz.at(0));
break;
case 'v':
version();
@@ -2842,6 +2842,11 @@ int parse_command_line(int argc, char* argv[]) {
}
}
+ if (optind < argc) {
+ cerr << "Error: Failed to parse command line: '" << argv[optind] << "' is seen as a positional argument. Expected no positional arguments.\n";
+ help();
+ }
+
if (in_path.length() == 0) {
cerr << "You must specify a path to the directory containing Stacks output files.\n";
help();
diff --git a/src/hstacks.cc b/src/hstacks.cc
index e8d725d..88157f2 100644
--- a/src/hstacks.cc
+++ b/src/hstacks.cc
@@ -46,6 +46,7 @@ int stack_dist = 0;
int n_limit = 4;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
@@ -98,6 +99,7 @@ int main (int argc, char* argv[]) {
write_homologous_loci(samples);
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int calc_kmer_distance(map<int, HLocus *> &loci, int stack_dist) {
diff --git a/src/input.cc b/src/input.cc
index 6252a25..6ffdd68 100644
--- a/src/input.cc
+++ b/src/input.cc
@@ -29,8 +29,9 @@ Seq::Seq() {
this->seq = NULL;
this->qual = NULL;
this->loc_str = NULL;
- this->aln_type = pri_aln;
- this->pct_aln = 1.0;
+ this->aln_type = AlnT::null;
+ this->pct_clipped = 0.0;
+ this->map_qual = 255;
}
Seq::Seq(const Seq& other)
@@ -60,8 +61,9 @@ Seq::Seq(const Seq& other)
loc_str = NULL;
}
- pct_aln = other.pct_aln;
+ pct_clipped = other.pct_clipped;
aln_type = other.aln_type;
+ map_qual = other.map_qual;
}
Seq::Seq(const char *id, const char *seq) {
@@ -73,8 +75,9 @@ Seq::Seq(const char *id, const char *seq) {
strcpy(this->id, id);
strcpy(this->seq, seq);
- this->aln_type = pri_aln;
- this->pct_aln = 1.0;
+ this->aln_type = AlnT::null;
+ this->pct_clipped = 0.0;
+ this->map_qual = 255;
}
Seq::Seq(const char *id, const char *seq, const char *qual) {
@@ -87,8 +90,9 @@ Seq::Seq(const char *id, const char *seq, const char *qual) {
strcpy(this->seq, seq);
strcpy(this->qual, qual);
- this->aln_type = pri_aln;
- this->pct_aln = 1.0;
+ this->aln_type = AlnT::null;
+ this->pct_clipped = 0.0;
+ this->map_qual = 255;
}
Seq::Seq(const char *id, const char *seq, const char *qual, const char *chr, uint bp, strand_type strand) {
@@ -112,11 +116,12 @@ Seq::Seq(const char *id, const char *seq, const char *qual, const char *chr, uin
this->seq = rev_comp(seq);
}
- this->aln_type = pri_aln;
- this->pct_aln = 1.0;
+ this->aln_type = AlnT::primary;
+ this->pct_clipped = 0.0;
+ this->map_qual = 255;
}
-Seq::Seq(const char *id, const char *seq, const char *qual, const char *chr, uint bp, strand_type strand, alnt aln_type, double pct_aln) {
+Seq::Seq(const char *id, const char *seq, const char *qual, const char *chr, uint bp, strand_type strand, AlnT aln_type, double pct_clipped, int map_qual) {
this->id = new char[strlen(id) + 1];
this->qual = new char[strlen(qual) + 1];
this->loc_str = new char[strlen(chr) + 15];
@@ -138,12 +143,13 @@ Seq::Seq(const char *id, const char *seq, const char *qual, const char *chr, uin
}
this->aln_type = aln_type;
- this->pct_aln = pct_aln;
+ this->pct_clipped = pct_clipped;
+ this->map_qual = map_qual;
}
void swap(Seq& s1, Seq& s2) {
char *ptr;
- alnt a;
+ AlnT a;
double p;
ptr = s1.id;
@@ -166,11 +172,13 @@ void swap(Seq& s1, Seq& s2) {
s1.aln_type = s2.aln_type;
s2.aln_type = a;
- p = s1.pct_aln;
- s1.pct_aln = s2.pct_aln;
- s2.pct_aln = p;
+ p = s1.pct_clipped;
+ s1.pct_clipped = s2.pct_clipped;
+ s2.pct_clipped = p;
swap(s1.loc, s2.loc);
+
+ std::swap(s1.map_qual, s2.map_qual);
}
Input::Input() {
diff --git a/src/input.h b/src/input.h
index 6a09284..1edbac9 100644
--- a/src/input.h
+++ b/src/input.h
@@ -41,7 +41,7 @@ using std::endl;
#include "utils.h"
#include "stacks.h"
-enum alnt {pri_aln, sec_aln, sup_aln};
+enum class AlnT {null, primary, secondary, supplementary};
class Seq {
public:
@@ -52,8 +52,9 @@ class Seq {
//
// Information for an aligned sequence.
//
- alnt aln_type;
- double pct_aln;
+ AlnT aln_type;
+ double pct_clipped;
+ int map_qual;
char *loc_str;
PhyLoc loc;
@@ -62,7 +63,7 @@ class Seq {
Seq(const char *, const char *);
Seq(const char *, const char *, const char *);
Seq(const char *, const char *, const char *, const char *, uint, strand_type);
- Seq(const char *, const char *, const char *, const char *, uint, strand_type, alnt, double);
+ Seq(const char *, const char *, const char *, const char *, uint, strand_type, AlnT, double, int);
~Seq( void ) {
if (id != NULL)
delete[] id;
diff --git a/src/kmer_filter.cc b/src/kmer_filter.cc
index c2971eb..477e3cb 100644
--- a/src/kmer_filter.cc
+++ b/src/kmer_filter.cc
@@ -55,6 +55,7 @@ int num_threads = 1;
int barcode_size = 0;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
@@ -232,6 +233,7 @@ int main (int argc, char* argv[]) {
}
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int process_paired_reads(string in_path_1,
diff --git a/src/locus.cc b/src/locus.cc
index ef31b68..4b55616 100644
--- a/src/locus.cc
+++ b/src/locus.cc
@@ -73,7 +73,7 @@ Locus::populate_alleles()
vector<SNP *>::iterator i;
map<string, int>::iterator j;
string s;
- int k;
+ uint k;
if (this->len > strlen(this->con))
cerr << "Recorded locus->len: " << this->len << "; consensus length: " << strlen(this->con) << "\n";
@@ -97,9 +97,10 @@ Locus::populate_alleles()
k = 0;
for (i = this->snps.begin(); i != this->snps.end(); i++) {
- if ((*i)->col < this->len)
+ if ((*i)->type == snp_type_het && (*i)->col < this->len && k < j->first.length()) {
s.replace((*i)->col, 1, 1, j->first[k]);
- k++;
+ k++;
+ }
}
this->strings.push_back(make_pair(j->first, s));
diff --git a/src/log_utils.cc b/src/log_utils.cc
index 7fa799c..aefc5e3 100644
--- a/src/log_utils.cc
+++ b/src/log_utils.cc
@@ -18,8 +18,16 @@
// along with Stacks. If not, see <http://www.gnu.org/licenses/>.
//
+#include <ctime>
+#include <fstream>
+#include <sstream>
+#include <iomanip>
+
+#include "constants.h"
#include "log_utils.h"
+using namespace std;
+
int
init_log(ofstream &fh, int argc, char **argv)
{
@@ -44,3 +52,10 @@ init_log(ofstream &fh, int argc, char **argv)
return 0;
}
+
+std::string as_percentage(double d) {
+ stringstream ss;
+ ss << std::fixed << std::setprecision(1);
+ ss << d*100 << "%";
+ return ss.str();
+}
diff --git a/src/log_utils.h b/src/log_utils.h
index 78a74f2..cd27731 100644
--- a/src/log_utils.h
+++ b/src/log_utils.h
@@ -21,20 +21,13 @@
#ifndef __LOG_UTILS_H__
#define __LOG_UTILS_H__
-#include <time.h>
-#include <iostream>
+#include <string>
#include <fstream>
-using std::ifstream;
using std::ofstream;
-using std::cin;
-using std::cout;
-using std::cerr;
-using std::endl;
-#include <sstream>
-using std::stringstream;
-
-#include "constants.h"
int init_log(ofstream &, int, char **);
+// Returns e.g. "23.2%".
+std::string as_percentage(double d);
+
#endif // __LOG_UTILS_H__
diff --git a/src/mst.cc b/src/mst.cc
index 6daf63c..20a3cb5 100644
--- a/src/mst.cc
+++ b/src/mst.cc
@@ -45,6 +45,9 @@ bool min_span_tree_cmp(const Node *lhs, const Node *rhs) {
Node *MinSpanTree::add_node(int id) {
Node *n = new Node(id);
+ if (this->nodes.count(id) > 0)
+ delete this->nodes[id];
+
this->nodes[id] = n;
return n;
@@ -56,6 +59,11 @@ Node *MinSpanTree::add_node(string label) {
//
uint id = this->id_cnt;
+ if (this->nodes.count(id) > 0) {
+ cerr << "Error constructing minimum spanning tree.\n";
+ delete this->nodes[id];
+ }
+
Node *n = new Node(id);
n->label = label;
diff --git a/src/mst.h b/src/mst.h
index 71c4b5a..63e07f6 100644
--- a/src/mst.h
+++ b/src/mst.h
@@ -72,8 +72,11 @@ public:
}
~Node() {
+ this->min_adj_list.clear();
+
for (uint i = 0; i < this->edges.size(); i++)
delete this->edges[i];
+ this->edges.clear();
}
Edge *add_edge(Node *, int);
@@ -87,8 +90,9 @@ class MinSpanTree {
public:
MinSpanTree() { id_cnt = 0; }
~MinSpanTree() {
- for (uint i = 0; i < this->nodes.size(); i++)
- delete this->nodes[i];
+ for (map<int, Node *>::iterator i = this->nodes.begin(); i != this->nodes.end(); i++)
+ delete i->second;
+ this->nodes.clear();
}
Node *add_node(int id);
diff --git a/src/phasedstacks.cc b/src/phasedstacks.cc
index 998fca5..10ad249 100644
--- a/src/phasedstacks.cc
+++ b/src/phasedstacks.cc
@@ -50,6 +50,7 @@ map<string, int> pop_map;
map<int, int> pop_cnts;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
@@ -249,6 +250,7 @@ int main (int argc, char* argv[]) {
log_fh.close();
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int
diff --git a/src/populations.cc b/src/populations.cc
index 2ea9f72..2bc1a5d 100644
--- a/src/populations.cc
+++ b/src/populations.cc
@@ -22,6 +22,7 @@
// populations -- generate population genetic statistics and output
// haplotypes in a population context.
//
+#include <cctype>
#include <dirent.h>
#include <sys/types.h>
@@ -117,6 +118,7 @@ map<string, int> renz_len;
map<string, int> renz_olap;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
#ifndef HAVE_LIBZ
cerr << "Stacks was compiled without zlib, and will refuse to parse compressed files.\n";
@@ -134,21 +136,21 @@ int main (int argc, char* argv[]) {
//
parse_command_line(argc, argv);
- cerr
- << "Fst kernel smoothing: " << (kernel_smoothed == true ? "on" : "off") << "\n"
- << "Bootstrap resampling: ";
+ cerr << "populations parameters selected:\n"
+ << " Fst kernel smoothing: " << (kernel_smoothed == true ? "on" : "off") << "\n"
+ << " Bootstrap resampling: ";
if (bootstrap)
cerr << "on, " << (bootstrap_type == bs_exact ? "exact; " : "approximate; ") << bootstrap_reps << " reptitions\n";
else
cerr << "off\n";
cerr
- << "Percent samples limit per population: " << sample_limit << "\n"
- << "Locus Population limit: " << population_limit << "\n"
- << "Minimum stack depth: " << min_stack_depth << "\n"
- << "Log liklihood filtering: " << (filter_lnl == true ? "on" : "off") << "; threshold: " << lnl_limit << "\n"
- << "Minor allele frequency cutoff: " << minor_allele_freq << "\n"
- << "Maximum observed heterozygosity cutoff: " << max_obs_het << "\n"
- << "Applying Fst correction: ";
+ << " Percent samples limit per population: " << sample_limit << "\n"
+ << " Locus Population limit: " << population_limit << "\n"
+ << " Minimum stack depth: " << min_stack_depth << "\n"
+ << " Log liklihood filtering: " << (filter_lnl == true ? "on" : "off") << "; threshold: " << lnl_limit << "\n"
+ << " Minor allele frequency cutoff: " << minor_allele_freq << "\n"
+ << " Maximum observed heterozygosity cutoff: " << max_obs_het << "\n"
+ << " Applying Fst correction: ";
switch(fst_correction) {
case p_value:
cerr << "P-value correction.\n";
@@ -163,19 +165,18 @@ int main (int argc, char* argv[]) {
cerr << "none.\n";
break;
}
+ cerr << "\n";
//
// Open and initialize the log file.
//
- struct stat path_stat;
- if (stat(out_path.c_str(), &path_stat) == 0) {
+ struct stat out_path_stat;
+ if (stat(out_path.substr(0, out_path.length()-1).c_str(), &out_path_stat) == 0) {
// Path exists, check that it is a directory
- DIR* d = opendir(out_path.c_str());
- if (d == NULL) {
- cerr << "Error: Failed to open '" << out_path << "' as a directory.\n";
+ if (!S_ISDIR(out_path_stat.st_mode)) {
+ cerr << "Error: '" << out_path.substr(0, out_path.length()-1) << "' is not a directory.\n";
return -1;
}
- closedir(d);
} else if (mkdir(out_path.c_str(), ACCESSPERMS) != 0) {
// Failed to create the directory.
cerr << "Error: Failed to create directory '" << out_path << "'.\n";
@@ -213,10 +214,6 @@ int main (int argc, char* argv[]) {
if (not pmap_path.empty()) {
cerr << "Parsing population map...\n";
mpopi.init_popmap(pmap_path);
- if (mpopi.samples().empty()) {
- cerr << "Error: Failed to open or parse population map file '" << pmap_path << "'.\n";
- return -1;
- }
cerr << "The population map contained " << mpopi.samples().size() << " samples, "
<< mpopi.pops().size() << " population(s), " << mpopi.groups().size() << " group(s).\n";
}
@@ -228,10 +225,6 @@ int main (int argc, char* argv[]) {
if (pmap_path.empty()) {
cerr << "No population map specified, building file list...\n";
mpopi.init_directory(in_path);
- if (mpopi.samples().empty()) {
- cerr << "Error: Failed to find sample files in directory '" << in_path << "'.\n";
- return -1;
- }
}
// Check that at least one sample file exists in the directory.
@@ -282,10 +275,10 @@ int main (int argc, char* argv[]) {
vector<CatMatch *>& m = catalog_matches.back();
load_catalog_matches(in_path + mpopi.samples().at(i).name, m);
- if (m.size() == 0) {
- cerr << "Warning: Absent or malformed matches file '"
- << mpopi.samples()[i].name << ".matches.tsv(.gz)"
- <<"', excluding this sample from population analysis.\n";
+ if (m.size() == 0 || m[0]->batch_id != batch_id) {
+ cerr << "Warning: File '" << mpopi.samples()[i].name << ".matches.tsv(.gz)'"
+ " is absent, malformed, or does not match the catalog batch ID. Excluding"
+ " this sample from population analysis.\n";
samples_to_remove.push_back(i);
catalog_matches.pop_back(); // This introduces an index shift between catalog_matches and [i]/[mpopi],
// which will be resolved by a call to MetaPopInfo::delete_samples().
@@ -616,6 +609,11 @@ int main (int argc, char* argv[]) {
}
}
+ //
+ // Log the SNPs per locus distribution.
+ //
+ log_snps_per_loc_distrib(log_fh, catalog);
+
calculate_haplotype_stats(catalog, pmap, psum);
if (calc_fstats) {
@@ -703,6 +701,7 @@ int main (int argc, char* argv[]) {
cerr << "Populations is done.\n";
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
void vcfcomp_simplify_pmap (map<int, CSLocus*>& catalog, PopMap<CSLocus>* pmap) {
@@ -1839,25 +1838,7 @@ merge_datums(int sample_cnt,
cerr << "Unexpected condition in merging datums: one datum is NULL while the other is not.\n";
//
- // 1. Reverse complement the SNP coordinates in the sink locus so that they are
- // enumerated on the positive strand. Complement the alleles as well.
- //
- for (uint j = 0; j < sink[i]->snps.size(); j++) {
- sink[i]->snps[j]->col = sink[i]->len - sink[i]->snps[j]->col - 1;
- sink[i]->snps[j]->rank_1 = reverse(sink[i]->snps[j]->rank_1);
- sink[i]->snps[j]->rank_2 = reverse(sink[i]->snps[j]->rank_2);
- sink[i]->snps[j]->rank_3 = reverse(sink[i]->snps[j]->rank_3);
- sink[i]->snps[j]->rank_4 = reverse(sink[i]->snps[j]->rank_4);
- }
-
- //
- // 2. Adjust the SNP coordinates in the src locus to account for the now, longer length.
- //
- for (uint j = 0; j < src[i]->snps.size(); j++)
- src[i]->snps[j]->col = sink[i]->len + src[i]->snps[j]->col - renz_olap[enz];
-
- //
- // 3. Reverse complement the observed haplotypes in the sink locus.
+ // 1. Reverse complement the observed haplotypes in the sink locus.
//
haplen = strlen(sink[i]->obshap[0]);
for (uint j = 0; j < sink[i]->obshap.size(); j++) {
@@ -1866,24 +1847,11 @@ merge_datums(int sample_cnt,
tmphap[haplen] = '\0';
strcpy(sink[i]->obshap[j], tmphap);
}
-
- //
- // 4. Combine SNPs between the two datums: add the SNPs from the sink (formerly on the
- // negative strand) in reverse order, followed by the SNPs from the src.
- //
- tmpsnp.clear();
- for (int j = (int) sink[i]->snps.size() - 1; j >= 0; j--)
- tmpsnp.push_back(sink[i]->snps[j]);
- for (uint j = 0; j < src[i]->snps.size(); j++)
- tmpsnp.push_back(src[i]->snps[j]);
- sink[i]->snps.clear();
- for (uint j = 0; j < tmpsnp.size(); j++)
- sink[i]->snps.push_back(tmpsnp[j]);
}
//
- // 5. Combine observed haplotypes between the two datums while phasing them.
- // 5.1 First combine the haplotypes from samples that are already in phase.
+ // 2. Combine observed haplotypes between the two datums while phasing them.
+ // 2.1 First combine the haplotypes from samples that are already in phase.
//
string merged_hap;
vector<int> to_be_phased;
@@ -1933,7 +1901,7 @@ merge_datums(int sample_cnt,
}
}
//
- // 5.2 Phase and combine the haplotypes from the remaining samples.
+ // 2.2 Phase and combine the haplotypes from the remaining samples.
//
int index;
for (uint i = 0; i < to_be_phased.size(); i++) {
@@ -1979,7 +1947,7 @@ merge_datums(int sample_cnt,
}
//
- // 6. Merge model calls; Set the length; combine the two depth and lnl measures together.
+ // 3. Merge model calls; Set the length; combine the two depth and lnl measures together.
//
string model_calls;
char *p;
@@ -2134,6 +2102,9 @@ int write_genomic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap) {
exit(1);
}
+ uint rcnt = enz.length() ? renz_cnt[enz] : 0;
+ uint rlen = enz.length() ? renz_len[enz] : 0;
+
//
// Count the number of markers that have enough samples to output.
//
@@ -2144,7 +2115,14 @@ int write_genomic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap) {
for (cit = catalog.begin(); cit != catalog.end(); cit++) {
loc = cit->second;
- num_loci += loc->len - renz_len[enz];
+ uint start = 0;
+ uint end = loc->len;
+ if (end > rlen) {
+ for (uint n = 0; n < rcnt; n++)
+ if (strncmp(loc->con, renz[enz][n], rlen) == 0)
+ start += renz_len[enz];
+ }
+ num_loci += end - start;
}
cerr << "Writing " << num_loci << " nucleotide positions to genomic file, '" << file << "'\n";
@@ -2159,10 +2137,6 @@ int write_genomic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap) {
map<string, vector<CSLocus *> >::iterator it;
int a, b;
- uint rcnt = enz.length() ? renz_cnt[enz] : 0;
- uint rlen = enz.length() ? renz_len[enz] : 0;
- char *p;
-
for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
for (uint i = 0; i < it->second.size(); i++) {
loc = it->second[i];
@@ -2180,14 +2154,10 @@ int write_genomic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap) {
// Check for the existence of the restriction enzyme cut site, mask off
// its output.
//
- for (uint n = 0; n < rcnt; n++)
- if (strncmp(loc->con, renz[enz][n], rlen) == 0)
- start += renz_len[enz];
- if (start == 0) {
- p = loc->con + (loc->len - rlen);
- for (uint n = rcnt; n < rcnt + rcnt; n++)
- if (strncmp(p, renz[enz][n], rlen) == 0)
- end -= renz_len[enz];
+ if (end > rlen) {
+ for (uint n = 0; n < rcnt; n++)
+ if (strncmp(loc->con, renz[enz][n], rlen) == 0)
+ start += renz_len[enz];
}
uint k = 0;
@@ -3658,6 +3628,31 @@ haplotype_d_est(Datum **d, LocSum **s, vector<int> &pop_ids)
return d_est;
}
+void log_snps_per_loc_distrib(std::ostream& log_fh, map<int, CSLocus*>& catalog)
+{
+
+ // N.B. The method below gives the same numbers as by counting the SNPs that satisfy
+ // `LocTally::nucs[col].allele_cnt >= 2`.
+ // This is different than the sumstats file, that uses `LocTally::nucs[col].allele_cnt == 2`;
+ // The difference seems to be about 1/1000.
+
+ // Bin loci by number of SNPs.
+ map<size_t, size_t> snps_per_loc_distrib;
+ for (auto& cloc : catalog)
+ ++snps_per_loc_distrib[cloc.second->snps.size()];
+
+ // Fill the gaps in the distribution.
+ size_t n_max = snps_per_loc_distrib.rbegin()->first;
+ for(size_t i=0; i<n_max; ++i)
+ snps_per_loc_distrib.insert({i, 0});
+
+ // Write the distribution.
+ log_fh << "# Distribution of the number of SNPs per locus.\n"
+ "#n_snps\tn_loci\n";
+ for(const auto& n_snps : snps_per_loc_distrib)
+ log_fh << n_snps.first << "\t" << n_snps.second << "\n";
+}
+
int
calculate_summary_stats(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum)
{
@@ -5198,8 +5193,8 @@ int parse_command_line(int argc, char* argv[]) {
{"hzar", no_argument, NULL, 'Z'},
{"treemix", no_argument, NULL, 'U'},
{"merge_sites", no_argument, NULL, 'D'},
- {"window_size", required_argument, NULL, 'w'},
- {"threads", required_argument, NULL, 't'},
+ {"sigma", required_argument, NULL, 1005},
+ {"threads", required_argument, NULL, 't'},
{"batch_id", required_argument, NULL, 'b'},
{"in_path", required_argument, NULL, 'P'},
{"out_path", required_argument, NULL, 'O'},
@@ -5460,12 +5455,13 @@ int parse_command_line(int argc, char* argv[]) {
break;
case 'e':
enz = optarg;
+ enz.at(0) = tolower(enz.at(0));
if (renz.count(enz) == 0) {
cerr << "Unrecognized restriction enzyme specified: '" << enz.c_str() << "'.\n";
help();
}
break;
- case 'w':
+ case 1005: //sigma
sigma = atof(optarg);
break;
case 'v':
@@ -5505,6 +5501,11 @@ int parse_command_line(int argc, char* argv[]) {
}
}
+ if (optind < argc) {
+ cerr << "Error: Failed to parse command line: '" << argv[optind] << "' is seen as a positional argument. Expected no positional arguments.\n";
+ help();
+ }
+
//
// Check argument constrains.
//
@@ -5527,8 +5528,16 @@ int parse_command_line(int argc, char* argv[]) {
cerr << "A population map was not specified, all samples will be read from '" << in_path << "' as a single popultaion.\n";
if (batch_id < 0) {
- cerr << "You must specify a batch ID.\n";
- help();
+ vector<int> cat_ids = find_catalogs(in_path);
+ if (cat_ids.size() == 1) {
+ batch_id = cat_ids[0];
+ } else if (cat_ids.empty()) {
+ cerr << "Error: Unable to find a catalog in '" << in_path << "'.\n";
+ help();
+ } else {
+ cerr << "Error: Input directory contains several catalogs, please specify -b.\n";
+ help();
+ }
}
if (out_path.empty())
@@ -5576,15 +5585,15 @@ void version() {
void help() {
cerr << "populations " << VERSION << "\n"
<< "Usage:\n"
- << "populations -P dir -b batch_id [-O dir] [-M popmap] (filters) [--fstats] [-k [--window_size=150000] [--bootstrap [-N 100]]] (output formats)\n"
+ << "populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats)\n"
<< "populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats)\n"
<< "\n"
<< " -P,--in_path: path to the directory containing the Stacks files.\n"
- << " -b,--batch_id: Batch ID to examine when exporting from the catalog (required by -P).\n"
<< " -V,--in_vcf: path to an input VCF file.\n"
<< " -O,--out_path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.)\n"
- << " -M,--popmap: path to a population map. (Format is 'SAMPLE1\tPOP1\\n...'.)\n"
+ << " -M,--popmap: path to a population map. (Format is 'SAMPLE1 \\t POP1 \\n SAMPLE2 ...'.)\n"
<< " -t,--threads: number of threads to run in parallel sections of code.\n"
+ << " -b,--batch_id: ID of the catalog to consider (default: guess).\n"
<< " -s,--sql_out: output a file to import results into an SQL database.\n"
<< "\n"
<< "Data Filtering:\n"
diff --git a/src/populations.h b/src/populations.h
index 38dbb56..b35d802 100644
--- a/src/populations.h
+++ b/src/populations.h
@@ -124,6 +124,8 @@ double haplotype_d_est(Datum **, LocSum **, vector<int> &);
LocStat *haplotype_diversity(int, int, Datum **);
double count_haplotypes_at_locus(int, int, Datum**, map<string, double>&);
+void log_snps_per_loc_distrib(std::ostream&, map<int, CSLocus*>&);
+
//int tally_ref_alleles(LocSum **, int, int, char &, char &); //unused; also commented out in the .cc
//int load_snp_calls(string, PopMap<CSLocus> *); //no implementation
diff --git a/src/process_radtags.cc b/src/process_radtags.cc
index f94953f..05d9634 100644
--- a/src/process_radtags.cc
+++ b/src/process_radtags.cc
@@ -25,9 +25,13 @@
//
#include <iomanip>
+#include <cstdlib>
+#include "constants.h"
#include "process_radtags.h"
+using namespace std;
+
//
// Global variables to hold command-line options.
//
@@ -93,6 +97,7 @@ map<string, int> renz_cnt;
map<string, int> renz_len;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
initialize_renz(renz, renz_cnt, renz_len);
@@ -128,7 +133,7 @@ int main (int argc, char* argv[]) {
init_adapter_seq(kmer_size, adapter_2, adp_2_len, adp_2_kmers);
}
- cerr << " " << distance << " mismatches allowed to adapter sequence.\n";
+ cerr << " " << ::distance << " mismatches allowed to adapter sequence.\n";
}
vector<pair<string, string> > files;
@@ -230,6 +235,7 @@ int main (int argc, char* argv[]) {
print_results(argc, argv, barcodes, counters, barcode_log);
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
template <typename fhType>
@@ -576,7 +582,7 @@ process_reads(string prefix,
}
if (discards && !r->retain)
- result = out_file_type == FileT::fastq ?
+ result = out_file_type == FileT::fastq || out_file_type == FileT::gzfastq ?
write_fastq(discard_fh, s) :
write_fasta(discard_fh, s);
@@ -687,10 +693,10 @@ process_singlet(Read *href,
int res = 1;
if (paired_end == true && adp_2_len > 0)
res = filter_adapter_seq(href, adapter_2, adp_2_len, adp_2_kmers,
- kmer_size, distance, len_limit);
+ kmer_size, ::distance, len_limit);
if (paired_end == false && adp_1_len > 0)
res = filter_adapter_seq(href, adapter_1, adp_1_len, adp_1_kmers,
- kmer_size, distance, len_limit);
+ kmer_size, ::distance, len_limit);
if (res <= 0) {
// cerr << "Sequence " << href->seq << " contains adapter.\n";
counter["adapter"]++;
@@ -754,6 +760,16 @@ print_results(int argc, char **argv,
map<string, map<string, long> >::iterator it;
string log_path = out_path + "process_radtags.log";
+ if (!in_path_1.empty()) {
+ // In directory mode, use `$out_path/process_radtags.$(basename $in_path).log`.
+ // For consistency we always use realpath().
+ char abspath [PATH_MAX];
+ realpath(in_path_1.c_str(), abspath);
+ string abspath_s (abspath);
+ size_t p = abspath_s.find_last_of('/');
+ string in_dir_name = abspath_s.substr(p+1);
+ log_path = out_path + "process_radtags." + in_dir_name + ".log";
+ }
ofstream log(log_path.c_str());
if (log.fail()) {
@@ -810,17 +826,13 @@ print_results(int argc, char **argv,
c["retained"] += it->second["retained"];
}
- std::ostream cerr_bis (cerr.rdbuf());
- cerr_bis << std::fixed << std::setprecision(1);
-
- auto print_nreads = [&cerr_bis,&c] (long n, const string& legend) {
- size_t nspaces = std::to_string(c["total"]).length() - std::to_string(n).length();
- cerr_bis << string(nspaces, ' ')
- << n << " " << legend
- << " (" << (double) n / c["total"] * 100 << "%)\n";
+ auto print_nreads = [&c] (long n, const string& legend) {
+ size_t nspaces = to_string(c["total"]).length() - to_string(n).length();
+ cerr << string(nspaces, ' ') << n << " " << legend
+ << " (" << as_percentage((double) n / c["total"]) << ")\n";
};
- cerr_bis << c["total"] << " total sequences\n";
+ cerr << c["total"] << " total sequences\n";
if (filter_illumina)
print_nreads(c["ill_filtered"], "failed Illumina filtered reads");
if (filter_adapter)
@@ -861,8 +873,8 @@ print_results(int argc, char **argv,
if (bc_names)
log << "Filename\t";
log << "Total\t"
- << "No RadTag\t"
- << "Low Quality\t"
+ << "NoRadTag\t"
+ << "LowQuality\t"
<< "Retained\n";
set<BarcodePair> barcode_list;
@@ -915,7 +927,6 @@ int compare_barcodes(pair<BarcodePair, int> a, pair<BarcodePair, int> b) {
}
int parse_command_line(int argc, char* argv[]) {
- FileT ftype;
int c;
while (1) {
@@ -1007,22 +1018,18 @@ int parse_command_line(int argc, char* argv[]) {
break;
case 'f':
in_file = optarg;
- ftype = FileT::fastq;
break;
case 'p':
in_path_1 = optarg;
in_path_2 = in_path_1;
- ftype = FileT::fastq;
break;
case '1':
paired = true;
in_file_p1 = optarg;
- ftype = FileT::fastq;
break;
case '2':
paired = true;
in_file_p2 = optarg;
- ftype = FileT::fastq;
break;
case 'P':
paired = true;
@@ -1053,9 +1060,11 @@ int parse_command_line(int argc, char* argv[]) {
break;
case 'e':
renz_1 = optarg;
+ renz_1.at(0) = tolower(renz_1.at(0));
break;
case 'z':
renz_2 = optarg;
+ renz_2.at(0) = tolower(renz_2.at(0));
break;
case 'b':
barcode_file = optarg;
@@ -1063,7 +1072,7 @@ int parse_command_line(int argc, char* argv[]) {
barcode_type = inline_null;
break;
case 'm':
- merge = true;
+ ::merge = true;
break;
case 'D':
discards = true;
@@ -1106,7 +1115,7 @@ int parse_command_line(int argc, char* argv[]) {
filter_adapter = true;
break;
case 'T':
- distance = is_integer(optarg);
+ ::distance = is_integer(optarg);
break;
case 'H':
retain_header = true;
@@ -1135,6 +1144,11 @@ int parse_command_line(int argc, char* argv[]) {
}
}
+ if (optind < argc) {
+ cerr << "Error: Failed to parse command line: '" << argv[optind] << "' is seen as a positional argument. Expected no positional arguments.\n";
+ help();
+ }
+
if (in_file.length() == 0 && in_path_1.length() == 0 && in_file_p1.length() == 0) {
cerr << "You must specify an input file of a directory path to a set of input files.\n";
help();
@@ -1167,8 +1181,16 @@ int parse_command_line(int argc, char* argv[]) {
if (out_path.at(out_path.length() - 1) != '/')
out_path += "/";
- if (in_file_type == FileT::unknown)
- in_file_type = ftype;
+ if (in_file_type == FileT::unknown) {
+ if (!in_file.empty())
+ in_file_type = guess_file_type(in_file);
+ else if (!in_file_p1.empty())
+ in_file_type = guess_file_type(in_file_p1);
+ // In directory mode, just use the default.
+
+ if (in_file_type == FileT::unknown)
+ in_file_type = FileT::gzfastq;
+ }
if (in_file_type == FileT::bam && paired == true && interleaved == false) {
cerr << "You may only specify a BAM input file for paired-end data if the read pairs are interleaved.\n";
@@ -1188,7 +1210,7 @@ int parse_command_line(int argc, char* argv[]) {
if (barcode_file.length() == 0)
cerr << "No barcodes specified, files will not be demultiplexed.\n";
- if (barcode_file.length() > 0 && merge) {
+ if (barcode_file.length() > 0 && ::merge) {
cerr << "You may specify a set of barcodes, or that all files should be merged, not both.\n";
help();
}
@@ -1234,26 +1256,29 @@ void version() {
void help() {
std::cerr << "process_radtags " << VERSION << "\n"
- << "process_radtags [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir -e enz [-c] [-q] [-r] [-t len] [-D] [-w size] [-s lim] [-h]\n"
- << " f: path to the input file if processing single-end sequences.\n"
- << " i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ.\n"
- << " y: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default is to match the input file type).\n"
+ << "process_radtags -p in_dir [--paired [--interleaved]] [-i format] -b barcode_file -o out_dir -e enz [-c] [-q] [-r] [-t len] [-D] [-w size] [-s lim]\n"
+ << "process_radtags -f in_file [-i format] -b barcode_file -o out_dir -e enz [-c] [-q] [-r] [-t len] [-D] [-w size] [-s lim]\n"
+ << "process_radtags -1 pair_1 -2 pair_2 [-i format] -b barcode_file -o out_dir -e enz [-c] [-q] [-r] [-t len] [-D] [-w size] [-s lim]\n"
+ << "\n"
<< " p: path to a directory of files.\n"
- << " P: files contained within directory specified by '-p' are paired.\n"
- << " I: specify that the paired-end reads are interleaved in single files.\n"
+ << " P,--paired: files contained within the directory are paired.\n"
+ << " I,--interleaved: specify that the paired-end reads are interleaved in single files.\n"
+ << " i: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to).\n"
+ << " b: path to a file containing barcodes for this run.\n"
+ << " o: path to output the processed files.\n"
+ << " f: path to the input file if processing single-end sequences.\n"
<< " 1: first input file in a set of paired-end sequences.\n"
<< " 2: second input file in a set of paired-end sequences.\n"
- << " o: path to output the processed files.\n"
- << " b: path to a file containing barcodes for this run.\n"
<< " c: clean data, remove any read with an uncalled base.\n"
<< " q: discard reads with low quality scores.\n"
<< " r: rescue barcodes and RAD-Tags.\n"
<< " t: truncate final read length to this value.\n"
- << " E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+, Sanger, default) or 'phred64' (Illumina 1.3 - 1.5).\n"
<< " D: capture discarded reads to a file.\n"
+ << " E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5).\n"
<< " w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15).\n"
<< " s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10).\n"
- << " h: display this help messsage." << "\n\n"
+ << " y: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type).\n"
+ << "\n"
<< " Barcode options:\n"
<< " --inline_null: barcode is inline with sequence, occurs only on single-end read (default).\n"
<< " --index_null: barcode is provded in FASTQ header (Illumina i5 or i7 read).\n"
@@ -1261,7 +1286,8 @@ void help() {
<< " --inline_inline: barcode is inline with sequence, occurs on single and paired-end read.\n"
<< " --index_index: barcode is provded in FASTQ header (Illumina i5 and i7 reads).\n"
<< " --inline_index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read).\n"
- << " --index_inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data).\n\n"
+ << " --index_inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data).\n"
+ << "\n"
<< " Restriction enzyme options:\n"
<< " -e <enz>, --renz_1 <enz>: provide the restriction enzyme used (cut site occurs on single-end read)\n"
<< " --renz_2 <enz>: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read).\n"
@@ -1283,6 +1309,7 @@ void help() {
it++;
}
+ cerr << "\n";
std::cerr << "\n"
<< " Adapter options:\n"
diff --git a/src/process_shortreads.cc b/src/process_shortreads.cc
index cf84b25..83bf2f8 100644
--- a/src/process_shortreads.cc
+++ b/src/process_shortreads.cc
@@ -86,6 +86,7 @@ int adp_2_len = 0;
AdapterHash adp_1_kmers, adp_2_kmers;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
@@ -219,6 +220,7 @@ int main (int argc, char* argv[]) {
print_results(argc, argv, barcodes, counters, barcode_log);
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
template<typename fhType>
@@ -826,7 +828,6 @@ int compare_barcodes(pair<BarcodePair, int> a, pair<BarcodePair, int> b) {
}
int parse_command_line(int argc, char* argv[]) {
- FileT ftype;
int c;
while (1) {
@@ -914,22 +915,18 @@ int parse_command_line(int argc, char* argv[]) {
break;
case 'f':
in_file = optarg;
- ftype = FileT::fastq;
break;
case 'p':
in_path_1 = optarg;
in_path_2 = in_path_1;
- ftype = FileT::fastq;
break;
case '1':
paired = true;
in_file_p1 = optarg;
- ftype = FileT::fastq;
break;
case '2':
paired = true;
in_file_p2 = optarg;
- ftype = FileT::fastq;
break;
case 'P':
paired = true;
@@ -1042,6 +1039,11 @@ int parse_command_line(int argc, char* argv[]) {
}
}
+ if (optind < argc) {
+ cerr << "Error: Failed to parse command line: '" << argv[optind] << "' is seen as a positional argument. Expected no positional arguments.\n";
+ help();
+ }
+
if (in_file.length() == 0 && in_path_1.length() == 0 && in_file_p1.length() == 0) {
cerr << "You must specify an input file of a directory path to a set of input files.\n";
help();
@@ -1085,7 +1087,7 @@ int parse_command_line(int argc, char* argv[]) {
}
if (in_file_type == FileT::unknown)
- in_file_type = ftype;
+ in_file_type = FileT::gzfastq;
if (in_file_type == FileT::bam && paired == true && interleaved == false) {
cerr << "You may only specify a BAM input file for paired-end data if the read pairs are interleaved.\n";
@@ -1132,13 +1134,13 @@ void help() {
<< " P: specify that input is paired (for use with '-p').\n"
<< " I: specify that the paired-end reads are interleaved in single files.\n"
<< " o: path to output the processed files.\n"
- << " y: output type, either 'fastq' or 'fasta' (default fastq).\n"
+ << " y: output type, either 'fastq' or 'fasta' (default gzfastq).\n"
<< " b: a list of barcodes for this run.\n"
<< " c: clean data, remove any read with an uncalled base.\n"
<< " q: discard reads with low quality scores.\n"
<< " r: rescue barcodes.\n"
<< " t: truncate final read length to this value.\n"
- << " E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+, Sanger) or 'phred64' (Illumina 1.3 - 1.5, default).\n"
+ << " E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5).\n"
<< " D: capture discarded reads to a file.\n"
<< " w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15).\n"
<< " s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10).\n"
diff --git a/src/pstacks.cc b/src/pstacks.cc
index 56a2566..77f8039 100644
--- a/src/pstacks.cc
+++ b/src/pstacks.cc
@@ -22,18 +22,21 @@
// pstacks -- search an existing set of stacks for polymorphisms
//
+#include "log_utils.h"
+
#include "pstacks.h"
+using namespace std;
//
// Global variables to hold command-line options.
//
FileT in_file_type;
string in_file;
-FileT out_file_type;
string out_path;
-int sql_id = 0;
+int sql_id = -1;
int min_stack_cov = 3;
-double req_pct_aln = 0.85;
+double max_clipped = 0.15;
+int min_mapping_qual = 10;
bool keep_sec_alns = false;
int num_threads = 1;
@@ -50,23 +53,12 @@ double heterozygote_limit = -3.84;
double homozygote_limit = 3.84;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
- cerr << "Min depth of coverage to report a stack: " << min_stack_cov << "\n"
- << "Model type: ";
- switch (model_type) {
- case snp:
- cerr << "SNP\n";
- break;
- case fixed:
- cerr << "Fixed\n";
- break;
- case bounded:
- cerr << "Bounded; lower epsilon bound: " << bound_low << "; upper bound: " << bound_high << "\n";
- break;
- }
- cerr << "Alpha significance level for model: " << alpha << "\n";
+ report_options(cerr);
+ cerr << std::fixed << std::setprecision(2);
//
// Set limits to call het or homozygote according to chi-square distribution with one
@@ -94,80 +86,67 @@ int main (int argc, char* argv[]) {
omp_set_num_threads(num_threads);
#endif
+ map<int, PStack *> unique; // Unique {sequence, alignment position} combinations.
HashMap* radtags = new HashMap();
- map<int, PStack *> unique;
-
load_radtags(in_file, *radtags);
-
reduce_radtags(*radtags, unique);
-
for (auto& stack : *radtags)
for (Seq* read : stack.second)
delete read;
delete radtags;
- //dump_stacks(unique);
-
map<int, MergedStack *> merged;
-
populate_merged_tags(unique, merged);
- //dump_merged_stacks(merged);
+ delete_low_cov_loci(merged, unique);
// Call the consensus sequence again, now that remainder tags have been merged.
- cerr << "Identifying polymorphic sites and calling consensus sequences...";
call_consensus(merged, unique, true);
- cerr << "done.\n";
- count_raw_reads(unique, merged);
-
- calc_coverage_distribution(unique, merged);
-
- cerr << "Writing loci, SNPs, alleles to '" << out_path << "...'\n";
write_results(merged, unique);
+ cerr << "pstacks is done.\n";
+
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
-int call_alleles(MergedStack *mtag, vector<DNANSeq *> &reads) {
- int row;
- int height = reads.size();
- string allele;
- char base;
- vector<SNP *>::iterator snp;
- DNANSeq *d;
-
- for (row = 0; row < height; row++) {
- allele.clear();
+void call_alleles(MergedStack *mtag, vector<DNANSeq *> &reads) {
- uint snp_cnt = 0;
+ vector<SNP*> het_snps;
+ for (SNP* snp : mtag->snps)
+ if (snp->type == snp_type_het)
+ het_snps.push_back(snp);
- for (snp = mtag->snps.begin(); snp != mtag->snps.end(); snp++) {
- if ((*snp)->type != snp_type_het) continue;
-
- snp_cnt++;
-
- d = reads[row];
- base = (*d)[(*snp)->col];
+ if (!het_snps.empty()) {
+ string allele;
+ allele.reserve(het_snps.size());
+ for (DNANSeq* r : reads) {
+ allele.clear();
+ for(SNP* hsnp : het_snps) {
+ //
+ // Check to make sure the nucleotide at the location of this SNP is
+ // of one of the two possible states the multinomial model called.
+ //
+ char base = (*r)[hsnp->col];
+ if (base != hsnp->rank_1 && base != hsnp->rank_2)
+ break;
+ allele.push_back(base);
+ }
- //
- // Check to make sure the nucleotide at the location of this SNP is
- // of one of the two possible states the multinomial model called.
- //
- if (base == (*snp)->rank_1 || base == (*snp)->rank_2)
- allele += base;
- else
- break;
+ if (allele.length() == het_snps.size())
+ mtag->alleles[allele]++;
}
- if (snp_cnt > 0 && allele.length() == snp_cnt)
- mtag->alleles[allele]++;
+ if (mtag->alleles.empty())
+ mtag->blacklisted = true;
}
-
- return 0;
}
int call_consensus(map<int, MergedStack *> &merged, map<int, PStack *> &unique, bool invoke_model) {
+
+ cerr << "Identifying polymorphic sites and calling consensus sequences...";
+
//
// OpenMP can't parallelize random access iterators, so we convert
// our map to a vector of integer keys.
@@ -251,7 +230,7 @@ int call_consensus(map<int, MergedStack *> &merged, map<int, PStack *> &unique,
case bounded:
call_bounded_multinomial_snp(mtag, col, nuc, true);
break;
- case fixed:
+ case ::fixed:
call_multinomial_fixed(mtag, col, nuc);
break;
}
@@ -260,7 +239,7 @@ int call_consensus(map<int, MergedStack *> &merged, map<int, PStack *> &unique,
if (invoke_model) {
call_alleles(mtag, reads);
- if (model_type == fixed) {
+ if (model_type == ::fixed) {
//
// Mask nucleotides that are not fixed.
//
@@ -273,94 +252,57 @@ int call_consensus(map<int, MergedStack *> &merged, map<int, PStack *> &unique,
}
mtag->add_consensus(con.c_str());
-
- //
- // If SNPs were called at this locus but no alleles could be determined,
- // blacklist this tag. This can occur if there are two many uncalled bases
- // in the locus (Ns), such that haplotypes can't be consistently read
- // due to the presence of the Ns in the reads.
- //
- if (mtag->alleles.empty())
- for (uint j = 0; j < mtag->snps.size(); j++)
- if (mtag->snps[j]->type == snp_type_het) {
- mtag->blacklisted = 1;
- break;
- }
}
}
+ size_t n_blacklisted = 0;
+ for (const auto& mtag : merged)
+ if (mtag.second->blacklisted)
+ ++n_blacklisted;
+
+ cerr << "done. (" << n_blacklisted << " loci were blacklisted.)\n";
+
return 0;
}
-double calc_coverage_distribution(map<int, PStack *> &unique, map<int, MergedStack *> &merged) {
- map<int, MergedStack *>::iterator it;
- vector<int>::iterator k;
- PStack *tag;
- double depth = 0.0;
- double total = 0.0;
- double sum = 0.0;
- double mean = 0.0;
- double max = 0.0;
- double stdev = 0.0;
-
- for (it = merged.begin(); it != merged.end(); it++) {
- depth = 0.0;
- for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
- tag = unique[*k];
- depth += tag->count;
- }
-
- if (depth < min_stack_cov)
+void
+calc_coverage_distribution(const map<int, PStack*> &unique,
+ const map<int, MergedStack*> &merged,
+ double &mean, double &stdev, double &max)
+{
+ max = 0.0;
+ mean = 0.0;
+ stdev = 0.0;
+
+ size_t not_blacklisted = 0;
+ for (const pair<int, MergedStack*>& mtag : merged) {
+ if (mtag.second->blacklisted)
continue;
- if (depth > max)
- max = depth;
- sum += depth;
- total++;
- }
-
- mean = sum / total;
+ ++not_blacklisted;
- //
- // Calculate the standard deviation
- //
- for (it = merged.begin(); it != merged.end(); it++) {
- depth = 0.0;
- for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
- tag = unique[*k];
- depth += tag->count;
- }
-
- if (depth < min_stack_cov)
- continue;
+ double depth = 0.0;
+ for (int utag_id : mtag.second->utags)
+ depth += unique.at(utag_id)->count;
- sum += pow((depth - mean), 2);
+ mean += depth;
+ if (depth > max)
+ max = depth;
}
+ mean /= not_blacklisted;
- stdev = sqrt(sum / (total - 1));
-
- cerr << " Mean coverage depth is " << mean << "; Std Dev: " << stdev << "; Max: " << max << "\n";
+ for (const pair<int, MergedStack*>& mtag : merged) {
+ if (mtag.second->blacklisted)
+ continue;
- return mean;
-}
+ double depth = 0.0;
+ for (int utag_id : mtag.second->utags)
+ depth += unique.at(utag_id)->count;
-int count_raw_reads(map<int, PStack *> &unique, map<int, MergedStack *> &merged) {
- map<int, MergedStack *>::iterator it;
- vector<int>::iterator k;
- PStack *tag;
- long int m = 0;
-
- for (it = merged.begin(); it != merged.end(); it++) {
- for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
- tag = unique[*k];
- m += tag->count;
- }
- m += it->second->remtags.size();
+ stdev += pow(depth - mean, 2);
}
-
- cerr << " Number of utilized reads " << m << "\n";
-
- return 0;
+ stdev /= not_blacklisted;
+ stdev = sqrt(stdev);
}
int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
@@ -373,18 +315,20 @@ int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
PStack *tag_2;
stringstream sstr;
- bool gzip = (in_file_type == FileT::bam) ? true : false;
-
//
// Parse the input file name to create the output files
//
size_t pos_1 = in_file.find_last_of("/");
size_t pos_2 = in_file.find_last_of(".");
- string tag_file = out_path + in_file.substr(pos_1 + 1, (pos_2 - pos_1 - 1)) + ".tags.tsv";
- string snp_file = out_path + in_file.substr(pos_1 + 1, (pos_2 - pos_1 - 1)) + ".snps.tsv";
- string all_file = out_path + in_file.substr(pos_1 + 1, (pos_2 - pos_1 - 1)) + ".alleles.tsv";
- string mod_file = out_path + in_file.substr(pos_1 + 1, (pos_2 - pos_1 - 1)) + ".models.tsv";
+ string prefix = out_path + in_file.substr(pos_1 + 1, (pos_2 - pos_1 - 1));
+ string tag_file = prefix + ".tags.tsv";
+ string snp_file = prefix + ".snps.tsv";
+ string all_file = prefix + ".alleles.tsv";
+ string mod_file = prefix + ".models.tsv";
+ cerr << "Writing tags, models, snps, and alleles files...\n";
+
+ bool gzip = (in_file_type == FileT::bam) ? true : false;
if (gzip) {
tag_file += ".gz";
snp_file += ".gz";
@@ -481,9 +425,6 @@ int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
int id;
char *buf; // = new char[m.begin()->second->len + 1];
- int wrote = 0;
- int excluded = 0;
- int blacklisted = 0;
for (i = m.begin(); i != m.end(); i++) {
tag_1 = i->second;
@@ -492,21 +433,12 @@ int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
for (k = tag_1->utags.begin(); k != tag_1->utags.end(); k++)
total += u[*k]->count;
- if (total < min_stack_cov) {
- excluded++;
- continue;
- }
-
//
// Calculate the log likelihood of this merged stack.
//
tag_1->gen_matrix(u);
tag_1->calc_likelihood();
- wrote++;
-
- if (tag_1->blacklisted) blacklisted++;
-
// First write the consensus sequence
sstr << "0" << "\t"
<< sql_id << "\t"
@@ -629,12 +561,10 @@ int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
alle.close();
}
- cerr << " Wrote " << wrote << " loci, excluded " << excluded << " loci due to insuffient depth of coverage; blacklisted " << blacklisted << " loci.\n";
-
return 0;
}
-int populate_merged_tags(map<int, PStack *> &unique, map<int, MergedStack *> &merged) {
+void populate_merged_tags(map<int, PStack *> &unique, map<int, MergedStack *> &merged) {
map<int, PStack *>::iterator i;
map<int, MergedStack *>::iterator it_new, it_old;
map<string, set<int> > locations;
@@ -687,9 +617,48 @@ int populate_merged_tags(map<int, PStack *> &unique, map<int, MergedStack *> &me
global_id++;
}
- cerr << " Merged " << unique.size() << " unique Stacks into " << merged.size() << " loci.\n";
+ double mean;
+ double stdev;
+ double max;
+ calc_coverage_distribution(unique, merged, mean, stdev, max);
- return 0;
+ cerr << "Created " << merged.size() << " loci; mean coverage is " << mean << " (stdev: " << stdev << ", max: " << size_t(max) << ").\n";
+}
+
+void delete_low_cov_loci(map<int, MergedStack *>& merged, const map<int, PStack*>& unique) {
+
+ size_t n_deleted = 0;
+ size_t n_reads = 0;
+ size_t n_rm_reads = 0;
+ vector<int> to_erase;
+
+ for (auto& mtag : merged) {
+ int depth = 0;
+ for (int utag_id : mtag.second->utags)
+ depth += unique.at(utag_id)->count;
+
+ n_reads += depth;
+ if (depth < min_stack_cov) {
+ delete mtag.second;
+ to_erase.push_back(mtag.first);
+
+ n_deleted++;
+ n_rm_reads += depth;
+ }
+ }
+
+ for (int id : to_erase)
+ merged.erase(id);
+
+ double mean;
+ double stdev;
+ double max;
+ calc_coverage_distribution(unique, merged, mean, stdev, max);
+
+ cerr << "Discarded " << n_deleted << " low coverage loci comprising " << n_rm_reads
+ << " (" << as_percentage((double) n_rm_reads/ n_reads) << ") reads.\n"
+ << "Kept " << merged.size() << " loci; mean coverage is "
+ << mean << " (stdev: " << stdev << ", max: " << size_t(max) << ").\n";
}
//
@@ -738,8 +707,6 @@ int reduce_radtags(HashMap &radtags, map<int, PStack *> &unique) {
}
}
- cerr << " " << radtags.size() << " unique stacks were aligned to " << unique.size() << " genomic locations.\n";
-
return 0;
}
@@ -747,7 +714,7 @@ int reduce_radtags(HashMap &radtags, map<int, PStack *> &unique) {
// We expect tags to have already been aligned to a reference genome. Therefore, the tags
// are identified by their chromosome and basepair location.
//
-int load_radtags(string in_file, HashMap &radtags) {
+void load_radtags(string in_file, HashMap &radtags) {
Input *fh = NULL;
Seq c;
@@ -760,37 +727,48 @@ int load_radtags(string in_file, HashMap &radtags) {
else if (in_file_type == FileT::tsv)
fh = new Tsv(in_file.c_str());
- cerr << "Parsing " << in_file.c_str() << "\n";
+ cerr << "Reading alignments...\n";
- int secondary = 0;
- int supplementary = 0;
- int below_req_aln = 0;
- int i = 0;
- cerr << "Loading aligned sequences...";
+ int primary_kept = 0;
+ int primary_qual = 0;
+ int primary_clipped = 0;
+ int secondary_kept = 0;
+ int secondary_disc = 0;
+ int supplementary = 0;
+ int unmapped = 0;
while ((fh->next_seq(c)) != 0) {
- if (i % 1000000 == 0 && i>0)
- cerr << i/1000000 << "M...";
-
- i++;
- switch (c.aln_type) {
- case sec_aln:
- secondary++;
- if (!keep_sec_alns)
+ switch (c.aln_type) {
+ case AlnT::null:
+ unmapped++;
+ continue;
+ break;
+ case AlnT::primary:
+ if (c.map_qual < min_mapping_qual) {
+ primary_qual++;
continue;
- break;
- case sup_aln:
- supplementary++;
- continue;
- break;
- case pri_aln:
- default:
- break;
- }
-
- if (c.pct_aln < req_pct_aln) {
- below_req_aln++;
+ } else if (c.pct_clipped > max_clipped) {
+ primary_clipped++;
+ continue;
+ } else {
+ primary_kept++;
+ }
+ break;
+ case AlnT::secondary:
+ if (keep_sec_alns && c.pct_clipped <= max_clipped) {
+ secondary_kept++;
+ } else {
+ secondary_disc++;
+ continue;
+ }
+ break;
+ case AlnT::supplementary:
+ supplementary++;
continue;
+ break;
+ default:
+ // assert(false);
+ break;
}
HashMap::iterator element = radtags.insert({DNANSeq(strlen(c.seq), c.seq), vector<Seq*>()}).first;
@@ -805,28 +783,29 @@ int load_radtags(string in_file, HashMap &radtags) {
the_seq.qual = NULL;
}
}
- cerr << "done\n";
- if (i == 0) {
- cerr << "Error: Unable to load data from '" << in_file.c_str() << "'.\n";
- exit(-1);
+ int n_primary = primary_kept+primary_qual+primary_clipped;
+ cerr << "Done reading alignment records:\n"
+ << " Kept " << primary_kept << " primary alignments\n"
+ << " Skipped " << primary_qual << " (" << as_percentage((double) primary_qual / n_primary)
+ << ") primary alignments with insufficient mapping qualities\n"
+ << " Skipped " << primary_clipped << " (" << as_percentage((double) primary_clipped / n_primary)
+ << ") excessively soft-clipped primary alignments\n"
+ << " Skipped " << secondary_disc << " secondary alignments\n"
+ << " Skipped " << supplementary << " supplementary alignments\n"
+ << " Skipped " << unmapped << " unmapped reads\n";
+
+ if(keep_sec_alns)
+ cerr << " Kept " << secondary_kept << " secondary alignments\n";
+
+ if (radtags.empty()) {
+ cerr << "Error: No input.\n";
+ throw std::exception();
}
- cerr << "Loaded " << i << " sequence reads; "
- << "identified " << radtags.size() << " unique stacks from those reads.\n"
- << " Discarded " << below_req_aln << " reads where the aligned percentage of the read was too low.\n";
- if (keep_sec_alns)
- cerr << " Kept " << secondary << " secondarily aligned reads (reads may be present in the data set more than once).\n";
- else
- cerr << " Discarded " << secondary << " secondarily aligned reads (primary alignments were retained).\n";
- cerr << " Discarded " << supplementary << " supplementary aligned (chimeric) reads.\n";
+ cerr << "Collapsed reads into " << radtags.size() << " stacks.\n";
- //
- // Close the file and delete the Input object.
- //
delete fh;
-
- return 0;
}
int dump_stacks(map<int, PStack *> &u) {
@@ -886,14 +865,14 @@ int parse_command_line(int argc, char* argv[]) {
while (1) {
static struct option long_options[] = {
{"help", no_argument, NULL, 'h'},
- {"version", no_argument, NULL, 'v'},
+ {"version", no_argument, NULL, 1000},
{"infile_type", required_argument, NULL, 't'},
- {"outfile_type", required_argument, NULL, 'y'},
{"file", required_argument, NULL, 'f'},
{"outpath", required_argument, NULL, 'o'},
{"id", required_argument, NULL, 'i'},
{"min_cov", required_argument, NULL, 'm'},
- {"pct_aln", required_argument, NULL, 'a'},
+ {"max_clipped", required_argument, NULL, 1001},
+ {"min_mapq", required_argument, NULL, 1002},
{"keep_sec_aln", required_argument, NULL, 'k'},
{"num_threads", required_argument, NULL, 'p'},
{"bc_err_freq", required_argument, NULL, 'e'},
@@ -907,7 +886,7 @@ int parse_command_line(int argc, char* argv[]) {
// getopt_long stores the option index here.
int option_index = 0;
- c = getopt_long(argc, argv, "hkvOT:a:A:L:U:f:o:i:e:p:m:s:f:t:y:", long_options, &option_index);
+ c = getopt_long(argc, argv, "hkvOT:a:A:L:U:f:o:i:e:p:m:s:f:t:", long_options, &option_index);
// Detect the end of the options.
if (c == -1)
@@ -929,12 +908,6 @@ int parse_command_line(int argc, char* argv[]) {
else
in_file_type = FileT::unknown;
break;
- case 'y':
- if (strcmp(optarg, "sam") == 0)
- out_file_type = FileT::sam;
- else
- out_file_type = FileT::sql;
- break;
case 'f':
in_file = optarg;
break;
@@ -943,21 +916,24 @@ int parse_command_line(int argc, char* argv[]) {
break;
case 'i':
sql_id = is_integer(optarg);
- if (sql_id < 0) {
- cerr << "SQL ID (-i) must be an integer, e.g. 1, 2, 3\n";
- help();
- }
break;
case 'm':
min_stack_cov = atoi(optarg);
break;
- case 'a':
- req_pct_aln = is_double(optarg);
- if (req_pct_aln > 1)
- req_pct_aln = req_pct_aln / 100;
+ case 1001: //max_clipped
+ max_clipped = is_double(optarg);
+ if (max_clipped > 1)
+ max_clipped = max_clipped / 100;
- if (req_pct_aln < 0 || req_pct_aln > 1.0) {
- cerr << "Unable to parse the required alignment percentage.\n";
+ if (max_clipped < 0 || max_clipped > 1.0) {
+ cerr << "Unable to parse the maximum clipped proportion.\n";
+ help();
+ }
+ break;
+ case 1002:
+ min_mapping_qual = is_integer(optarg);
+ if (min_mapping_qual < 0) {
+ cerr << "Unable to parse the minimum mapping quality.\n";
help();
}
break;
@@ -971,13 +947,14 @@ int parse_command_line(int argc, char* argv[]) {
if (strcmp(optarg, "snp") == 0) {
model_type = snp;
} else if (strcmp(optarg, "fixed") == 0) {
- model_type = fixed;
+ model_type = ::fixed;
} else if (strcmp(optarg, "bounded") == 0) {
model_type = bounded;
} else {
cerr << "Unknown model type specified '" << optarg << "'\n";
help();
}
+ break;
case 'L':
bound_low = atof(optarg);
break;
@@ -990,7 +967,7 @@ int parse_command_line(int argc, char* argv[]) {
case 'p':
num_threads = atoi(optarg);
break;
- case 'v':
+ case 1000:
version();
break;
case '?':
@@ -1005,6 +982,11 @@ int parse_command_line(int argc, char* argv[]) {
}
}
+ if (optind < argc) {
+ cerr << "Error: Failed to parse command line: '" << argv[optind] << "' is seen as a positional argument. Expected no positional arguments.\n";
+ help();
+ }
+
if (alpha != 0.1 && alpha != 0.05 && alpha != 0.01 && alpha != 0.001) {
cerr << "SNP model alpha significance level must be either 0.1, 0.05, 0.01, or 0.001.\n";
help();
@@ -1024,8 +1006,21 @@ int parse_command_line(int argc, char* argv[]) {
model_type = bounded;
}
- if (in_file.length() == 0 || in_file_type == FileT::unknown) {
- cerr << "You must specify an input file of a supported type.\n";
+ if (in_file.empty()) {
+ cerr << "You must specify an input file.\n";
+ help();
+ }
+
+ if (in_file_type == FileT::unknown) {
+ in_file_type = guess_file_type(in_file);
+ if (in_file_type == FileT::unknown) {
+ cerr << "Unable to recongnize the extention of file '" << in_file << "'.\n";
+ help();
+ }
+ }
+
+ if (sql_id < 0) {
+ cerr << "A sample ID must be provided.\n";
help();
}
@@ -1035,7 +1030,7 @@ int parse_command_line(int argc, char* argv[]) {
if (out_path.at(out_path.length() - 1) != '/')
out_path += "/";
- if (model_type == fixed && barcode_err_freq == 0) {
+ if (model_type == ::fixed && barcode_err_freq == 0) {
cerr << "You must specify the barcode error frequency.\n";
help();
}
@@ -1051,25 +1046,50 @@ void version() {
void help() {
std::cerr << "pstacks " << VERSION << "\n"
- << "pstacks -t file_type -f file_path [-o path] [-i id] [-m min_cov] [-p num_threads] [-h]" << "\n"
- << " t: input file Type. Supported types: bowtie, sam, or bam.\n"
+ << "pstacks -f file_path -i id -o path [-m min_cov] [-p num_threads]" << "\n"
<< " f: input file path.\n"
- << " o: output path to write results.\n"
- << " i: SQL ID to insert into the output to identify this sample.\n"
+ << " i: a unique integer ID for this sample.\n"
+ << " o: output directory.\n"
<< " m: minimum depth of coverage to report a stack (default 3).\n"
<< " p: enable parallel execution with num_threads threads.\n"
- << " h: display this help messsage.\n"
- << " --pct_aln <num>: require read alignments to use at least this percentage of the read (default 85%).\n"
+ << " t: input file Type. Supported types: bam, sam, bowtie (default: guess).\n"
+ << " --max_clipped <float>: alignments with more than this fraction of soft-clipped bases are discarded (default 15%).\n"
+ << " --min_mapq <int>: minimum required quality (default 10).\n"
<< " --keep_sec_alns: keep secondary alignments (default: false, only keep primary alignments).\n"
+ << "\n"
<< " Model options:\n"
<< " --model_type <type>: either 'snp' (default), 'bounded', or 'fixed'\n"
- << " For the SNP or Bounded SNP model:\n"
- << " --alpha <num>: chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001.\n"
- << " For the Bounded SNP model:\n"
- << " --bound_low <num>: lower bound for epsilon, the error rate, between 0 and 1.0 (default 0).\n"
- << " --bound_high <num>: upper bound for epsilon, the error rate, between 0 and 1.0 (default 1).\n"
- << " For the Fixed model:\n"
- << " --bc_err_freq <num>: specify the barcode error frequency, between 0 and 1.0.\n";
+ << " For the SNP or Bounded SNP model:\n"
+ << " --alpha <num>: chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001.\n"
+ << " For the Bounded SNP model:\n"
+ << " --bound_low <num>: lower bound for epsilon, the error rate, between 0 and 1.0 (default 0).\n"
+ << " --bound_high <num>: upper bound for epsilon, the error rate, between 0 and 1.0 (default 1).\n"
+ << " For the Fixed model:\n"
+ << " --bc_err_freq <num>: specify the barcode error frequency, between 0 and 1.0.\n";
exit(0);
}
+
+void report_options(std::ostream& os) {
+ os << "pstacks parameters selected:\n"
+ << " Alignments file: " << in_file << "\n"
+ << " Output directory: " << out_path << "\n"
+ << " Sample ID: " << sql_id << "\n"
+ << " Min locus depth: " << min_stack_cov << "\n"
+ << " Max clipped proportion: " << max_clipped << "\n"
+ << " Min mapping quality: " << min_mapping_qual << "\n";
+
+ // Model.
+ if (model_type == snp) {
+ os << " Model: snp\n"
+ << " Model alpha: " << alpha << "\n";
+ } else if (model_type == bounded) {
+ os << " Model: snp\n"
+ << " Model alpha: " << alpha << "\n"
+ << " Model lower bound: " << bound_low << "\n"
+ << " Model higher bound: " << bound_high << "\n";
+ } else if (model_type == ::fixed) {
+ os << " Model: fixed\n"
+ << " Model barcode err. prob.: " << barcode_err_freq << "\n";
+ }
+}
diff --git a/src/pstacks.h b/src/pstacks.h
index 3a10cb2..de4ecf0 100644
--- a/src/pstacks.h
+++ b/src/pstacks.h
@@ -76,16 +76,17 @@ typedef unordered_map<DNANSeq, vector<Seq*> > HashMap;
void help( void );
void version( void );
int parse_command_line(int, char**);
-int load_radtags(string, HashMap &);
+void load_radtags(string, HashMap &);
int reduce_radtags(HashMap &, map<int, PStack *> &);
-int populate_merged_tags(map<int, PStack *> &, map<int, MergedStack *> &);
+void populate_merged_tags(map<int, PStack *> &, map<int, MergedStack *> &);
+void delete_low_cov_loci(map<int, MergedStack *>&, const map<int, PStack *>&);
int call_consensus(map<int, MergedStack *> &, map<int, PStack *> &, bool);
-int call_alleles(MergedStack *, vector<DNANSeq *> &);
-int count_raw_reads(map<int, PStack *> &, map<int, MergedStack *> &);
-double calc_coverage_distribution(map<int, PStack *> &, map<int, MergedStack *> &);
+void call_alleles(MergedStack *, vector<DNANSeq *> &);
+void calc_coverage_distribution(const map<int, PStack*>&, const map<int, MergedStack *>&, double&, double&, double&);
int write_results(map<int, MergedStack *> &, map<int, PStack *> &);
-//
+void report_options(std::ostream& os);
+
// Debugging
//
int dump_stacks(map<int, PStack *> &);
diff --git a/src/renz.cc b/src/renz.cc
index c153069..78f13ec 100644
--- a/src/renz.cc
+++ b/src/renz.cc
@@ -12,22 +12,24 @@ const char *ageI[] = {"CCGGT", // A/CCGGT, AgeI
"ACCGG"};
const char *aluI[] = {"CT", // AG/CT, AluI
"AG"};
+const char *apaLI[] = {"TGCAC", // G/TGCAC, ApaLI
+ "GTGCA"};
const char *apeKI[] = {"CAGC", "CTGC", // G/CWGC, ApeKI; W=A or T
- "GTCG", "GACG"};
+ "GTCG", "GACG"};
const char *apoI[] = {"AATTC", "AATTT", // R/AATTY, ApoI (also known as XapI)
"GAATT", "AAATT"};
const char *aseI[] = {"TAAT", // AT/TAAT, AseI
"ATTA"};
const char *bamHI[] = {"GATCC", // G/GATCC, BamHI
- "GGATC"};
+ "GGATC"};
const char *bfaI[] = {"TAG", // C/TAG, BfaI
"CTA"};
const char *bgIII[] = {"GATCT", // A/GATCT, BgIII
- "AGATC"};
+ "AGATC"};
const char *bsaHI[] = {"CGCC", "CGTC", // GR/CGYC, BsaHI
"GGCG", "GACG"};
const char *bspDI[] = {"CGAT", // AT/CGAT, BspDI
- "ATCG"};
+ "ATCG"};
const char *bstYI[] = {"GATCC", "GATCT", // R/GATCY, BstYI (also known as PsuI)
"GGATC", "AGATC"};
const char *claI[] = {"CGAT", // AT/CGAT, ClaI
@@ -35,29 +37,31 @@ const char *claI[] = {"CGAT", // AT/CGAT, ClaI
const char *csp6I[] = {"TAC", // G/TAC, Csp6I
"GTA"};
const char *ddeI[] = {"TAAG", "TCAG", "TGAG", "TTAG", // C/TNAG, DdeI
- "CTTA", "CTGA", "CTCA", "CTAA"};
+ "CTTA", "CTGA", "CTCA", "CTAA"};
const char *dpnII[] = {"GATC", // GATC, DpnII
- "GATC"};
+ "GATC"};
const char *eaeI[] = {"GGCCA", "GGCCG", // Y/GGCCR, EaeI
- "TGGCC", "CGGCC"};
+ "TGGCC", "CGGCC"};
const char *ecoRI[] = {"AATTC", // G/AATTC, EcoRI
- "GAATT"};
+ "GAATT"};
const char *ecoRV[] = {"ATC", // GAT/ATC, EcoRV
- "GAT"};
+ "GAT"};
const char *ecoT22I[] = {"TGCAT", // A/TGCAT, EcoT22I
- "ATGCA"};
+ "ATGCA"};
+const char *haeIII[] = {"CC", // GG/CC, HaeIII
+ "GG"};
const char *hindIII[] = {"AGCTT", // A/AGCTT, HindIII
- "TCGAA"};
+ "TCGAA"};
const char *hpaII[] = {"CGG", // C/CGG, HpaII
"CCG"};
const char *kpnI[] = {"GTACC", // C/CATGG, KpnI
- "GGTAC"};
+ "GGTAC"};
const char *mluCI[] = {"AATT", // AATT, MluCI
- "AATT"};
+ "AATT"};
const char *mseI[] = {"TAA", // T/TAA, MseI
- "TTA"};
+ "TTA"};
const char *mspI[] = {"CGG", // C/CGG, MspI
- "CCG"};
+ "CCG"};
const char *ncoI[] = {"CATGG", // C/CATGG, NcoI
"CCATG"};
const char *ndeI[] = {"TATG", // CA/TATG, NdeI
@@ -65,33 +69,33 @@ const char *ndeI[] = {"TATG", // CA/TATG, NdeI
const char *nheI[] = {"CTAGC", // G/CTAGC, NheI
"GCTAG"};
const char *nlaIII[] = {"CATG", // CATG, NlaIII
- "CATG"};
+ "CATG"};
const char *notI[] = {"GGCCGC", // GC/GGCCGC, NotI
- "GCGGCC"};
+ "GCGGCC"};
const char *nsiI[] = {"TGCAT", // ATGCA/T, NsiI
- "ATGCA"};
+ "ATGCA"};
const char *pstI[] = {"TGCAG", // CTGCA/G, PstI
- "CTGCA"};
+ "CTGCA"};
const char *rsaI[] = {"AC", // GT/AC, RsaI
"GT"};
const char *sacI[] = {"AGCTC", // GAGCT/C, SacI
- "GAGCT"};
+ "GAGCT"};
const char *sau3AI[] = {"GATC", // GATC, Sau3AI
- "GATC"};
+ "GATC"};
const char *sbfI[] = {"TGCAGG", // CCTGCA/GG, SbfI
- "CCTGCA"};
+ "CCTGCA"};
const char *sexAI[] = {"CCAGGT", "CCTGGT", // A/CCWGGT, SexAI; W=A or T
- "ACCTGG", "ACCAGG"};
+ "ACCTGG", "ACCAGG"};
const char *sgrAI[] = {"CCGGCG", "CCGGTG", // CR/CCGGYG, SgrAI; R=A or G; Y=C or T
- "CGCCGG", "CACCGG"};
+ "CGCCGG", "CACCGG"};
const char *speI[] = {"CTAGT", // A/CTAGT, SpeI
"ACTAG"};
const char *sphI[] = {"CATGC", // GCATG/C, SphI
- "GCATG"};
+ "GCATG"};
const char *taqI[] = {"CGA", // T/CGA, TaqI
- "TCG"};
+ "TCG"};
const char *xbaI[] = {"CTAGA", // T/CTAGA, XbaI
- "TCTAG"};
+ "TCTAG"};
const char *xhoI[] = {"TCGAG", // C/TCGAG, XhoI
"CTCGA"};
@@ -105,6 +109,7 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
renz["sgrAI"] = sgrAI; // CR/CCGGYG, SgrAI; R=A or G; Y=C or T
renz["apeKI"] = apeKI; // G/CWGC, ApeKI; W=A or T
renz["hindIII"] = hindIII; // A/AGCTT, HindIII
+ renz["haeIII"] = haeIII; // GG/CC, HaeIII
renz["dpnII"] = dpnII; // GATC, DpnII
renz["sphI"] = sphI; // GCATG/C, SphI
renz["nlaIII"] = nlaIII; // CATG, NlaIII
@@ -142,6 +147,7 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
renz["bsaHI"] = bsaHI; // GR/CGYC, BsaHI
renz["hpaII"] = hpaII; // C/CGG, HpaII
renz["ncoI"] = ncoI; // C/CATGG, NcoI
+ renz["apaLI"] = apaLI; // G/TGCAC, ApaLI
renz_cnt["sbfI"] = 1;
renz_cnt["pstI"] = 1;
@@ -150,6 +156,7 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
renz_cnt["sgrAI"] = 2;
renz_cnt["apeKI"] = 2;
renz_cnt["hindIII"] = 1;
+ renz_cnt["haeIII"] = 1;
renz_cnt["dpnII"] = 1;
renz_cnt["sphI"] = 1;
renz_cnt["nlaIII"] = 1;
@@ -187,6 +194,7 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
renz_cnt["bsaHI"] = 2;
renz_cnt["hpaII"] = 1;
renz_cnt["ncoI"] = 1;
+ renz_cnt["apaLI"] = 1;
renz_len["sbfI"] = 6;
renz_len["pstI"] = 5;
@@ -195,6 +203,7 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
renz_len["sgrAI"] = 6;
renz_len["apeKI"] = 4;
renz_len["hindIII"] = 5;
+ renz_len["haeIII"] = 2;
renz_len["dpnII"] = 4;
renz_len["sphI"] = 5;
renz_len["nlaIII"] = 4;
@@ -232,6 +241,7 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
renz_len["bsaHI"] = 4;
renz_len["hpaII"] = 3;
renz_len["ncoI"] = 5;
+ renz_len["apaLI"] = 5;
}
void
diff --git a/src/rxstacks.cc b/src/rxstacks.cc
index 87c71a4..9f7e702 100644
--- a/src/rxstacks.cc
+++ b/src/rxstacks.cc
@@ -24,6 +24,7 @@
//
#include "MetaPopInfo.h"
+#include "catalog_utils.h"
#include "rxstacks.h"
@@ -31,7 +32,7 @@ typedef MetaPopInfo::Sample Sample;
// Global variables to hold command-line options.
int num_threads = 1;
-int batch_id = 0;
+int batch_id = -1;
string in_path;
string out_path;
FileT in_file_type = FileT::sql;
@@ -58,6 +59,7 @@ double homozygote_limit = 2.71;
const int barcode_size = 5;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
@@ -95,10 +97,6 @@ int main (int argc, char* argv[]) {
MetaPopInfo mpopi;
mpopi.init_directory(in_path);
- if (mpopi.samples().empty()) {
- cerr << "Error: Failed to find sample files in directory '" << in_path << "'.\n";
- return -1;
- }
//
// Open and initialize the log files.
@@ -397,6 +395,7 @@ int main (int argc, char* argv[]) {
map<int, Locus *>::iterator stack_it;
for (stack_it = stacks.begin(); stack_it != stacks.end(); stack_it++)
delete stack_it->second;
+ stacks.clear();
cerr << "done.\n";
}
@@ -407,7 +406,22 @@ int main (int argc, char* argv[]) {
log_hap_fh.close();
}
+ //
+ // Free memory associated with the catalog and matches to the catalog.
+ //
+ for (map<int, CSLocus *>::iterator cat_it = catalog.begin(); cat_it != catalog.end(); cat_it++)
+ delete cat_it->second;
+ catalog.clear();
+
+ for (uint i = 0; i < catalog_matches.size(); i++) {
+ for (uint j = 0; j < catalog_matches[i].size(); j++)
+ delete catalog_matches[i][j];
+ catalog_matches[i].clear();
+ }
+
+ cerr << "rxstacks is done.\n";
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int
@@ -472,12 +486,12 @@ calc_lnl_means(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap)
mean += d[i]->lnl;
}
- if (lnls.size() == 0) continue;
+ if (lnls.size() == 0)
+ continue;
sort(lnls.begin(), lnls.end());
-
mid = lnls.size() / 2;
- median = lnls.size() % 2 == 0 ? lnls[mid] + lnls[mid+1] / 2.0 : lnls[mid+1];
+ median = lnls.size() % 2 == 0 ? lnls[mid-1] + lnls[mid] / 2.0 : lnls[mid];
mean = mean / (double) lnls.size();
cloc->lnl = mean;
@@ -551,14 +565,12 @@ prune_mst_haplotypes(CSLocus *cloc, Datum *d, Locus *loc, unsigned long &pruned_
MinSpanTree *mst = new MinSpanTree;
map<string, int>::iterator it;
- vector<uint> keys;
vector<string> haps;
Node *n;
for (it = cloc->hap_cnts.begin(); it != cloc->hap_cnts.end(); it++) {
- n = mst->add_node(it->first);
+ mst->add_node(it->first);
haps.push_back(it->first);
- keys.push_back(n->id);
}
//
@@ -609,8 +621,10 @@ prune_mst_haplotypes(CSLocus *cloc, Datum *d, Locus *loc, unsigned long &pruned_
//
sort(haplotypes.begin(), haplotypes.end(), compare_pair_haplotype_rev);
- if (size <= 2)
+ if (size <= 2) {
+ delete mst;
return 0;
+ }
//
// Pull out the two most frequently occuring haplotypes.
@@ -720,6 +734,8 @@ prune_mst_haplotypes(CSLocus *cloc, Datum *d, Locus *loc, unsigned long &pruned_
//
generate_matched_haplotypes(cloc, loc, d);
+ delete mst;
+
return 0;
}
@@ -1662,10 +1678,6 @@ parse_command_line(int argc, char* argv[])
break;
case 'b':
batch_id = is_integer(optarg);
- if (batch_id < 0) {
- cerr << "Batch ID (-b) must be an integer, e.g. 1, 2, 3\n";
- help();
- }
break;
case 'o':
out_path = optarg;
@@ -1674,7 +1686,7 @@ parse_command_line(int argc, char* argv[])
if (strcmp(optarg, "snp") == 0) {
model_type = snp;
} else if (strcmp(optarg, "fixed") == 0) {
- model_type = fixed;
+ model_type = ::fixed;
} else if (strcmp(optarg, "bounded") == 0) {
model_type = bounded;
} else {
@@ -1729,14 +1741,19 @@ parse_command_line(int argc, char* argv[])
}
}
+ if (optind < argc) {
+ cerr << "Error: Failed to parse command line: '" << argv[optind] << "' is seen as a positional argument. Expected no positional arguments.\n";
+ help();
+ }
+
if (in_path.length() == 0) {
cerr << "You must specify a path to the directory containing Stacks output files.\n";
help();
}
if (out_path.length() == 0) {
- cerr << "No output path specified, files in '" << in_path << "' will be overwritten.\n";
- out_path = in_path;
+ cerr << "You must specify a path to a directory where to write output files.\n";
+ help();
}
if (in_path.at(in_path.length() - 1) != '/')
@@ -1745,9 +1762,17 @@ parse_command_line(int argc, char* argv[])
if (out_path.at(out_path.length() - 1) != '/')
out_path += "/";
- if (batch_id == 0) {
- cerr << "You must specify a batch ID.\n";
- help();
+ if (batch_id < 0) {
+ vector<int> cat_ids = find_catalogs(in_path);
+ if (cat_ids.size() == 1) {
+ batch_id = cat_ids[0];
+ } else if (cat_ids.empty()) {
+ cerr << "Error: Unable to find a catalog in '" << in_path << "'.\n";
+ help();
+ } else {
+ cerr << "Error: Input directory contains several catalogs, please specify -b.\n";
+ help();
+ }
}
if (alpha != 0.1 && alpha != 0.05 && alpha != 0.01 && alpha != 0.001) {
@@ -1785,13 +1810,11 @@ void version() {
void help() {
std::cerr << "rxstacks " << VERSION << "\n"
- << "rxstacks -b batch_id -P path [-o path] [-t threads] [-v] [-h]" << "\n"
- << " b: Batch ID to examine when exporting from the catalog.\n"
+ << "rxstacks -P path -o path [-t threads] [-b batch_id]" << "\n"
<< " P: path to the Stacks output files.\n"
- << " o: output path to write results.\n"
+ << " o: output path to write results ('.' to override the current files).\n"
<< " t: number of threads to run in parallel sections of code.\n"
- << " v: print program version." << "\n"
- << " h: display this help messsage." << "\n\n"
+ << " b: database/batch ID of the input catalog to consider (default: guess).\n"
<< " Filtering options:\n"
<< " --lnl_filter: filter catalog loci based on the mean log likelihood of the catalog locus in the population.\n"
<< " --lnl_lim <limit>: minimum log likelihood required to keep a catalog locus.\n"
diff --git a/src/smoothing.h b/src/smoothing.h
index 547751b..0b84a3b 100644
--- a/src/smoothing.h
+++ b/src/smoothing.h
@@ -64,9 +64,10 @@ KSmooth<StatT>::smooth(vector<StatT *> &popstats)
int limit = 3 * sigma;
int dist;
uint pos_l, pos_u;
- double sum, final_weight;
+ double *sum, final_weight;
PopStat *c, *p;
+ sum = new double[this->size];
pos_l = 0;
pos_u = 0;
@@ -77,9 +78,10 @@ KSmooth<StatT>::smooth(vector<StatT *> &popstats)
if (c == NULL)
continue;
- for (uint i = 0; i < this->size; i++)
+ for (uint i = 0; i < this->size; i++) {
c->smoothed[i] = 0.0;
- sum = 0.0;
+ sum[i] = 0.0;
+ }
determine_window_limits(popstats, c->bp, pos_l, pos_u);
@@ -114,10 +116,12 @@ KSmooth<StatT>::smooth(vector<StatT *> &popstats)
// sites_cnt++;
final_weight = (p->alleles - 1) * this->weights[dist];
- for (uint i = 0; i < this->size; i++)
- c->smoothed[i] += p->stat[i] * final_weight;
- sum += final_weight;
-
+ for (uint i = 0; i < this->size; i++) {
+ if (p->stat[i] > -7.0) {
+ c->smoothed[i] += p->stat[i] * final_weight;
+ sum[i] += final_weight;
+ }
+ }
// if (c->loc_id == 9314) {
// cerr << " id: " << p->loc_id
// << "; dist: " << dist
@@ -139,8 +143,10 @@ KSmooth<StatT>::smooth(vector<StatT *> &popstats)
// c->snp_cnt = snp_cnt;
for (uint i = 0; i < this->size; i++)
- c->smoothed[i] /= sum;
+ c->smoothed[i] /= sum[i];
}
+
+ delete [] sum;
}
return 0;
diff --git a/src/sql_utilities.cc b/src/sql_utilities.cc
index 3143f2c..89f5b88 100644
--- a/src/sql_utilities.cc
+++ b/src/sql_utilities.cc
@@ -76,6 +76,8 @@ int load_catalog_matches(string sample, vector<CatMatch *> &matches) {
else
fh.close();
+ free(line);
+
return 0;
}
@@ -194,7 +196,7 @@ int load_model_results(string sample, map<int, ModRes *> &modres) {
else
fh.close();
- delete [] line;
+ free(line);
return 1;
}
@@ -293,7 +295,7 @@ int load_snp_calls(string sample, map<int, SNPRes *> &snpres) {
else
fh.close();
- delete [] line;
+ free(line);
return 1;
}
diff --git a/src/sstacks.cc b/src/sstacks.cc
index c23f995..48f2de7 100644
--- a/src/sstacks.cc
+++ b/src/sstacks.cc
@@ -22,17 +22,23 @@
// sstacks -- search for occurances of stacks in a catalog of stacks.
//
+#include <regex>
+
+#include "catalog_utils.h"
+#include "MetaPopInfo.h"
+
#include "sstacks.h"
+using namespace std;
+
// Global variables to hold command-line options.
queue<string> samples;
string catalog_path;
string out_path;
FileT in_file_type = FileT::sql;
-int num_threads = 1;
-int batch_id = 0;
-int samp_id = 0;
-int catalog = 0;
+int num_threads = 1;
+int batch_id = -1;
+int samp_id = 0;
bool verify_haplotypes = true;
bool impute_haplotypes = true;
bool require_uniq_haplotypes = false;
@@ -44,6 +50,7 @@ double max_gaps = 2.0;
int gapped_kmer_len = 19;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
@@ -92,7 +99,7 @@ int main (int argc, char* argv[]) {
sample_path = samples.front();
samples.pop();
- cerr << "Processing sample '" << sample_path << "' [" << i << " of " << sample_cnt << "]\n";
+ cerr << "\nProcessing sample '" << sample_path << "' [" << i << " of " << sample_cnt << "]\n";
res = load_loci(sample_path, sample, false, false, compressed);
@@ -144,9 +151,10 @@ int main (int argc, char* argv[]) {
//
for (map<int, Locus *>::iterator j = catalog.begin(); j != catalog.end(); j++)
delete j->second;
- catalog.clear();
+ cerr << "\nsstacks is done.\n";
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int
@@ -1288,29 +1296,29 @@ write_matches(string sample_path, map<int, QLocus *> &sample)
}
int parse_command_line(int argc, char* argv[]) {
- string sample_file;
- int c;
+ string in_dir;
+ string popmap_path;
while (1) {
static struct option long_options[] = {
{"help", no_argument, NULL, 'h'},
{"version", no_argument, NULL, 'v'},
- {"genomic_loc", no_argument, NULL, 'g'},
+ {"aligned", no_argument, NULL, 'g'},
{"verify_hap", no_argument, NULL, 'x'},
{"uniq_haplotypes", no_argument, NULL, 'u'},
{"gapped", no_argument, NULL, 'G'},
{"num_threads", required_argument, NULL, 'p'},
{"batch_id", required_argument, NULL, 'b'},
{"catalog", required_argument, NULL, 'c'},
- {"sample_2", required_argument, NULL, 's'},
+ {"sample_path", required_argument, NULL, 's'},
{"outpath", required_argument, NULL, 'o'},
+ {"in_dir", required_argument, NULL, 'P'},
+ {"popmap", required_argument, NULL, 'M'},
{0, 0, 0, 0}
};
- // getopt_long stores the option index here.
int option_index = 0;
-
- c = getopt_long(argc, argv, "hgGxuvs:c:o:b:p:", long_options, &option_index);
+ int c = getopt_long(argc, argv, "hgGxuvs:c:o:b:p:P:M:", long_options, &option_index);
// Detect the end of the options.
if (c == -1)
@@ -1331,8 +1339,7 @@ int parse_command_line(int argc, char* argv[]) {
}
break;
case 's':
- sample_file = optarg;
- samples.push(sample_file);
+ samples.push(optarg);
break;
case 'g':
search_type = genomic_loc;
@@ -1352,6 +1359,12 @@ int parse_command_line(int argc, char* argv[]) {
case 'G':
gapped_alignments = true;
break;
+ case 'P':
+ in_dir = optarg;
+ break;
+ case 'M':
+ popmap_path = optarg;
+ break;
case 'v':
version();
break;
@@ -1365,21 +1378,85 @@ int parse_command_line(int argc, char* argv[]) {
}
}
- if (catalog_path.length() == 0) {
- cerr << "You must specify the prefix path to the catalog.\n";
+ if (optind < argc) {
+ cerr << "Error: Failed to parse command line: '" << argv[optind] << "' is seen as a positional argument. Expected no positional arguments.\n";
help();
}
- if (samples.size() == 0) {
- cerr << "You must specify at least one sample file.\n";
+ if (in_dir.empty() && catalog_path.empty()) {
+ cerr << "Error: You must specify one of -P or -c.\n";
+ help();
+ } else if (
+ ((!in_dir.empty() || !popmap_path.empty()) // One of -P, or -M
+ && (!catalog_path.empty() || !samples.empty() || !out_path.empty())) // and one of -c, -s or -o
+ ) {
+ cerr << "Error: Please do not mix run modes (-P/-M or -c/-s/-o).\n";
help();
}
- if (out_path.length() == 0)
- out_path = ".";
+ if (!in_dir.empty()) {
+ if (popmap_path.empty()) {
+ cerr << "Error: Please specify some input samples (-M).\n";
+ help();
+ }
- if (out_path.at(out_path.length() - 1) != '/')
- out_path += "/";
+ if (batch_id < 0) {
+ vector<int> cat_ids = find_catalogs(in_dir);
+ if (cat_ids.size() == 1) {
+ batch_id = cat_ids[0];
+ } else if (cat_ids.empty()) {
+ cerr << "Error: Unable to find a catalog in '" << in_dir << "'.\n";
+ help();
+ } else {
+ cerr << "Error: Input directory contains several catalogs, please specify -b.\n";
+ help();
+ }
+ }
+
+ if (in_dir.back() != '/')
+ in_dir += "/";
+
+ // Set `catalog_path`.
+ catalog_path = in_dir + "batch_" + to_string(batch_id);
+
+ // Set `samples`.
+ if (!popmap_path.empty()) {
+ MetaPopInfo popmap;
+ popmap.init_popmap(popmap_path);
+ for (const MetaPopInfo::Sample& s : popmap.samples())
+ samples.push(in_dir + s.name);
+ }
+
+ // Set `out_path`.
+ out_path = in_dir;
+
+ } else if (!catalog_path.empty()) {
+ if (batch_id < 0) {
+ regex r ("batch_([0-9]+)");
+ smatch m;
+ regex_search(catalog_path, m, r);
+ if (m.size()==2) {
+ // full match plus one submatch
+ batch_id = stoi(m[1].str());
+ }
+
+ if (batch_id < 0) {
+ cerr << "Unable to guess batch ID.\n";
+ help();
+ }
+ }
+
+ if (samples.size() == 0) {
+ cerr << "You must specify at least one sample file.\n";
+ help();
+ }
+
+ if (out_path.length() == 0)
+ out_path = ".";
+
+ if (out_path.back() != '/')
+ out_path += "/";
+ }
return 0;
}
@@ -1392,18 +1469,20 @@ void version() {
void help() {
std::cerr << "sstacks " << VERSION << "\n"
- << "sstacks -b batch_id -c catalog_file -s sample_file [-s sample_file_2 ...] [-o path] [-p num_threads] [-g] [-x] [-v] [-h]" << "\n"
- << " p: enable parallel execution with num_threads threads.\n"
- << " b: MySQL ID of this batch." << "\n"
- << " c: TSV file from which to load the catalog loci." << "\n"
+ << "sstacks [--aligned] -P dir [-b batch_id] -M popmap [-p n_threads]" << "\n"
+ << "sstacks [--aligned] -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads]" << "\n"
+ << " b: database/batch ID of the catalog to consider (default: guess)." << "\n"
+ << " P: path to the directory containing Stacks files.\n"
+ << " M: path to a population map file from which to take sample names.\n"
<< " s: filename prefix from which to load sample loci." << "\n"
+ << " c: path to the catalog." << "\n"
+ << " g,--aligned: base matching on alignment position, not sequence identity." << "\n"
+ << " p: enable parallel execution with num_threads threads.\n"
<< " o: output path to write results." << "\n"
- << " g: base matching on genomic location, not sequence identity." << "\n"
<< " x: don't verify haplotype of matching locus." << "\n"
- << " v: print program version." << "\n"
- << " h: display this help messsage." << "\n\n"
- << " Gapped assembly options:\n"
- << " --gapped: preform gapped alignments between stacks.\n";
+ << "\n"
+ << "Gapped assembly options:\n"
+ << " --gapped: preform gapped alignments between stacks.\n";
exit(0);
}
diff --git a/src/stacks.h b/src/stacks.h
index 6a70d8e..364137e 100644
--- a/src/stacks.h
+++ b/src/stacks.h
@@ -73,8 +73,12 @@ public:
}
PhyLoc(const PhyLoc& other)
: bp(other.bp), strand(other.strand) {
- chr = new char[strlen(other.chr)+1];
- strcpy(chr, other.chr);
+ if (other.chr == NULL) {
+ chr = NULL;
+ } else {
+ chr = new char[strlen(other.chr)+1];
+ strcpy(chr, other.chr);
+ }
}
PhyLoc(const char *chr, uint bp) {
this->chr = new char[strlen(chr) + 1];
diff --git a/src/ustacks.cc b/src/ustacks.cc
index fb93412..eeb9388 100644
--- a/src/ustacks.cc
+++ b/src/ustacks.cc
@@ -24,6 +24,8 @@
#include "ustacks.h"
+using namespace std;
+
//
// Global variables to hold command-line options.
//
@@ -31,7 +33,7 @@ FileT in_file_type;
string in_file;
string out_path;
int num_threads = 1;
-int sql_id = 0;
+int sql_id = -1;
bool call_sec_hapl = true;
bool set_kmer_len = true;
int kmer_len = 0;
@@ -41,7 +43,7 @@ uint max_subgraph = 3;
int dump_graph = 0;
int retain_rem_reads = false;
int deleverage_stacks = 0;
-int remove_rep_stacks = 0;
+bool remove_rep_stacks = true;
int max_utag_dist = 2;
int max_rem_dist = -1;
bool gapped_alignments = false;
@@ -62,6 +64,7 @@ double heterozygote_limit = -3.84;
double homozygote_limit = 3.84;
int main (int argc, char* argv[]) {
+ IF_NDEBUG_TRY
parse_command_line(argc, argv);
@@ -71,7 +74,8 @@ int main (int argc, char* argv[]) {
//
if (max_rem_dist == -1) max_rem_dist = max_utag_dist + 2;
- cerr << "ustacks paramters selected:\n"
+ cerr << "ustacks parameters selected:\n"
+ << " Sample ID: " << sql_id << "\n"
<< " Min depth of coverage to create a stack: " << min_merge_cov << "\n"
<< " Max distance allowed between stacks: " << max_utag_dist << "\n"
<< " Max distance allowed to align secondary reads: " << max_rem_dist << "\n"
@@ -83,7 +87,7 @@ int main (int argc, char* argv[]) {
case snp:
cerr << "SNP\n";
break;
- case fixed:
+ case ::fixed:
cerr << "Fixed\n";
break;
case bounded:
@@ -134,27 +138,21 @@ int main (int argc, char* argv[]) {
double cov_mean, cov_stdev, cov_max;
- calc_coverage_distribution(unique, cov_mean, cov_stdev, cov_max);
- cerr << "Initial coverage mean: " << cov_mean << "; Std Dev: " << cov_stdev << "; Max: " << cov_max << "\n";
-
- calc_triggers(cov_mean, cov_stdev, 1, deleverage_trigger, removal_trigger);
-
- cerr << "Deleveraging trigger: " << deleverage_trigger << "; Removal trigger: " << removal_trigger << "\n";
-
map<int, MergedStack *> merged;
-
populate_merged_tags(unique, merged);
-
cerr << merged.size() << " initial stacks were populated; " << remainders.size() << " stacks were set aside as secondary reads.\n";
+ calc_coverage_distribution(unique, remainders, merged, cov_mean, cov_stdev, cov_max);
+ cerr << "Initial coverage mean: " << cov_mean << "; Std Dev: " << cov_stdev << "; Max: " << cov_max << "\n";
+ calc_triggers(cov_mean, cov_stdev, 1, deleverage_trigger, removal_trigger);
+ cerr << "Deleveraging trigger: " << deleverage_trigger << "; Removal trigger: " << removal_trigger << "\n";
if (remove_rep_stacks) {
cerr << "Calculating distance for removing repetitive stacks.\n";
calc_kmer_distance(merged, 1);
cerr << "Removing repetitive stacks.\n";
remove_repetitive_stacks(unique, merged);
}
-
- calc_coverage_distribution(unique, merged, cov_mean, cov_stdev, cov_max);
+ calc_coverage_distribution(unique, remainders, merged, cov_mean, cov_stdev, cov_max);
cerr << "Post-Repeat Removal, coverage depth Mean: " << cov_mean << "; Std Dev: " << cov_stdev << "; Max: " << cov_max << "\n";
cerr << "Calculating distance between stacks...\n";
@@ -165,7 +163,7 @@ int main (int argc, char* argv[]) {
call_consensus(merged, unique, remainders, false);
- calc_coverage_distribution(unique, merged, cov_mean, cov_stdev, cov_max);
+ calc_coverage_distribution(unique, remainders, merged, cov_mean, cov_stdev, cov_max);
cerr << "After merging, coverage depth Mean: " << cov_mean << "; Std Dev: " << cov_stdev << "; Max: " << cov_max << "\n";
//dump_merged_tags(merged);
@@ -200,7 +198,9 @@ int main (int argc, char* argv[]) {
write_results(merged, unique, remainders);
cerr << "done.\n";
+ cerr << "ustacks is done.\n";
return 0;
+ IF_NDEBUG_CATCH_ALL_EXCEPTIONS
}
int
@@ -868,7 +868,7 @@ call_consensus(map<int, MergedStack *> &merged, map<int, Stack *> &unique, map<i
case bounded:
call_bounded_multinomial_snp(mtag, col, nuc, true);
break;
- case fixed:
+ case ::fixed:
call_multinomial_fixed(mtag, col, nuc);
break;
}
@@ -877,7 +877,7 @@ call_consensus(map<int, MergedStack *> &merged, map<int, Stack *> &unique, map<i
if (invoke_model) {
call_alleles(mtag, reads, read_types);
- if (model_type == fixed) {
+ if (model_type == ::fixed) {
//
// Mask nucleotides that are not fixed.
//
@@ -1094,8 +1094,14 @@ merge_stacks(map<int, Stack *> &unique, map<int, Rem *> &rem, map<int, MergedSta
}
}
- uint new_cnt = new_merged.size();
- uint old_cnt = merged.size();
+ cerr << " " << merged.size() << " stacks merged into " << new_merged.size()
+ << " loci; deleveraged " << delev_cnt
+ << " loci; blacklisted " << blist_cnt << " loci.\n";
+
+ if (new_merged.empty()) {
+ cerr << "Error: Couldn't assemble any loci.\n";
+ throw exception();
+ }
//
// Free the memory from the old map of merged tags.
@@ -1103,12 +1109,7 @@ merge_stacks(map<int, Stack *> &unique, map<int, Rem *> &rem, map<int, MergedSta
for (it = merged.begin(); it != merged.end(); it++)
delete it->second;
- merged = new_merged;
-
- cerr << " " << old_cnt << " stacks merged into " << new_cnt
- << " stacks; deleveraged " << delev_cnt
- << " stacks; removed " << blist_cnt << " stacks.\n";
-
+ swap(merged, new_merged);
return 0;
}
@@ -1709,157 +1710,49 @@ int reduce_radtags(DNASeqHashMap &radtags, map<int, Stack *> &unique, map<int, R
return 0;
}
-int
-calc_coverage_distribution(map<int, Stack *> &unique,
- double &mean, double &stdev, double &max)
-{
- map<int, Stack *>::iterator i;
- double m = 0.0;
- double s = 0.0;
- double sum = 0.0;
- uint cnt = 0;
- double total = 0.0;
-
- mean = 0.0;
- max = 0.0;
- stdev = 0.0;
-
- map<int, int> depth_dist;
- map<int, int>::iterator j;
-
- for (i = unique.begin(); i != unique.end(); i++) {
- cnt = i->second->count();
- m += cnt;
- total++;
-
- depth_dist[cnt]++;
-
- if (cnt > max)
- max = cnt;
- }
-
- mean = m / total;
-
- //
- // Calculate the standard deviation
- //
- total = 0.0;
-
- for (i = unique.begin(); i != unique.end(); i++) {
- total++;
- s = i->second->count();
- sum += pow((s - mean), 2);
- }
-
- stdev = sqrt(sum / (total - 1));
-
- return 0;
-}
-
-int
-calc_coverage_distribution(map<int, Stack *> &unique,
- map<int, MergedStack *> &merged,
- double &mean, double &stdev, double &max)
-{
- map<int, MergedStack *>::iterator it;
- vector<int>::iterator k;
- Stack *tag;
- double m = 0.0;
- double s = 0.0;
- double sum = 0.0;
- double cnt = 0.0;
-
- mean = 0.0;
- max = 0.0;
- stdev = 0.0;
-
- for (it = merged.begin(); it != merged.end(); it++) {
- if (it->second->blacklisted) continue;
-
- cnt++;
- m = 0.0;
- for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
- tag = unique[*k];
- m += tag->count();
- }
- if (m > max) max = m;
-
- sum += m;
- }
-
- mean = sum / cnt;
-
- //
- // Calculate the standard deviation
- //
- for (it = merged.begin(); it != merged.end(); it++) {
- s = 0.0;
- for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
- tag = unique[*k];
- s += tag->count();
- }
- sum += pow((s - mean), 2);
- }
-
- stdev = sqrt(sum / (cnt - 1));
-
- return 0;
-}
-
-int
+void
calc_coverage_distribution(map<int, Stack *> &unique,
map<int, Rem *> &rem,
map<int, MergedStack *> &merged,
double &mean, double &stdev, double &max)
{
- map<int, MergedStack *>::iterator it;
- vector<int>::iterator k;
- Stack *tag;
- double m = 0.0;
- double s = 0.0;
- double sum = 0.0;
- double cnt = 0.0;
-
- mean = 0.0;
max = 0.0;
+ mean = 0.0;
stdev = 0.0;
- for (it = merged.begin(); it != merged.end(); it++) {
- if (it->second->blacklisted) continue;
+ size_t not_blacklisted = 0;
+ for (const pair<int, MergedStack*>& mtag : merged) {
+ if (mtag.second->blacklisted)
+ continue;
- cnt++;
- m = 0.0;
- for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
- tag = unique[*k];
- m += tag->count();
- }
- for (uint j = 0; j < it->second->remtags.size(); j++)
- m += rem[it->second->remtags[j]]->count();
+ ++not_blacklisted;
- if (m > max) max = m;
+ double depth = 0.0;
+ for (int utag_id : mtag.second->utags)
+ depth += unique[utag_id]->count();
+ for (int remtag_id : mtag.second->remtags)
+ depth += rem[remtag_id]->count();
- sum += m;
+ mean += depth;
+ if (depth > max)
+ max = depth;
}
+ mean /= not_blacklisted;
- mean = sum / cnt;
-
- //
- // Calculate the standard deviation
- //
- for (it = merged.begin(); it != merged.end(); it++) {
- s = 0.0;
- for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
- tag = unique[*k];
- s += tag->count();
- }
- for (uint j = 0; j < it->second->remtags.size(); j++)
- s += rem[it->second->remtags[j]]->count();
- sum += pow((s - mean), 2);
- }
+ for (const pair<int, MergedStack*>& mtag : merged) {
+ if (mtag.second->blacklisted)
+ continue;
- stdev = sqrt(sum / (cnt - 1));
+ double depth = 0.0;
+ for (int utag_id : mtag.second->utags)
+ depth += unique[utag_id]->count();
+ for (int remtag_id : mtag.second->remtags)
+ depth += rem[remtag_id]->count();
- return 0;
+ stdev += pow(depth - mean, 2);
+ }
+ stdev /= not_blacklisted;
+ stdev = sqrt(stdev);
}
int count_raw_reads(map<int, Stack *> &unique, map<int, Rem *> &rem, map<int, MergedStack *> &merged) {
@@ -2168,7 +2061,7 @@ write_results(map<int, MergedStack *> &m, map<int, Stack *> &u, map<int, Rem *>
break;
}
- sstr << std::fixed << std::setprecision(2)
+ sstr << std::fixed << setprecision(2)
<< (*s)->lratio << "\t"
<< (*s)->rank_1 << "\t"
<< (*s)->rank_2 << "\t\t\n";
@@ -2265,7 +2158,7 @@ int dump_stack_graph(string data_file,
double d, scale, scaled_d;
char label[32];
vector<string> colors;
- std::ofstream data(data_file.c_str());
+ ofstream data(data_file.c_str());
size_t pos_1 = data_file.find_last_of("/");
size_t pos_2 = data_file.find_last_of(".");
@@ -2585,7 +2478,7 @@ int parse_command_line(int argc, char* argv[]) {
{"k_len", required_argument, NULL, 'k'},
{"num_threads", required_argument, NULL, 'p'},
{"deleverage", no_argument, NULL, 'd'},
- {"remove_rep", no_argument, NULL, 'r'},
+ {"keep_high_cov", no_argument, NULL, 1000},
{"retain_rem", no_argument, NULL, 'R'},
{"graph", no_argument, NULL, 'g'},
{"sec_hapl", no_argument, NULL, 'H'},
@@ -2597,6 +2490,7 @@ int parse_command_line(int argc, char* argv[]) {
{"bound_low", required_argument, NULL, 'L'},
{"bound_high", required_argument, NULL, 'U'},
{"alpha", required_argument, NULL, 'A'},
+ {"r-deprecated", no_argument, NULL, 'r'},
{0, 0, 0, 0}
};
@@ -2635,10 +2529,6 @@ int parse_command_line(int argc, char* argv[]) {
break;
case 'i':
sql_id = is_integer(optarg);
- if (sql_id < 0) {
- cerr << "SQL ID (-i) must be an integer, e.g. 1, 2, 3\n";
- help();
- }
break;
case 'm':
min_merge_cov = is_integer(optarg);
@@ -2652,8 +2542,8 @@ int parse_command_line(int argc, char* argv[]) {
case 'd':
deleverage_stacks++;
break;
- case 'r':
- remove_rep_stacks++;
+ case 1000: // keep_high_cov
+ remove_rep_stacks = false;
break;
case 'K':
max_subgraph = is_integer(optarg);
@@ -2681,13 +2571,14 @@ int parse_command_line(int argc, char* argv[]) {
if (strcmp(optarg, "snp") == 0) {
model_type = snp;
} else if (strcmp(optarg, "fixed") == 0) {
- model_type = fixed;
+ model_type = ::fixed;
} else if (strcmp(optarg, "bounded") == 0) {
model_type = bounded;
} else {
cerr << "Unknown model type specified '" << optarg << "'\n";
help();
}
+ break;;
case 'e':
barcode_err_freq = is_double(optarg);
break;
@@ -2709,6 +2600,9 @@ int parse_command_line(int argc, char* argv[]) {
case 'v':
version();
break;
+ case 'r': // deprecated Dec 2016, v1.45
+ cerr << "Warning: Ignoring deprecated option -r (this has become the default).\n";
+ break;
case '?':
// getopt_long already printed an error message.
help();
@@ -2721,6 +2615,11 @@ int parse_command_line(int argc, char* argv[]) {
}
}
+ if (optind < argc) {
+ cerr << "Error: Failed to parse command line: '" << argv[optind] << "' is seen as a positional argument. Expected no positional arguments.\n";
+ help();
+ }
+
if (set_kmer_len == false && (kmer_len < 5 || kmer_len > 31)) {
cerr << "Kmer length must be between 5 and 31bp.\n";
help();
@@ -2745,8 +2644,21 @@ int parse_command_line(int argc, char* argv[]) {
model_type = bounded;
}
- if (in_file.length() == 0 || in_file_type == FileT::unknown) {
- cerr << "You must specify an input file of a supported type.\n";
+ if (in_file.empty()) {
+ cerr << "You must specify an input file.\n";
+ help();
+ }
+
+ if (in_file_type == FileT::unknown) {
+ in_file_type = guess_file_type(in_file);
+ if (in_file_type == FileT::unknown) {
+ cerr << "Unable to recongnize the extention of file '" << in_file << "'.\n";
+ help();
+ }
+ }
+
+ if (sql_id < 0) {
+ cerr << "A sample ID must be provided.\n";
help();
}
@@ -2756,7 +2668,7 @@ int parse_command_line(int argc, char* argv[]) {
if (out_path.at(out_path.length() - 1) != '/')
out_path += "/";
- if (model_type == fixed && barcode_err_freq == 0) {
+ if (model_type == ::fixed && barcode_err_freq == 0) {
cerr << "You must specify the barcode error frequency.\n";
help();
}
@@ -2765,28 +2677,28 @@ int parse_command_line(int argc, char* argv[]) {
}
void version() {
- std::cerr << "ustacks " << VERSION << "\n\n";
+ cerr << "ustacks " << VERSION << "\n\n";
exit(0);
}
void help() {
- std::cerr << "ustacks " << VERSION << "\n"
- << "ustacks -t file_type -f file_path [-d] [-r] [-o path] [-i id] [-m min_cov] [-M max_dist] [-p num_threads] [-R] [-H] [-h]" << "\n"
- << " t: input file Type. Supported types: fasta, fastq, gzfasta, or gzfastq.\n"
+ cerr << "ustacks " << VERSION << "\n"
+ << "ustacks -f file_path -i id -o path [-M max_dist] [-m min_cov] [-p num_threads]" << "\n"
<< " f: input file path.\n"
+ << " i: a unique integer ID for this sample.\n"
<< " o: output path to write results.\n"
- << " i: SQL ID to insert into the output to identify this sample.\n"
- << " m: Minimum depth of coverage required to create a stack (default 3).\n"
<< " M: Maximum distance (in nucleotides) allowed between stacks (default 2).\n"
+ << " m: Minimum depth of coverage required to create a stack (default 3).\n"
<< " N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2).\n"
+ << " p: enable parallel execution with num_threads threads.\n"
+ << " t: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess).\n"
<< " R: retain unused reads.\n"
<< " H: disable calling haplotypes from secondary reads.\n"
- << " p: enable parallel execution with num_threads threads.\n"
- << " h: display this help messsage.\n\n"
+ << "\n"
<< " Stack assembly options:\n"
- << " r: enable the Removal algorithm, to drop highly-repetitive stacks (and nearby errors) from the algorithm.\n"
- << " d: enable the Deleveraging algorithm, used for resolving over merged tags.\n"
+ << " d,--deleverage: enable the Deleveraging algorithm, used for resolving over merged tags.\n"
+ << " --keep_high_cov: disable the algorithm that removes highly-repetitive stacks and nearby errors.\n"
<< " --max_locus_stacks <num>: maximum number of stacks at a single de novo locus (default 3).\n"
<< " --k_len <len>: specify k-mer size for matching between alleles and loci (automatically calculated by default).\n\n"
<< " Gapped assembly options:\n"
@@ -2801,7 +2713,9 @@ void help() {
<< " --bound_low <num>: lower bound for epsilon, the error rate, between 0 and 1.0 (default 0).\n"
<< " --bound_high <num>: upper bound for epsilon, the error rate, between 0 and 1.0 (default 1).\n"
<< " For the Fixed model:\n"
- << " --bc_err_freq <num>: specify the barcode error frequency, between 0 and 1.0.\n";
+ << " --bc_err_freq <num>: specify the barcode error frequency, between 0 and 1.0.\n"
+ << "\n"
+ << " h: display this help messsage.\n";
exit(0);
}
diff --git a/src/ustacks.h b/src/ustacks.h
index 8d8d003..d3c485d 100644
--- a/src/ustacks.h
+++ b/src/ustacks.h
@@ -130,9 +130,7 @@ bool rank_alignments(Aln, Aln);
//
// Calculate depth of coverage statistics for stacks
//
-int calc_coverage_distribution(map<int, Stack *> &, double &, double &, double &);
-int calc_coverage_distribution(map<int, Stack *> &, map<int, MergedStack *> &, double &, double &, double &);
-int calc_coverage_distribution(map<int, Stack *> &, map<int, Rem *> &, map<int, MergedStack *> &, double &, double &, double &);
+void calc_coverage_distribution(map<int, Stack *> &, map<int, Rem *> &, map<int, MergedStack *> &, double &, double &, double &);
int count_raw_reads(map<int, Stack *> &, map<int, Rem *> &, map<int, MergedStack *> &);
//
diff --git a/src/utils.cc b/src/utils.cc
index 975ab41..d84c849 100644
--- a/src/utils.cc
+++ b/src/utils.cc
@@ -27,6 +27,8 @@
//
#include "utils.h"
+using namespace std;
+
char reverse(char c) {
switch (c) {
case 'A':
@@ -59,12 +61,44 @@ char reverse(char c) {
return 'N';
}
+string
+rev_comp(const string& seq)
+{
+ string s;
+ s.reserve(seq.length());
+ for (char c: seq) {
+ switch (c) {
+ case 'A':
+ case 'a':
+ s.push_back('T');
+ break;
+ case 'C':
+ case 'c':
+ s.push_back('G');
+ break;
+ case 'G':
+ case 'g':
+ s.push_back('C');
+ break;
+ case 'T':
+ case 't':
+ s.push_back('A');
+ break;
+ default:
+ s.push_back('N');
+ break;
+ }
+ }
+
+ return s;
+}
+
char *
rev_comp(const char *seq)
{
int len = strlen(seq);
int j = 0;
- char *com = new char[len + 1];
+ char *com = new char[len + 1]; // *** new
const char *p;
for (p = seq + len - 1; p >= seq; p--) {
diff --git a/src/utils.h b/src/utils.h
index 7bcda89..c538c9e 100644
--- a/src/utils.h
+++ b/src/utils.h
@@ -31,11 +31,16 @@ using std::endl;
#include <utility>
using std::pair;
using std::make_pair;
+#include <string>
+using std::string;
+
+#include <dirent.h>
#include "stacks.h"
char reverse(char);
char *rev_comp(const char *);
+string rev_comp(const string&);
void reverse_string(char *);
int is_integer(const char *);
double is_double(const char *);
@@ -72,4 +77,29 @@ struct int_decreasing {
}
};
+//
+// Wrapper for directory parsing functions.
+// e.g. for(DirIterator e (path); e; ++e) {...}
+//
+class DirIterator {
+ DIR* dir;
+ struct dirent* entry;
+public:
+ DirIterator(const std::string& dir_path) : dir(NULL), entry(NULL) {
+ dir = opendir(dir_path.c_str());
+ if (dir == NULL) {
+ cerr << "Error: Unable to open directory '" << dir_path << "' for reading.\n";
+ throw std::exception();
+ }
+ entry = readdir(dir);
+ }
+ ~DirIterator() {closedir(dir);}
+
+ const char* name() const {return entry->d_name;}
+
+ operator bool() const {return entry!=NULL;}
+ DirIterator& operator++() {entry = readdir(dir); return *this;}
+ dirent* operator*() {return entry;}
+};
+
#endif // __UTILS_H__
--
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