[med-svn] [idba] 01/04: Imported Upstream version 1.1.3
Andreas Tille
tille at debian.org
Fri Aug 5 22:19:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository idba.
commit 1c629cacdf8f935113a3c2042dc38654255710ce
Author: Andreas Tille <tille at debian.org>
Date: Sat Aug 6 00:09:06 2016 +0200
Imported Upstream version 1.1.3
---
Makefile.in | 323 ++++++++------
README | 77 ----
aclocal.m4 | 686 +++++++++++++++++++-----------
bin/Makefile.in | 784 ++++++++++++++++++++--------------
compile | 347 +++++++++++++++
configure | 654 +++++++++++++++++-----------
configure.ac | 4 +-
lib/Makefile.in | 590 +++++++++++++++-----------
script/Makefile.in | 110 ++++-
src/graph/contig_graph.cpp | 11 +-
src/graph/contig_graph.h | 5 +-
src/graph/hash_graph.h | 7 +-
src/misc/log.cpp | 7 +-
src/release/filterfa.cpp | 2 +-
src/release/idba_tran.cpp | 7 +-
src/sequence/sequence_reader.cpp | 4 +-
src/sequence/sequence_writer.cpp | 4 +-
test-driver | 139 ++++++
test/Makefile.am | 3 +-
test/Makefile.in | 894 +++++++++++++++++++++++++++++++--------
20 files changed, 3175 insertions(+), 1483 deletions(-)
diff --git a/Makefile.in b/Makefile.in
index ec7434f..2a78abb 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.11.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 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.
@@ -15,6 +14,51 @@
@SET_MAKE@
VPATH = @srcdir@
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
+ case $$MAKEFLAGS in \
+ *\\[\ \ ]*) \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
+ esac; \
+ done; \
+ test $$has_opt = yes
+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@
@@ -32,9 +76,9 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = .
-DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
- $(srcdir)/Makefile.in $(srcdir)/config.h.in \
- $(top_srcdir)/configure AUTHORS ChangeLog NEWS depcomp \
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+ $(top_srcdir)/configure $(am__configure_deps) \
+ $(srcdir)/config.h.in AUTHORS ChangeLog NEWS compile depcomp \
install-sh missing
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
@@ -46,22 +90,62 @@ mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
+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 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
SOURCES =
DIST_SOURCES =
-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
+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_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
distclean-recursive maintainer-clean-recursive
-AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
- $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
- distdir dist dist-all distcheck
+am__recursive_targets = \
+ $(RECURSIVE_TARGETS) \
+ $(RECURSIVE_CLEAN_TARGETS) \
+ $(am__extra_recursive_targets)
+AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
+ cscope 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,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
+CSCOPE = cscope
DIST_SUBDIRS = $(SUBDIRS)
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
distdir = $(PACKAGE)-$(VERSION)
@@ -72,6 +156,7 @@ am__remove_distdir = \
&& rm -rf "$(distdir)" \
|| { sleep 5 && rm -rf "$(distdir)"; }; \
else :; fi
+am__post_remove_distdir = $(am__remove_distdir)
am__relativize = \
dir0=`pwd`; \
sed_first='s,^\([^/]*\)/.*$$,\1,'; \
@@ -99,12 +184,14 @@ am__relativize = \
reldir="$$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$$'
distcleancheck_listfiles = find . -type f -print
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -236,8 +323,8 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
config.h: stamp-h1
- @if test ! -f $@; then rm -f stamp-h1; else :; fi
- @if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi
+ @test -f $@ || rm -f stamp-h1
+ @test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1
stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
@rm -f stamp-h1
@@ -251,22 +338,25 @@ distclean-hdr:
-rm -f config.h stamp-h1
# This directory's subdirectories are mostly independent; you can cd
-# into them and run `make' without going through this Makefile.
-# To change the values of `make' variables: instead of editing Makefiles,
-# (1) if the variable is set in `config.status', edit `config.status'
-# (which will cause the Makefiles to be regenerated when you run `make');
-# (2) otherwise, pass the desired values on the `make' command line.
-$(RECURSIVE_TARGETS):
- @fail= failcom='exit 1'; \
- for f in x $$MAKEFLAGS; do \
- case $$f in \
- *=* | --[!k]*);; \
- *k*) failcom='fail=yes';; \
- esac; \
- done; \
+# into them and run 'make' without going through this Makefile.
+# To change the values of 'make' variables: instead of editing Makefiles,
+# (1) if the variable is set in 'config.status', edit 'config.status'
+# (which will cause the Makefiles to be regenerated when you run 'make');
+# (2) otherwise, pass the desired values on the 'make' command line.
+$(am__recursive_targets):
+ @fail=; \
+ if $(am__make_keepgoing); then \
+ failcom='fail=yes'; \
+ else \
+ failcom='exit 1'; \
+ fi; \
dot_seen=no; \
target=`echo $@ | sed s/-recursive//`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
+ case "$@" in \
+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
+ *) list='$(SUBDIRS)' ;; \
+ esac; \
+ for subdir in $$list; do \
echo "Making $$target in $$subdir"; \
if test "$$subdir" = "."; then \
dot_seen=yes; \
@@ -281,57 +371,12 @@ $(RECURSIVE_TARGETS):
$(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
fi; test -z "$$fail"
-$(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 "$$fail"
-tags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
- test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
- done
-ctags-recursive:
- list='$(SUBDIRS)'; for subdir in $$list; do \
- test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
- done
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-recursive
+TAGS: tags
-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)
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
@@ -347,12 +392,7 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
fi; \
done; \
- 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[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -364,15 +404,11 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-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[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-recursive
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -381,9 +417,31 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscope: cscope.files
+ test ! -s cscope.files \
+ || $(CSCOPE) -b -q $(AM_CSCOPEFLAGS) $(CSCOPEFLAGS) -i cscope.files $(CSCOPE_ARGS)
+clean-cscope:
+ -rm -f cscope.files
+cscope.files: clean-cscope cscopelist
+cscopelist: cscopelist-recursive
+
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
+ case "$(srcdir)" in \
+ [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
+ *) sdir=$(subdir)/$(srcdir) ;; \
+ esac; \
+ for i in $$list; do \
+ if test -f "$$i"; then \
+ echo "$(subdir)/$$i"; \
+ else \
+ echo "$$sdir/$$i"; \
+ fi; \
+ done >> $(top_builddir)/cscope.files
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+ -rm -f cscope.out cscope.in.out cscope.po.out cscope.files
distdir: $(DISTFILES)
$(am__remove_distdir)
@@ -419,13 +477,10 @@ distdir: $(DISTFILES)
done
@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
if test "$$subdir" = .; then :; else \
- test -d "$(distdir)/$$subdir" \
- || $(MKDIR_P) "$(distdir)/$$subdir" \
- || exit 1; \
- fi; \
- done
- @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
- if test "$$subdir" = .; then :; else \
+ $(am__make_dryrun) \
+ || test -d "$(distdir)/$$subdir" \
+ || $(MKDIR_P) "$(distdir)/$$subdir" \
+ || exit 1; \
dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
$(am__relativize); \
new_distdir=$$reldir; \
@@ -454,40 +509,42 @@ distdir: $(DISTFILES)
|| chmod -R a+r "$(distdir)"
dist-gzip: distdir
tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
- $(am__remove_distdir)
+ $(am__post_remove_distdir)
dist-bzip2: distdir
tardir=$(distdir) && $(am__tar) | BZIP2=$${BZIP2--9} bzip2 -c >$(distdir).tar.bz2
- $(am__remove_distdir)
+ $(am__post_remove_distdir)
dist-lzip: distdir
tardir=$(distdir) && $(am__tar) | lzip -c $${LZIP_OPT--9} >$(distdir).tar.lz
- $(am__remove_distdir)
-
-dist-lzma: distdir
- tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
- $(am__remove_distdir)
+ $(am__post_remove_distdir)
dist-xz: distdir
tardir=$(distdir) && $(am__tar) | XZ_OPT=$${XZ_OPT--e} xz -c >$(distdir).tar.xz
- $(am__remove_distdir)
+ $(am__post_remove_distdir)
dist-tarZ: distdir
+ @echo WARNING: "Support for shar distribution archives is" \
+ "deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
- $(am__remove_distdir)
+ $(am__post_remove_distdir)
dist-shar: distdir
+ @echo WARNING: "Support for distribution archives compressed with" \
+ "legacy program 'compress' is deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
- $(am__remove_distdir)
+ $(am__post_remove_distdir)
dist-zip: distdir
-rm -f $(distdir).zip
zip -rq $(distdir).zip $(distdir)
- $(am__remove_distdir)
+ $(am__post_remove_distdir)
-dist dist-all: distdir
- tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
- $(am__remove_distdir)
+dist dist-all:
+ $(MAKE) $(AM_MAKEFLAGS) $(DIST_TARGETS) am__post_remove_distdir='@:'
+ $(am__post_remove_distdir)
# This target untars the dist file and tries a VPATH configuration. Then
# it guarantees that the distribution is self-contained by making another
@@ -498,8 +555,6 @@ distcheck: dist
GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
*.tar.bz2*) \
bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
- *.tar.lzma*) \
- lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
*.tar.lz*) \
lzip -dc $(distdir).tar.lz | $(am__untar) ;;\
*.tar.xz*) \
@@ -511,18 +566,19 @@ distcheck: dist
*.zip*) \
unzip $(distdir).zip ;;\
esac
- chmod -R a-w $(distdir); chmod a+w $(distdir)
- mkdir $(distdir)/_build
- mkdir $(distdir)/_inst
+ chmod -R a-w $(distdir)
+ chmod u+w $(distdir)
+ mkdir $(distdir)/_build $(distdir)/_inst
chmod a-w $(distdir)
test -d $(distdir)/_build || exit 0; \
dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
&& dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
&& am__cwd=`pwd` \
&& $(am__cd) $(distdir)/_build \
- && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+ && ../configure \
$(AM_DISTCHECK_CONFIGURE_FLAGS) \
$(DISTCHECK_CONFIGURE_FLAGS) \
+ --srcdir=.. --prefix="$$dc_install_base" \
&& $(MAKE) $(AM_MAKEFLAGS) \
&& $(MAKE) $(AM_MAKEFLAGS) dvi \
&& $(MAKE) $(AM_MAKEFLAGS) check \
@@ -545,7 +601,7 @@ distcheck: dist
&& $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
&& cd "$$am__cwd" \
|| exit 1
- $(am__remove_distdir)
+ $(am__post_remove_distdir)
@(echo "$(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'
@@ -679,13 +735,12 @@ ps-am:
uninstall-am:
-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
- ctags-recursive install-am install-strip tags-recursive
+.MAKE: $(am__recursive_targets) all install-am install-strip
-.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
- all all-am am--refresh check check-am clean clean-generic \
- ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \
- dist-lzip dist-lzma dist-shar dist-tarZ dist-xz dist-zip \
+.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
+ am--refresh check check-am clean clean-cscope clean-generic \
+ cscope cscopelist-am ctags ctags-am dist dist-all dist-bzip2 \
+ dist-gzip dist-lzip dist-shar dist-tarZ dist-xz dist-zip \
distcheck distclean distclean-generic distclean-hdr \
distclean-tags distcleancheck distdir distuninstallcheck dvi \
dvi-am html html-am info info-am install install-am \
@@ -695,8 +750,8 @@ uninstall-am:
install-pdf-am install-ps install-ps-am install-strip \
installcheck installcheck-am installdirs installdirs-am \
maintainer-clean maintainer-clean-generic mostlyclean \
- mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \
- uninstall uninstall-am
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
+ uninstall-am
scan:
diff --git a/README b/README
deleted file mode 100644
index 8355b44..0000000
--- a/README
+++ /dev/null
@@ -1,77 +0,0 @@
-###############################################################################
-Copyright (C) 2009 Yu Peng (ypeng at cs.hku.hk)
-
-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
-of the License, 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, write to the Free Software
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-Yu Peng (ypeng at cs.hku.hk)
-Dept. of Computer Science,
-The University of Hong Kong,
-Pokfulam Road,
-Hong Kong,
-China
-###############################################################################
-
-Requirement
-
-This software is suitable for all unix-like system with gcc installed.
-
-
-Installation Guide
-
-Exract the package, then use make to compile the source code.
-$ ./configure
-$ make
-
-
-Introduction
-
-IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads.
-IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth
-regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a
-generic purpose assembler and epspacially good for single-cell and metagenomic sequencing data.
-IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference
-genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for
-RNA-Seq data.
-
-The basic IDBA is included for comparison, you should use more specific assemblers for your data.
-If you are assembling genomic data without reference, please use IDBA-UD.
-If you are assembling genomic data with a similar reference genome, please use IDBA-Hybrid.
-If you are assembling transcriptome data, please use IDBA-Tran.
-
-
-Comments
-
-Note that IDBA assemblers are designed for short reads (around 100bp). If you want to assemble
-paired-end reads with longer read length, please modify the constant kMaxShortSequence in
-src/sequence/short_sequence.h to support longer read length.
-
-Please find the manual by running the assembler without any parameters. For example:
-$ bin/idba
-
-IDBA series assemblers accept fasta format reads. Fastq format reads can be converted by
-fq2fa program in the packcage.
-$ bin/fq2fa read.fq read.fa
-
-IDBA-UD IDBA-Hybrid and IDBA-Tran require paired-end reads stored in single FastA file and a pair of
-reads is in consecutive two lines. If not, please use fq2fa to merge two
-FastQ read files to single file.
-$ bin/fq2fa --merge --filter read_1.fq read_2.fq read.fa
-or convert a FastQ read file to FastA file.
-$ bin/fq2fa --paired --filter read.fq read.fa
-
-The this tools assume the paired-end reads are in order (->, <-). If your data is in order (<-, ->),
-please convert it by yourself.
-
-
diff --git a/aclocal.m4 b/aclocal.m4
index da06da5..3a9a040 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,8 +1,7 @@
-# generated automatically by aclocal 1.11.3 -*- Autoconf -*-
+# generated automatically by aclocal 1.14.1 -*- Autoconf -*-
+
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
-# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2007, 2008, 2009, 2010, 2011 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.
@@ -12,33 +11,31 @@
# 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]), [2.68],,
-[m4_warning([this file was generated for autoconf 2.68.
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.69],,
+[m4_warning([this file was generated for autoconf 2.69.
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, 2003, 2005, 2006, 2007, 2008, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 2002-2013 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 1
-
# AM_AUTOMAKE_VERSION(VERSION)
# ----------------------------
# Automake X.Y traces this macro to ensure aclocal.m4 has been
# 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='1.11'
+[am__api_version='1.14'
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], [1.11.3], [],
+m4_if([$1], [1.14.1], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -54,24 +51,22 @@ 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([1.11.3])dnl
+[AM_AUTOMAKE_VERSION([1.14.1])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, 2003, 2005, 2011 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 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 1
-
# 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
@@ -90,7 +85,7 @@ _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,
@@ -116,22 +111,19 @@ am_aux_dir=`cd $ac_aux_dir && pwd`
# AM_CONDITIONAL -*- Autoconf -*-
-# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 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
- ifelse([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])],
- [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
+[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_SUBST([$1_TRUE])dnl
AC_SUBST([$1_FALSE])dnl
_AM_SUBST_NOTMAKE([$1_TRUE])dnl
@@ -150,16 +142,14 @@ AC_CONFIG_COMMANDS_PRE(
Usually this means the macro was only invoked conditionally.]])
fi])])
-# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009,
-# 2010, 2011 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 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 12
-# 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
@@ -169,7 +159,7 @@ fi])])
# _AM_DEPENDENCIES(NAME)
# ----------------------
# See how the compiler implements dependency checking.
-# NAME is "CC", "CXX", "GCJ", or "OBJC".
+# NAME is "CC", "CXX", "OBJC", "OBJCXX", "UPC", or "GJC".
# 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
@@ -182,12 +172,13 @@ AC_REQUIRE([AM_OUTPUT_DEPENDENCY_COMMANDS])dnl
AC_REQUIRE([AM_MAKE_INCLUDE])dnl
AC_REQUIRE([AM_DEP_TRACK])dnl
-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="$$1" am_compiler_list=])
+m4_if([$1], [CC], [depcc="$CC" am_compiler_list=],
+ [$1], [CXX], [depcc="$CXX" am_compiler_list=],
+ [$1], [OBJC], [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
+ [$1], [OBJCXX], [depcc="$OBJCXX" am_compiler_list='gcc3 gcc'],
+ [$1], [UPC], [depcc="$UPC" am_compiler_list=],
+ [$1], [GCJ], [depcc="$GCJ" am_compiler_list='gcc3 gcc'],
+ [depcc="$$1" am_compiler_list=])
AC_CACHE_CHECK([dependency style of $depcc],
[am_cv_$1_dependencies_compiler_type],
@@ -195,8 +186,8 @@ 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'.
+ # making a dummy file named 'D' -- because '-MD' means "put the output
+ # in D".
rm -rf conftest.dir
mkdir conftest.dir
# Copy depcomp to subdir because otherwise we won't find it if we're
@@ -236,16 +227,16 @@ 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$i.h' creates only sub/conftst1.h with
- # Solaris 8's {/usr,}/bin/sh.
- touch sub/conftst$i.h
+ # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
+ # Solaris 10 /bin/sh.
+ echo '/* dummy */' > sub/conftst$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
@@ -254,8 +245,8 @@ 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
@@ -263,7 +254,7 @@ AC_CACHE_CHECK([dependency style of $depcc],
fi
;;
msvc7 | msvc7msys | msvisualcpp | msvcmsys)
- # This compiler won't grok `-c -o', but also, the minuso test has
+ # This compiler won't grok '-c -o', but also, the minuso test has
# not run yet. These depmodes are late enough in the game, and
# so weak that their functioning should not be impacted.
am__obj=conftest.${OBJEXT-o}
@@ -311,7 +302,7 @@ 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
@@ -321,9 +312,13 @@ AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
# AM_DEP_TRACK
# ------------
AC_DEFUN([AM_DEP_TRACK],
-[AC_ARG_ENABLE(dependency-tracking,
-[ --disable-dependency-tracking speeds up one-time build
- --enable-dependency-tracking do not reject slow dependency extractors])
+[AC_ARG_ENABLE([dependency-tracking], [dnl
+AS_HELP_STRING(
+ [--enable-dependency-tracking],
+ [do not reject slow dependency extractors])
+AS_HELP_STRING(
+ [--disable-dependency-tracking],
+ [speeds up one-time build])])
if test "x$enable_dependency_tracking" != xno; then
am_depcomp="$ac_aux_dir/depcomp"
AMDEPBACKSLASH='\'
@@ -338,20 +333,18 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
# Generate code to set up dependency tracking. -*- Autoconf -*-
-# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 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],
[{
- # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # Older Autoconf 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 $CONFIG_FILES in
@@ -364,7 +357,7 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
# Strip MF so we end up with the name of the file.
mf=`echo "$mf" | sed -e 's/:.*$//'`
# Check whether this is an Automake generated Makefile or not.
- # We used to match only the files named `Makefile.in', but
+ # We used to match only the files named 'Makefile.in', but
# some people rename them; so instead we look at the file content.
# Grep'ing the first line is not enough: some people post-process
# each Makefile.in and add a new line on top of each file to say so.
@@ -376,21 +369,19 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
continue
fi
# Extract the definition of DEPDIR, am__include, and am__quote
- # from the Makefile without running `make'.
+ # from the Makefile without running 'make'.
DEPDIR=`sed -n 's/^DEPDIR = //p' < "$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' -e 's/\$U/'"$U"'/g'`; do
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
# Make sure the directory exists.
test -f "$dirpart/$file" && continue
fdir=`AS_DIRNAME(["$file"])`
@@ -408,7 +399,7 @@ AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
# This macro should only be invoked once -- use via AC_REQUIRE.
#
# This code is only required when automatic dependency tracking
-# is enabled. FIXME. This creates each `.P' file that we will
+# is enabled. FIXME. This creates each '.P' file that we will
# need in order to bootstrap the dependency handling code.
AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
[AC_CONFIG_COMMANDS([depfiles],
@@ -418,18 +409,21 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# Do all the work for Automake. -*- Autoconf -*-
-# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2008, 2009 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 16
-
# This macro actually does too much. Some checks are only needed if
# your package does certain things. But this isn't really a big deal.
+dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.
+m4_define([AC_PROG_CC],
+m4_defn([AC_PROG_CC])
+[_AM_PROG_CC_C_O
+])
+
# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
# AM_INIT_AUTOMAKE([OPTIONS])
# -----------------------------------------------
@@ -442,7 +436,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# arguments mandatory, and then we can depend on a new Autoconf
# release and drop the old call support.
AC_DEFUN([AM_INIT_AUTOMAKE],
-[AC_PREREQ([2.62])dnl
+[AC_PREREQ([2.65])dnl
dnl Autoconf wants to disallow AM_ names. We explicitly allow
dnl the ones we care about.
m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
@@ -471,31 +465,40 @@ AC_SUBST([CYGPATH_W])
# Define the identity of the package.
dnl Distinguish between old-style and new-style calls.
m4_ifval([$2],
-[m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
+[AC_DIAGNOSE([obsolete],
+ [$0: two- and three-arguments forms are deprecated.])
+m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
AC_SUBST([PACKAGE], [$1])dnl
AC_SUBST([VERSION], [$2])],
[_AM_SET_OPTIONS([$1])dnl
dnl Diagnose old-style AC_INIT with new-style AM_AUTOMAKE_INIT.
-m4_if(m4_ifdef([AC_PACKAGE_NAME], 1)m4_ifdef([AC_PACKAGE_VERSION], 1), 11,,
+m4_if(
+ m4_ifdef([AC_PACKAGE_NAME], [ok]):m4_ifdef([AC_PACKAGE_VERSION], [ok]),
+ [ok:ok],,
[m4_fatal([AC_INIT should be called with package and version arguments])])dnl
AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl
AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl
_AM_IF_OPTION([no-define],,
-[AC_DEFINE_UNQUOTED(PACKAGE, "$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-${am__api_version}])
+AM_MISSING_PROG([AUTOHEADER], [autoheader])
+AM_MISSING_PROG([MAKEINFO], [makeinfo])
AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
-AC_REQUIRE([AM_PROG_MKDIR_P])dnl
+AC_REQUIRE([AC_PROG_MKDIR_P])dnl
+# For better backward compatibility. To be removed once Automake 1.9.x
+# dies out for good. For more background, see:
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
AC_REQUIRE([AC_PROG_AWK])dnl
@@ -506,34 +509,78 @@ _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)],
- [define([AC_PROG_CC],
- defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl
+ [_AM_DEPENDENCIES([CC])],
+ [m4_define([AC_PROG_CC],
+ m4_defn([AC_PROG_CC])[_AM_DEPENDENCIES([CC])])])dnl
AC_PROVIDE_IFELSE([AC_PROG_CXX],
- [_AM_DEPENDENCIES(CXX)],
- [define([AC_PROG_CXX],
- defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
+ [_AM_DEPENDENCIES([CXX])],
+ [m4_define([AC_PROG_CXX],
+ m4_defn([AC_PROG_CXX])[_AM_DEPENDENCIES([CXX])])])dnl
AC_PROVIDE_IFELSE([AC_PROG_OBJC],
- [_AM_DEPENDENCIES(OBJC)],
- [define([AC_PROG_OBJC],
- defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl
+ [_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_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_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.
AC_CONFIG_COMMANDS_PRE(dnl
[m4_provide_if([_AM_COMPILER_EXEEXT],
[AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
-])
-dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
+# 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 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.
@@ -555,15 +602,12 @@ 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, 2003, 2005, 2008, 2011 Free Software Foundation,
-# Inc.
+# Copyright (C) 2001-2013 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 1
-
# AM_PROG_INSTALL_SH
# ------------------
# Define $install_sh.
@@ -577,16 +621,14 @@ if test x"${install_sh}" != xset; then
install_sh="\${SHELL} $am_aux_dir/install-sh"
esac
fi
-AC_SUBST(install_sh)])
+AC_SUBST([install_sh])])
-# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
+# Copyright (C) 2003-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 2
-
# Check whether the underlying file-system supports filenames
# with a leading dot. For instance MS-DOS doesn't.
AC_DEFUN([AM_SET_LEADING_DOT],
@@ -602,14 +644,12 @@ AC_SUBST([am__leading_dot])])
# Check to see how 'make' treats includes. -*- Autoconf -*-
-# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 4
-
# AM_MAKE_INCLUDE()
# -----------------
# Check to see how make treats includes.
@@ -627,7 +667,7 @@ am__quote=
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
-# Ignore all kinds of additional output from `make'.
+# Ignore all kinds of additional output from 'make'.
case `$am_make -s -f confmf 2> /dev/null` in #(
*the\ am__doit\ target*)
am__include=include
@@ -654,15 +694,12 @@ rm -f confinc confmf
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
-# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 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],
@@ -670,11 +707,10 @@ AC_DEFUN([AM_MISSING_PROG],
$1=${$1-"${am_missing_run}$2"}
AC_SUBST($1)])
-
# AM_MISSING_HAS_RUN
# ------------------
-# Define MISSING if not defined so far and test if it supports --run.
-# If it does, set am_missing_run to use it, otherwise, to nothing.
+# Define MISSING if not defined so far and test if it is modern enough.
+# If it is, set am_missing_run to use it, otherwise, to nothing.
AC_DEFUN([AM_MISSING_HAS_RUN],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
AC_REQUIRE_AUX_FILE([missing])dnl
@@ -687,54 +723,22 @@ if test x"${MISSING+set}" != xset; then
esac
fi
# Use eval to expand $SHELL
-if eval "$MISSING --run true"; then
- am_missing_run="$MISSING --run "
+if eval "$MISSING --is-lightweight"; then
+ am_missing_run="$MISSING "
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, 2011 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 1
-
-# 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, 2002, 2003, 2005, 2008, 2010 Free Software
-# Foundation, Inc.
+# Copyright (C) 2001-2013 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_MANGLE_OPTION(NAME)
# -----------------------
AC_DEFUN([_AM_MANGLE_OPTION],
@@ -744,7 +748,7 @@ AC_DEFUN([_AM_MANGLE_OPTION],
# --------------------
# 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)
# ------------------------
@@ -758,24 +762,82 @@ AC_DEFUN([_AM_SET_OPTIONS],
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
-# Check to make sure that the build environment is sane. -*- Autoconf -*-
+# Copyright (C) 1999-2013 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 $CC"
+fi
+AC_LANG_POP([C])])
+
+# For backward compatibility.
+AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
-# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 5
+# AM_RUN_LOG(COMMAND)
+# -------------------
+# Run COMMAND, save the exit status in ac_status, and log it.
+# (This has been adapted from Autoconf's _AC_RUN_LOG macro.)
+AC_DEFUN([AM_RUN_LOG],
+[{ echo "$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) 1996-2013 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_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='
@@ -786,32 +848,40 @@ 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 (
- 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
-
+ 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 $am_try -eq 2; then
+ break
+ fi
+ # Just in case.
+ sleep 1
+ am_has_slept=yes
+ done
test "$[2]" = conftest.file
)
then
@@ -821,46 +891,118 @@ else
AC_MSG_ERROR([newly created file is older than distributed files!
Check your system clock])
fi
-AC_MSG_RESULT(yes)])
+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) 2001, 2003, 2005, 2011 Free Software Foundation, Inc.
+# Copyright (C) 2009-2013 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 1
+# 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
+])
+
+# Copyright (C) 2001-2013 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_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, 2008, 2010 Free Software Foundation, Inc.
+# Copyright (C) 2006-2013 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 3
-
# _AM_SUBST_NOTMAKE(VARIABLE)
# ---------------------------
# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
@@ -874,18 +1016,16 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# Check how to create a tarball. -*- Autoconf -*-
-# Copyright (C) 2004, 2005, 2012 Free Software Foundation, Inc.
+# Copyright (C) 2004-2013 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 $(am__tar) that is a command
# writing to stdout a FORMAT-tarball containing the directory
@@ -895,76 +1035,114 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# 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], ['$${TAR-tar}'])
-m4_if([$1], [v7],
- [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} 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.
+
+# We'll 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 $1 -d'
- ;;
- none)
- am__tar=false
- am__tar_=false
- am__untar=false
- ;;
- esac
- # If the value was cached, stop now. We just wanted to have am__tar
- # and am__untar set.
- test -n "${am_cv_prog_tar_$1}" && break
+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
- # 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])
+ # 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
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/bin/Makefile.in b/bin/Makefile.in
index 9190167..003d43f 100644
--- a/bin/Makefile.in
+++ b/bin/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.11.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 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.
@@ -16,6 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
+ case $$MAKEFLAGS in \
+ *\\[\ \ ]*) \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
+ esac; \
+ done; \
+ test $$has_opt = yes
+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 = $(libdir)/@PACKAGE@
@@ -46,7 +90,8 @@ noinst_PROGRAMS = shuffle_reads$(EXEEXT) scaffold$(EXEEXT) \
sim_reads_tran$(EXEEXT) filterfa$(EXEEXT) idba$(EXEEXT) \
split_scaffold$(EXEEXT) sim_reads$(EXEEXT)
subdir = bin
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+ $(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -149,15 +194,39 @@ validate_reads_blat_LDADD = $(LDADD)
am_validate_rna_OBJECTS = validate_rna.$(OBJEXT)
validate_rna_OBJECTS = $(am_validate_rna_OBJECTS)
validate_rna_LDADD = $(LDADD)
+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 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/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 =
SOURCES = $(fa2fq_SOURCES) $(filter_blat_SOURCES) \
$(filter_contigs_SOURCES) $(filterfa_SOURCES) $(fq2fa_SOURCES) \
$(idba_SOURCES) $(idba_hybrid_SOURCES) $(idba_tran_SOURCES) \
@@ -186,11 +255,34 @@ DIST_SOURCES = $(fa2fq_SOURCES) $(filter_blat_SOURCES) \
$(validate_component_SOURCES) $(validate_contigs_blat_SOURCES) \
$(validate_contigs_mummer_SOURCES) \
$(validate_reads_blat_SOURCES) $(validate_rna_SOURCES)
+am__can_run_installinfo = \
+ case $$AM_UPDATE_INFO_DIR in \
+ n|no|NO) false;; \
+ *) (install-info --version) >/dev/null 2>&1;; \
+ esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -349,14 +441,18 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
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/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -377,7 +473,8 @@ uninstall-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$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
@@ -387,96 +484,126 @@ clean-binPROGRAMS:
clean-noinstPROGRAMS:
-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
+
fa2fq$(EXEEXT): $(fa2fq_OBJECTS) $(fa2fq_DEPENDENCIES) $(EXTRA_fa2fq_DEPENDENCIES)
@rm -f fa2fq$(EXEEXT)
- $(CXXLINK) $(fa2fq_OBJECTS) $(fa2fq_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(fa2fq_OBJECTS) $(fa2fq_LDADD) $(LIBS)
+
filter_blat$(EXEEXT): $(filter_blat_OBJECTS) $(filter_blat_DEPENDENCIES) $(EXTRA_filter_blat_DEPENDENCIES)
@rm -f filter_blat$(EXEEXT)
- $(CXXLINK) $(filter_blat_OBJECTS) $(filter_blat_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(filter_blat_OBJECTS) $(filter_blat_LDADD) $(LIBS)
+
filter_contigs$(EXEEXT): $(filter_contigs_OBJECTS) $(filter_contigs_DEPENDENCIES) $(EXTRA_filter_contigs_DEPENDENCIES)
@rm -f filter_contigs$(EXEEXT)
- $(CXXLINK) $(filter_contigs_OBJECTS) $(filter_contigs_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(filter_contigs_OBJECTS) $(filter_contigs_LDADD) $(LIBS)
+
filterfa$(EXEEXT): $(filterfa_OBJECTS) $(filterfa_DEPENDENCIES) $(EXTRA_filterfa_DEPENDENCIES)
@rm -f filterfa$(EXEEXT)
- $(CXXLINK) $(filterfa_OBJECTS) $(filterfa_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(filterfa_OBJECTS) $(filterfa_LDADD) $(LIBS)
+
fq2fa$(EXEEXT): $(fq2fa_OBJECTS) $(fq2fa_DEPENDENCIES) $(EXTRA_fq2fa_DEPENDENCIES)
@rm -f fq2fa$(EXEEXT)
- $(CXXLINK) $(fq2fa_OBJECTS) $(fq2fa_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(fq2fa_OBJECTS) $(fq2fa_LDADD) $(LIBS)
+
idba$(EXEEXT): $(idba_OBJECTS) $(idba_DEPENDENCIES) $(EXTRA_idba_DEPENDENCIES)
@rm -f idba$(EXEEXT)
- $(CXXLINK) $(idba_OBJECTS) $(idba_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(idba_OBJECTS) $(idba_LDADD) $(LIBS)
+
idba_hybrid$(EXEEXT): $(idba_hybrid_OBJECTS) $(idba_hybrid_DEPENDENCIES) $(EXTRA_idba_hybrid_DEPENDENCIES)
@rm -f idba_hybrid$(EXEEXT)
- $(CXXLINK) $(idba_hybrid_OBJECTS) $(idba_hybrid_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(idba_hybrid_OBJECTS) $(idba_hybrid_LDADD) $(LIBS)
+
idba_tran$(EXEEXT): $(idba_tran_OBJECTS) $(idba_tran_DEPENDENCIES) $(EXTRA_idba_tran_DEPENDENCIES)
@rm -f idba_tran$(EXEEXT)
- $(CXXLINK) $(idba_tran_OBJECTS) $(idba_tran_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(idba_tran_OBJECTS) $(idba_tran_LDADD) $(LIBS)
+
idba_tran_test$(EXEEXT): $(idba_tran_test_OBJECTS) $(idba_tran_test_DEPENDENCIES) $(EXTRA_idba_tran_test_DEPENDENCIES)
@rm -f idba_tran_test$(EXEEXT)
- $(CXXLINK) $(idba_tran_test_OBJECTS) $(idba_tran_test_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(idba_tran_test_OBJECTS) $(idba_tran_test_LDADD) $(LIBS)
+
idba_ud$(EXEEXT): $(idba_ud_OBJECTS) $(idba_ud_DEPENDENCIES) $(EXTRA_idba_ud_DEPENDENCIES)
@rm -f idba_ud$(EXEEXT)
- $(CXXLINK) $(idba_ud_OBJECTS) $(idba_ud_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(idba_ud_OBJECTS) $(idba_ud_LDADD) $(LIBS)
+
parallel_blat$(EXEEXT): $(parallel_blat_OBJECTS) $(parallel_blat_DEPENDENCIES) $(EXTRA_parallel_blat_DEPENDENCIES)
@rm -f parallel_blat$(EXEEXT)
- $(CXXLINK) $(parallel_blat_OBJECTS) $(parallel_blat_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(parallel_blat_OBJECTS) $(parallel_blat_LDADD) $(LIBS)
+
parallel_rna_blat$(EXEEXT): $(parallel_rna_blat_OBJECTS) $(parallel_rna_blat_DEPENDENCIES) $(EXTRA_parallel_rna_blat_DEPENDENCIES)
@rm -f parallel_rna_blat$(EXEEXT)
- $(CXXLINK) $(parallel_rna_blat_OBJECTS) $(parallel_rna_blat_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(parallel_rna_blat_OBJECTS) $(parallel_rna_blat_LDADD) $(LIBS)
+
print_graph$(EXEEXT): $(print_graph_OBJECTS) $(print_graph_DEPENDENCIES) $(EXTRA_print_graph_DEPENDENCIES)
@rm -f print_graph$(EXEEXT)
- $(CXXLINK) $(print_graph_OBJECTS) $(print_graph_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(print_graph_OBJECTS) $(print_graph_LDADD) $(LIBS)
+
raw_n50$(EXEEXT): $(raw_n50_OBJECTS) $(raw_n50_DEPENDENCIES) $(EXTRA_raw_n50_DEPENDENCIES)
@rm -f raw_n50$(EXEEXT)
- $(CXXLINK) $(raw_n50_OBJECTS) $(raw_n50_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(raw_n50_OBJECTS) $(raw_n50_LDADD) $(LIBS)
+
sample_reads$(EXEEXT): $(sample_reads_OBJECTS) $(sample_reads_DEPENDENCIES) $(EXTRA_sample_reads_DEPENDENCIES)
@rm -f sample_reads$(EXEEXT)
- $(CXXLINK) $(sample_reads_OBJECTS) $(sample_reads_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(sample_reads_OBJECTS) $(sample_reads_LDADD) $(LIBS)
+
scaffold$(EXEEXT): $(scaffold_OBJECTS) $(scaffold_DEPENDENCIES) $(EXTRA_scaffold_DEPENDENCIES)
@rm -f scaffold$(EXEEXT)
- $(CXXLINK) $(scaffold_OBJECTS) $(scaffold_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(scaffold_OBJECTS) $(scaffold_LDADD) $(LIBS)
+
shuffle_reads$(EXEEXT): $(shuffle_reads_OBJECTS) $(shuffle_reads_DEPENDENCIES) $(EXTRA_shuffle_reads_DEPENDENCIES)
@rm -f shuffle_reads$(EXEEXT)
- $(CXXLINK) $(shuffle_reads_OBJECTS) $(shuffle_reads_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(shuffle_reads_OBJECTS) $(shuffle_reads_LDADD) $(LIBS)
+
sim_reads$(EXEEXT): $(sim_reads_OBJECTS) $(sim_reads_DEPENDENCIES) $(EXTRA_sim_reads_DEPENDENCIES)
@rm -f sim_reads$(EXEEXT)
- $(CXXLINK) $(sim_reads_OBJECTS) $(sim_reads_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(sim_reads_OBJECTS) $(sim_reads_LDADD) $(LIBS)
+
sim_reads_tran$(EXEEXT): $(sim_reads_tran_OBJECTS) $(sim_reads_tran_DEPENDENCIES) $(EXTRA_sim_reads_tran_DEPENDENCIES)
@rm -f sim_reads_tran$(EXEEXT)
- $(CXXLINK) $(sim_reads_tran_OBJECTS) $(sim_reads_tran_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(sim_reads_tran_OBJECTS) $(sim_reads_tran_LDADD) $(LIBS)
+
sort_psl$(EXEEXT): $(sort_psl_OBJECTS) $(sort_psl_DEPENDENCIES) $(EXTRA_sort_psl_DEPENDENCIES)
@rm -f sort_psl$(EXEEXT)
- $(CXXLINK) $(sort_psl_OBJECTS) $(sort_psl_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(sort_psl_OBJECTS) $(sort_psl_LDADD) $(LIBS)
+
sort_reads$(EXEEXT): $(sort_reads_OBJECTS) $(sort_reads_DEPENDENCIES) $(EXTRA_sort_reads_DEPENDENCIES)
@rm -f sort_reads$(EXEEXT)
- $(CXXLINK) $(sort_reads_OBJECTS) $(sort_reads_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(sort_reads_OBJECTS) $(sort_reads_LDADD) $(LIBS)
+
split_fa$(EXEEXT): $(split_fa_OBJECTS) $(split_fa_DEPENDENCIES) $(EXTRA_split_fa_DEPENDENCIES)
@rm -f split_fa$(EXEEXT)
- $(CXXLINK) $(split_fa_OBJECTS) $(split_fa_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(split_fa_OBJECTS) $(split_fa_LDADD) $(LIBS)
+
split_fq$(EXEEXT): $(split_fq_OBJECTS) $(split_fq_DEPENDENCIES) $(EXTRA_split_fq_DEPENDENCIES)
@rm -f split_fq$(EXEEXT)
- $(CXXLINK) $(split_fq_OBJECTS) $(split_fq_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(split_fq_OBJECTS) $(split_fq_LDADD) $(LIBS)
+
split_scaffold$(EXEEXT): $(split_scaffold_OBJECTS) $(split_scaffold_DEPENDENCIES) $(EXTRA_split_scaffold_DEPENDENCIES)
@rm -f split_scaffold$(EXEEXT)
- $(CXXLINK) $(split_scaffold_OBJECTS) $(split_scaffold_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(split_scaffold_OBJECTS) $(split_scaffold_LDADD) $(LIBS)
+
test$(EXEEXT): $(test_OBJECTS) $(test_DEPENDENCIES) $(EXTRA_test_DEPENDENCIES)
@rm -f test$(EXEEXT)
- $(CXXLINK) $(test_OBJECTS) $(test_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(test_OBJECTS) $(test_LDADD) $(LIBS)
+
validate_component$(EXEEXT): $(validate_component_OBJECTS) $(validate_component_DEPENDENCIES) $(EXTRA_validate_component_DEPENDENCIES)
@rm -f validate_component$(EXEEXT)
- $(CXXLINK) $(validate_component_OBJECTS) $(validate_component_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(validate_component_OBJECTS) $(validate_component_LDADD) $(LIBS)
+
validate_contigs_blat$(EXEEXT): $(validate_contigs_blat_OBJECTS) $(validate_contigs_blat_DEPENDENCIES) $(EXTRA_validate_contigs_blat_DEPENDENCIES)
@rm -f validate_contigs_blat$(EXEEXT)
- $(CXXLINK) $(validate_contigs_blat_OBJECTS) $(validate_contigs_blat_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(validate_contigs_blat_OBJECTS) $(validate_contigs_blat_LDADD) $(LIBS)
+
validate_contigs_mummer$(EXEEXT): $(validate_contigs_mummer_OBJECTS) $(validate_contigs_mummer_DEPENDENCIES) $(EXTRA_validate_contigs_mummer_DEPENDENCIES)
@rm -f validate_contigs_mummer$(EXEEXT)
- $(CXXLINK) $(validate_contigs_mummer_OBJECTS) $(validate_contigs_mummer_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(validate_contigs_mummer_OBJECTS) $(validate_contigs_mummer_LDADD) $(LIBS)
+
validate_reads_blat$(EXEEXT): $(validate_reads_blat_OBJECTS) $(validate_reads_blat_DEPENDENCIES) $(EXTRA_validate_reads_blat_DEPENDENCIES)
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validate_reads_blat.o: $(top_srcdir)/src/tools/validate_reads_blat.cpp
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/tools/validate_reads_blat.cpp' object='validate_reads_blat.o' libtool=no @AMDEPBACKSLASH@
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-
-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 $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o validate_rna.obj `if test -f '$(top_srcdir)/src/tools/validate_rna.cpp'; then $(CYGPATH_W) '$(top_srcdir)/src/tools/validate_rna.cpp'; else $(CYGPATH_W) '$(srcdir)/$(top_srcdir)/src/tools/validate_rna.cpp'; fi`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(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[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -980,15 +1096,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(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[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -997,6 +1109,21 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
+
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
+ case "$(srcdir)" in \
+ [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
+ *) sdir=$(subdir)/$(srcdir) ;; \
+ esac; \
+ for i in $$list; do \
+ if test -f "$$i"; then \
+ echo "$(subdir)/$$i"; \
+ else \
+ echo "$$sdir/$$i"; \
+ fi; \
+ done >> $(top_builddir)/cscope.files
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
@@ -1140,18 +1267,19 @@ uninstall-am: uninstall-binPROGRAMS
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic clean-noinstPROGRAMS ctags distclean \
- distclean-compile distclean-generic distclean-tags distdir dvi \
- dvi-am html html-am info info-am install install-am \
- install-binPROGRAMS install-data install-data-am install-dvi \
- install-dvi-am install-exec install-exec-am install-html \
- install-html-am install-info install-info-am install-man \
- install-pdf install-pdf-am install-ps install-ps-am \
- install-strip installcheck installcheck-am installdirs \
- maintainer-clean maintainer-clean-generic mostlyclean \
- mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
- tags uninstall uninstall-am uninstall-binPROGRAMS
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic clean-noinstPROGRAMS \
+ cscopelist-am ctags ctags-am distclean distclean-compile \
+ distclean-generic distclean-tags distdir dvi dvi-am html \
+ html-am info info-am install install-am install-binPROGRAMS \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-compile \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
+ uninstall-am uninstall-binPROGRAMS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/compile b/compile
new file mode 100755
index 0000000..531136b
--- /dev/null
+++ b/compile
@@ -0,0 +1,347 @@
+#! /bin/sh
+# Wrapper for compilers which do not understand '-c -o'.
+
+scriptversion=2012-10-14.11; # UTC
+
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Written by Tom Tromey <tromey at cygnus.com>.
+#
+# 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>.
+
+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
+ 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
+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'.
+
+Report bugs to <bug-automake at gnu.org>.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "compile $scriptversion"
+ exit $?
+ ;;
+ cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
+ func_cl_wrapper "$@" # Doesn't return...
+ ;;
+esac
+
+ofile=
+cfile=
+
+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'.
+ # So we strip '-o arg' only if arg is an object.
+ eat=1
+ case $2 in
+ *.o | *.obj)
+ ofile=$2
+ ;;
+ *)
+ set x "$@" -o "$2"
+ shift
+ ;;
+ esac
+ ;;
+ *.c)
+ cfile=$1
+ set x "$@" "$1"
+ shift
+ ;;
+ *)
+ set x "$@" "$1"
+ shift
+ ;;
+ esac
+ fi
+ shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+ # If no '-o' option was seen then we might have been invoked from a
+ # pattern rule where we don't need one. That is ok -- this is a
+ # normal compilation that the losing compiler can handle. If no
+ # '.c' file was seen then we are probably linking. That is also
+ # ok.
+ exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+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
+# 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 "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
+while true; do
+ if mkdir "$lockdir" >/dev/null 2>&1; then
+ break
+ fi
+ sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+ test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+ test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/configure b/configure
index 95dff19..6d41564 100755
--- a/configure
+++ b/configure
@@ -1,13 +1,11 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68 for idba 1.1.2.
+# Generated by GNU Autoconf 2.69 for idba 1.1.3.
#
# Report bugs to <loneknightpy at gmail.com>.
#
#
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
-# Foundation, Inc.
+# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
#
#
# This configure script is free software; the Free Software Foundation
@@ -136,6 +134,31 @@ export LANGUAGE
# CDPATH.
(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+# Use a proper internal environment variable to ensure we don't fall
+ # into an infinite loop, continuously re-executing ourselves.
+ if test x"${_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
@@ -169,7 +192,8 @@ 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\$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'\" &&
@@ -214,21 +238,25 @@ IFS=$as_save_IFS
if test "x$CONFIG_SHELL" != x; then :
- # 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
- export CONFIG_SHELL
- 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" ${1+"$@"}
+ 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 :
@@ -331,6 +359,14 @@ $as_echo X"$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 "$1"
+} # as_fn_executable_p
# as_fn_append VAR VALUE
# ----------------------
# Append the text in VALUE to the end of the definition contained in VAR. Take
@@ -452,6 +488,10 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits
chmod +x "$as_me.lineno" ||
{ $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+ # If 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).
@@ -486,16 +526,16 @@ if (echo >conf$$.file) 2>/dev/null; then
# ... but there are two gotchas:
# 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
# 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
- # In both cases, we have to default to `cp -p'.
+ # In both cases, we have to default to `cp -pR'.
ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
elif ln conf$$.file conf$$ 2>/dev/null; then
as_ln_s=ln
else
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
fi
else
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null
@@ -507,28 +547,8 @@ else
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
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
# 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%[^_$as_cr_alnum]%_%g'"
@@ -560,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='idba'
PACKAGE_TARNAME='idba'
-PACKAGE_VERSION='1.1.2'
-PACKAGE_STRING='idba 1.1.2'
+PACKAGE_VERSION='1.1.3'
+PACKAGE_STRING='idba 1.1.3'
PACKAGE_BUGREPORT='loneknightpy at gmail.com'
PACKAGE_URL=''
@@ -633,6 +653,10 @@ CPPFLAGS
LDFLAGS
CXXFLAGS
CXX
+AM_BACKSLASH
+AM_DEFAULT_VERBOSITY
+AM_DEFAULT_V
+AM_V
am__untar
am__tar
AMTAR
@@ -697,6 +721,7 @@ SHELL'
ac_subst_files=''
ac_user_opts='
enable_option_checking
+enable_silent_rules
enable_dependency_tracking
'
ac_precious_vars='build_alias
@@ -1166,8 +1191,6 @@ target=$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
@@ -1253,7 +1276,7 @@ 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 idba 1.1.2 to adapt to many kinds of systems.
+\`configure' configures idba 1.1.3 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1319,7 +1342,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of idba 1.1.2:";;
+ short | recursive ) echo "Configuration of idba 1.1.3:";;
esac
cat <<\_ACEOF
@@ -1327,8 +1350,12 @@ Optional Features:
--disable-option-checking ignore unrecognized --enable/--with options
--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
- --disable-dependency-tracking speeds up one-time build
- --enable-dependency-tracking do not reject slow dependency extractors
+ --enable-silent-rules less verbose build output (undo: "make V=1")
+ --disable-silent-rules verbose build output (undo: "make V=0")
+ --enable-dependency-tracking
+ do not reject slow dependency extractors
+ --disable-dependency-tracking
+ speeds up one-time build
Some influential environment variables:
CXX C++ compiler command
@@ -1408,10 +1435,10 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-idba configure 1.1.2
-generated by GNU Autoconf 2.68
+idba configure 1.1.3
+generated by GNU Autoconf 2.69
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2012 Free Software Foundation, Inc.
This configure script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it.
_ACEOF
@@ -1689,7 +1716,7 @@ $as_echo "$ac_try_echo"; } >&5
test ! -s conftest.err
} && test -s conftest$ac_exeext && {
test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
+ test -x conftest$ac_exeext
}; then :
ac_retval=0
else
@@ -1778,8 +1805,8 @@ 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 idba $as_me 1.1.2, which was
-generated by GNU Autoconf 2.68. Invocation command line was
+It was created by idba $as_me 1.1.3, which was
+generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2129,7 +2156,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
ac_config_headers="$ac_config_headers config.h"
-am__api_version='1.11'
+am__api_version='1.14'
ac_aux_dir=
for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
@@ -2197,7 +2224,7 @@ case $as_dir/ in #((
# by default.
for ac_prog in ginstall scoinst install; do
for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if as_fn_executable_p "$as_dir/$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.
@@ -2255,9 +2282,6 @@ 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_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='
@@ -2268,32 +2292,40 @@ case `pwd` in
esac
case $srcdir in
*[\\\"\#\$\&\'\`$am_lf\ \ ]*)
- as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
+ as_fn_error $? "unsafe srcdir value: '$srcdir'" "$LINENO" 5;;
esac
-# Do `set' in a subshell so we don't clobber the current shell's
+# Do 'set' in a subshell so we don't clobber the current shell's
# arguments. Must try -L first in case configure is actually a
# symlink; some systems play weird games with the mod time of symlinks
# (eg FreeBSD returns the mod time of the symlink's containing
# directory).
if (
- set X `ls -Lt "$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_fn_error $? "ls -t appears to fail. Make sure there is not a broken
-alias in your environment" "$LINENO" 5
- fi
-
+ 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
test "$2" = conftest.file
)
then
@@ -2305,6 +2337,16 @@ Check your system clock" "$LINENO" 5
fi
{ $as_echo "$as_me:${as_lineno-$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.
@@ -2327,12 +2369,12 @@ if test x"${MISSING+set}" != xset; then
esac
fi
# Use eval to expand $SHELL
-if eval "$MISSING --run true"; then
- am_missing_run="$MISSING --run "
+if eval "$MISSING --is-lightweight"; then
+ am_missing_run="$MISSING "
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:${as_lineno-$LINENO}: WARNING: 'missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: 'missing' script is too old or missing" >&2;}
fi
if test x"${install_sh}" != xset; then
@@ -2344,10 +2386,10 @@ if test x"${install_sh}" != 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 "${ac_tool_prefix}strip", so it can be a program name with args.
@@ -2366,7 +2408,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$as_dir/$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$ac_exec_ext" >&5
break 2
@@ -2406,7 +2448,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$as_dir/$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$ac_exec_ext" >&5
break 2
@@ -2457,7 +2499,7 @@ do
test -z "$as_dir" && as_dir=.
for ac_prog in mkdir gmkdir; do
for ac_exec_ext in '' $ac_executable_extensions; do
- { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
+ as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext" || continue
case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
'mkdir (GNU coreutils) '* | \
'mkdir (coreutils) '* | \
@@ -2486,12 +2528,6 @@ fi
{ $as_echo "$as_me:${as_lineno-$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.
@@ -2510,7 +2546,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_prog_AWK="$ac_prog"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
@@ -2574,6 +2610,45 @@ else
fi
rmdir .tst 2>/dev/null
+# Check whether --enable-silent-rules was given.
+if test "${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 $(srcdir) != ., so that make's output
# is not polluted with repeated "-I."
@@ -2595,8 +2670,9 @@ fi
# Define the identity of the package.
+
PACKAGE=idba
- VERSION=1.1.2
+ VERSION=1.1.3
cat >>confdefs.h <<_ACEOF
@@ -2624,12 +2700,22 @@ AUTOHEADER=${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. 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 -'
@@ -2637,6 +2723,48 @@ am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} 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
+
# Checks for programs.
ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
@@ -2666,7 +2794,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$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
break 2
@@ -2710,7 +2838,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$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
break 2
@@ -3163,7 +3291,7 @@ 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
@@ -3219,8 +3347,8 @@ else
# 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'.
+ # making a dummy file named 'D' -- because '-MD' means "put the output
+ # in D".
rm -rf conftest.dir
mkdir conftest.dir
# Copy depcomp to subdir because otherwise we won't find it if we're
@@ -3255,16 +3383,16 @@ 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 8's {/usr,}/bin/sh.
- touch sub/conftst$i.h
+ # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
+ # Solaris 10 /bin/sh.
+ echo '/* dummy */' > 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
@@ -3273,8 +3401,8 @@ 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
@@ -3282,7 +3410,7 @@ else
fi
;;
msvc7 | msvc7msys | msvisualcpp | msvcmsys)
- # This compiler won't grok `-c -o', but also, the minuso test has
+ # 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}
@@ -3358,7 +3486,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$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
break 2
@@ -3398,7 +3526,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$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
break 2
@@ -3451,7 +3579,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$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
break 2
@@ -3492,7 +3620,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$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
@@ -3550,7 +3678,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$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
break 2
@@ -3594,7 +3722,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$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
break 2
@@ -3790,8 +3918,7 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <stdarg.h>
#include <stdio.h>
-#include <sys/types.h>
-#include <sys/stat.h>
+struct stat;
/* 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);
@@ -3876,6 +4003,65 @@ 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
@@ -3887,8 +4073,8 @@ else
# 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'.
+ # making a dummy file named 'D' -- because '-MD' means "put the output
+ # in D".
rm -rf conftest.dir
mkdir conftest.dir
# Copy depcomp to subdir because otherwise we won't find it if we're
@@ -3923,16 +4109,16 @@ 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 8's {/usr,}/bin/sh.
- touch sub/conftst$i.h
+ # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
+ # Solaris 10 /bin/sh.
+ echo '/* dummy */' > 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
@@ -3941,8 +4127,8 @@ 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
@@ -3950,7 +4136,7 @@ else
fi
;;
msvc7 | msvc7msys | msvisualcpp | msvcmsys)
- # This compiler won't grok `-c -o', but also, the minuso test has
+ # 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}
@@ -4025,7 +4211,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
@@ -4065,7 +4251,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
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 as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_prog_ac_ct_RANLIB="ranlib"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
@@ -4259,7 +4445,7 @@ 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"
- { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
+ as_fn_executable_p "$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
@@ -4325,7 +4511,7 @@ 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"
- { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
+ as_fn_executable_p "$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
@@ -4510,60 +4696,60 @@ else
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* 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];
+ /* 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;
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);
+ 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);
;
return 0;
@@ -4578,7 +4764,7 @@ 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 "$ac_cv_header_stdbool_h" >&6; }
-ac_fn_c_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
+ ac_fn_c_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
if test "x$ac_cv_type__Bool" = xyes; then :
cat >>confdefs.h <<_ACEOF
@@ -4588,6 +4774,7 @@ _ACEOF
fi
+
if test $ac_cv_header_stdbool_h = yes; then
$as_echo "#define HAVE_STDBOOL_H 1" >>confdefs.h
@@ -4605,11 +4792,11 @@ else
int
main ()
{
-/* FIXME: Include the comments suggested by Paul. */
+
#ifndef __cplusplus
- /* Ultrix mips cc rejects this. */
+ /* Ultrix mips cc rejects this sort of thing. */
typedef int charset[2];
- const charset cs;
+ const charset cs = { 0, 0 };
/* SunOS 4.1.1 cc rejects this. */
char const *const *pcpcc;
char **ppc;
@@ -4626,8 +4813,9 @@ main ()
++pcpcc;
ppc = (char**) pcpcc;
pcpcc = (char const *const *) ppc;
- { /* SCO 3.2v4 cc rejects this. */
- char *t;
+ { /* SCO 3.2v4 cc rejects this sort of thing. */
+ char tx;
+ char *t = &tx;
char const *s = 0 ? (char *) 0 : (char const *) 0;
*t++ = 0;
@@ -4643,10 +4831,10 @@ main ()
iptr p = 0;
++p;
}
- { /* AIX XL C 1.02.0.0 rejects this saying
+ { /* AIX XL C 1.02.0.0 rejects this sort of thing, saying
"k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */
- struct s { int j; const int *ap[3]; };
- struct s *b; b->j = 5;
+ struct s { int j; const int *ap[3]; } bx;
+ struct s *b = &bx; b->j = 5;
}
{ /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */
const int foo = 10;
@@ -4880,6 +5068,14 @@ 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='#'
@@ -5198,16 +5394,16 @@ 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 -p'.
+ # In both cases, we have to default to `cp -pR'.
ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
elif ln conf$$.file conf$$ 2>/dev/null; then
as_ln_s=ln
else
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
fi
else
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null
@@ -5267,28 +5463,16 @@ else
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
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+ test -f "$1" && test -x "$1"
+} # as_fn_executable_p
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
# Sed expression to map a string onto a valid CPP name.
as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
@@ -5309,8 +5493,8 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by idba $as_me 1.1.2, which was
-generated by GNU Autoconf 2.68. Invocation command line was
+This file was extended by idba $as_me 1.1.3, which was
+generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
CONFIG_HEADERS = $CONFIG_HEADERS
@@ -5375,11 +5559,11 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-idba config.status 1.1.2
-configured by $0, generated by GNU Autoconf 2.68,
+idba config.status 1.1.3
+configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2012 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."
@@ -5470,7 +5654,7 @@ fi
_ACEOF
cat >>$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'
@@ -6107,7 +6291,7 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
case $ac_file$ac_mode in
"depfiles":C) test x"$AMDEP_TRUE" != x"" || {
- # Autoconf 2.62 quotes --file arguments for eval, but not when files
+ # Older Autoconf 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
@@ -6120,7 +6304,7 @@ $as_echo "$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.
@@ -6154,21 +6338,19 @@ $as_echo X"$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' -e 's/\$U/'"$U"'/g'`; do
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
# Make sure the directory exists.
test -f "$dirpart/$file" && continue
fdir=`$as_dirname -- "$file" ||
diff --git a/configure.ac b/configure.ac
index 198ea08..67d11e8 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,10 +2,10 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
-AC_INIT(idba, 1.1.2, loneknightpy at gmail.com)
+AC_INIT(idba, 1.1.3, loneknightpy at gmail.com)
AC_CONFIG_SRCDIR([src/basic/kmer.h])
AC_CONFIG_HEADER([config.h])
-AM_INIT_AUTOMAKE(idba, 1.1.2)
+AM_INIT_AUTOMAKE(idba, 1.1.3)
# Checks for programs.
AC_PROG_CXX
diff --git a/lib/Makefile.in b/lib/Makefile.in
index 603604c..a5948ba 100644
--- a/lib/Makefile.in
+++ b/lib/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.11.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 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.
@@ -16,6 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
+ case $$MAKEFLAGS in \
+ *\\[\ \ ]*) \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
+ esac; \
+ done; \
+ test $$has_opt = yes
+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@
@@ -33,7 +77,8 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = lib
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+ $(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -45,6 +90,10 @@ CONFIG_CLEAN_VPATH_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
+AM_V_AR = $(am__v_AR_ at AM_V@)
+am__v_AR_ = $(am__v_AR_ at AM_DEFAULT_V@)
+am__v_AR_0 = @echo " AR " $@;
+am__v_AR_1 =
libassembly_a_AR = $(AR) $(ARFLAGS)
libassembly_a_LIBADD =
am_libassembly_a_OBJECTS = math.$(OBJEXT) hash_aligner.$(OBJEXT) \
@@ -62,26 +111,81 @@ libgtest_a_AR = $(AR) $(ARFLAGS)
libgtest_a_LIBADD =
am_libgtest_a_OBJECTS = gtest_main.$(OBJEXT) gtest-all.$(OBJEXT)
libgtest_a_OBJECTS = $(am_libgtest_a_OBJECTS)
+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 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/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 = $(libassembly_a_SOURCES) $(libgtest_a_SOURCES)
DIST_SOURCES = $(libassembly_a_SOURCES) $(libgtest_a_SOURCES)
+am__can_run_installinfo = \
+ case $$AM_UPDATE_INFO_DIR in \
+ n|no|NO) false;; \
+ *) (install-info --version) >/dev/null 2>&1;; \
+ esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -283,14 +387,16 @@ $(am__aclocal_m4_deps):
clean-noinstLIBRARIES:
-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
+
libassembly.a: $(libassembly_a_OBJECTS) $(libassembly_a_DEPENDENCIES) $(EXTRA_libassembly_a_DEPENDENCIES)
- -rm -f libassembly.a
- $(libassembly_a_AR) libassembly.a $(libassembly_a_OBJECTS) $(libassembly_a_LIBADD)
- $(RANLIB) libassembly.a
+ $(AM_V_at)-rm -f libassembly.a
+ $(AM_V_AR)$(libassembly_a_AR) libassembly.a $(libassembly_a_OBJECTS) $(libassembly_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libassembly.a
+
libgtest.a: $(libgtest_a_OBJECTS) $(libgtest_a_DEPENDENCIES) $(EXTRA_libgtest_a_DEPENDENCIES)
- -rm -f libgtest.a
- $(libgtest_a_AR) libgtest.a $(libgtest_a_OBJECTS) $(libgtest_a_LIBADD)
- $(RANLIB) libgtest.a
+ $(AM_V_at)-rm -f libgtest.a
+ $(AM_V_AR)$(libgtest_a_AR) libgtest.a $(libgtest_a_OBJECTS) $(libgtest_a_LIBADD)
+ $(AM_V_at)$(RANLIB) libgtest.a
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -322,361 +428,350 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/utils.Po at am__quote@
.cc.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cc.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
math.o: $(top_srcdir)/src/basic/math.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT math.o -MD -MP -MF $(DEPDIR)/math.Tpo -c -o math.o `test -f '$(top_srcdir)/src/basic/math.cpp' || echo '$(srcdir)/'`$(top_srcdir)/src/basic/math.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/math.Tpo $(DEPDIR)/math.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/basic/math.cpp' object='math.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT math.o -MD -MP -MF $(DEPDIR)/math.Tpo -c -o math.o `test -f '$(top_srcdir)/src/basic/math.cpp' || echo '$(srcdir)/'`$(top_srcdir)/src/basic/math.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/math.Tpo $(DEPDIR)/math.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$(top_srcdir)/src/basic/math.cpp' object='math.o' libtool=no @AMDEPBACKSLASH@
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-
-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 $$unique
-tags: TAGS
-
-TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+ID: $(am__tagged_files)
+ $(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
+
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
- list='$(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[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ $(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
@@ -688,15 +783,11 @@ TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
$$unique; \
fi; \
fi
-ctags: CTAGS
-CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
- $(TAGS_FILES) $(LISP)
- list='$(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[$$0] = 1; nonempty = 1; } \
- END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+ $(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
@@ -705,6 +796,21 @@ GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
+cscopelist: cscopelist-am
+
+cscopelist-am: $(am__tagged_files)
+ list='$(am__tagged_files)'; \
+ case "$(srcdir)" in \
+ [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
+ *) sdir=$(subdir)/$(srcdir) ;; \
+ esac; \
+ for i in $$list; do \
+ if test -f "$$i"; then \
+ echo "$(subdir)/$$i"; \
+ else \
+ echo "$$sdir/$$i"; \
+ fi; \
+ done >> $(top_builddir)/cscope.files
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
@@ -844,17 +950,17 @@ uninstall-am:
.MAKE: install-am install-strip
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
- clean-noinstLIBRARIES ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-data \
- install-data-am install-dvi install-dvi-am install-exec \
- install-exec-am install-html install-html-am install-info \
- install-info-am install-man install-pdf install-pdf-am \
- install-ps install-ps-am install-strip installcheck \
- installcheck-am installdirs maintainer-clean \
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean clean-generic \
+ clean-noinstLIBRARIES cscopelist-am ctags ctags-am distclean \
+ distclean-compile distclean-generic distclean-tags distdir dvi \
+ dvi-am html html-am info info-am install install-am \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
uninstall-am
diff --git a/script/Makefile.in b/script/Makefile.in
index e657634..98ef3ef 100644
--- a/script/Makefile.in
+++ b/script/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.11.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 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.
@@ -16,6 +15,51 @@
@SET_MAKE@
VPATH = @srcdir@
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
+ case $$MAKEFLAGS in \
+ *\\[\ \ ]*) \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
+ esac; \
+ done; \
+ test $$has_opt = yes
+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@
@@ -33,8 +77,8 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = script
-DIST_COMMON = $(dist_bin_SCRIPTS) $(srcdir)/Makefile.am \
- $(srcdir)/Makefile.in
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+ $(dist_bin_SCRIPTS)
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -72,11 +116,30 @@ am__uninstall_files_from_dir = { \
}
am__installdirs = "$(DESTDIR)$(bindir)"
SCRIPTS = $(dist_bin_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 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
SOURCES =
DIST_SOURCES =
+am__can_run_installinfo = \
+ case $$AM_UPDATE_INFO_DIR in \
+ n|no|NO) false;; \
+ *) (install-info --version) >/dev/null 2>&1;; \
+ esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -207,8 +270,11 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
install-dist_binSCRIPTS: $(dist_bin_SCRIPTS)
@$(NORMAL_INSTALL)
- test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
@list='$(dist_bin_SCRIPTS)'; test -n "$(bindir)" || list=; \
+ if test -n "$$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 "$$p"; else :; fi; \
@@ -237,11 +303,11 @@ uninstall-dist_binSCRIPTS:
files=`for p in $$list; do echo "$$p"; done | \
sed -e 's,.*/,,;$(transform)'`; \
dir='$(DESTDIR)$(bindir)'; $(am__uninstall_files_from_dir)
-tags: TAGS
-TAGS:
+tags TAGS:
+
+ctags CTAGS:
-ctags: CTAGS
-CTAGS:
+cscope cscopelist:
distdir: $(DISTFILES)
@@ -379,17 +445,17 @@ uninstall-am: uninstall-dist_binSCRIPTS
.MAKE: install-am install-strip
-.PHONY: all all-am check check-am clean clean-generic distclean \
- distclean-generic distdir dvi dvi-am html html-am info info-am \
- install install-am install-data install-data-am \
- install-dist_binSCRIPTS install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
- pdf-am ps ps-am uninstall uninstall-am \
- uninstall-dist_binSCRIPTS
+.PHONY: all all-am check check-am clean clean-generic cscopelist-am \
+ ctags-am distclean distclean-generic distdir dvi dvi-am html \
+ html-am info info-am install install-am install-data \
+ install-data-am install-dist_binSCRIPTS install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
+ install-html-am install-info install-info-am install-man \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-generic pdf pdf-am ps ps-am tags-am uninstall \
+ uninstall-am uninstall-dist_binSCRIPTS
# Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/src/graph/contig_graph.cpp b/src/graph/contig_graph.cpp
index 1d8f3c4..754f607 100644
--- a/src/graph/contig_graph.cpp
+++ b/src/graph/contig_graph.cpp
@@ -37,6 +37,11 @@ void ContigGraph::InitializeTable()
const double err = 0.01;
double p_err = err/3 * pow(1-err, double(kmer_size_-1));
+ p_table.resize(10);
+ for (unsigned i = 0; i < 10; ++i) {
+ p_table.resize(1000);
+ }
+
for (int m = 1; m < 10; ++m)
{
for (int x = 1; x < 1000; ++x)
@@ -219,7 +224,6 @@ void ContigGraph::MergeSimilarPath()
if (current.out_edges().size() > 1)
{
- ContigGraphVertexAdaptor end(NULL);
deque<ContigGraphVertexAdaptor> neighbors;
GetNeighbors(current, neighbors);
sort(neighbors.begin(), neighbors.end(), CompareContigCoverage);
@@ -247,7 +251,6 @@ void ContigGraph::MergeSimilarPath()
}
Refresh();
MergeSimplePaths();
-
}
int64_t ContigGraph::Prune(int min_length)
@@ -1244,6 +1247,9 @@ void ContigGraph::GetContigs(deque<Sequence> &contigs, deque<ContigInfo> &contig
double ContigGraph::GetSimilarity(const Sequence &a, const Sequence &b)
{
+ if (a.size() >= kMaxCheckSimilarity || b.size() > kMaxCheckSimilarity)
+ return 0;
+
vector<vector<int> > table;
table.resize(a.size() + 1);
for (unsigned i = 0; i < table.size(); ++i)
@@ -1471,4 +1477,3 @@ double ContigGraph::FindSimilarPath(ContigGraphVertexAdaptor target, ContigGraph
}
}
-
diff --git a/src/graph/contig_graph.h b/src/graph/contig_graph.h
index 13203ff..4048aca 100644
--- a/src/graph/contig_graph.h
+++ b/src/graph/contig_graph.h
@@ -260,6 +260,8 @@ private:
double FindSimilarPath(ContigGraphVertexAdaptor target, ContigGraphVertexAdaptor start);
double FindSimilarPath(ContigGraphVertexAdaptor target, ContigGraphPath &path, int &time);
+ static const uint32_t kMaxCheckSimilarity = 1024;
+
HashMap<Kmer, uint32_t> begin_kmer_map_;
std::deque<ContigGraphVertex> vertices_;
uint64_t num_edges_;
@@ -268,8 +270,7 @@ private:
HashMap<Kmer, uint32_t> in_kmer_count_table_;
HashGraph edge_count_table_;
- double p_table[10][10000];
+ std::vector<std::vector<double> > p_table;
};
#endif
-
diff --git a/src/graph/hash_graph.h b/src/graph/hash_graph.h
index 79a0b8e..5f5152c 100644
--- a/src/graph/hash_graph.h
+++ b/src/graph/hash_graph.h
@@ -188,8 +188,13 @@ public:
void clear() { vertex_table_.clear(); num_edges_ = 0; }
private:
+#if __cplusplus >= 201103L
+ HashGraph(const HashGraph &) = delete;
+ const HashGraph &operator =(const HashGraph &) = delete;
+#else
HashGraph(const HashGraph &);
const HashGraph &operator =(const HashGraph &);
+#endif
bool GetNextVertexAdaptor(const HashGraphVertexAdaptor ¤t, HashGraphVertexAdaptor &next)
{
@@ -428,7 +433,7 @@ inline std::ostream &operator <<(std::ostream &os, HashGraph &hash_graph)
namespace std
{
-template <> inline void swap(HashGraph &x, HashGraph &y)
+inline void swap(HashGraph &x, HashGraph &y)
{ x.swap(y); }
}
diff --git a/src/misc/log.cpp b/src/misc/log.cpp
index 53ba507..f502452 100644
--- a/src/misc/log.cpp
+++ b/src/misc/log.cpp
@@ -48,7 +48,7 @@ LogProcess::LogProcess(const string &log_file)
dup2(pipe_fds[0], STDIN_FILENO);
close(pipe_fds[0]);
- char line[kMaxLine];
+ char *line = new char[kMaxLine];
FILE *flog = OpenFile(log_file, "wb");
while (fgets(line, kMaxLine, stdin) != NULL)
{
@@ -57,6 +57,7 @@ LogProcess::LogProcess(const string &log_file)
fflush(NULL);
}
+ delete[] line;
exit(0);
}
else
@@ -114,7 +115,7 @@ void *LogThread::LogThreadFunc(void *p)
FILE *flog = OpenFile(log_thread.log_file_, "wb");
- char line[kMaxLine];
+ char *line = new char[kMaxLine];
int len = 0;
while ((len = read(log_thread.in_fd, line, kMaxLine)) > 0)
{
@@ -124,6 +125,6 @@ void *LogThread::LogThreadFunc(void *p)
}
fclose(flog);
+ delete[] line;
return p;
}
-
diff --git a/src/release/filterfa.cpp b/src/release/filterfa.cpp
index 9ba25e4..77bf74f 100644
--- a/src/release/filterfa.cpp
+++ b/src/release/filterfa.cpp
@@ -44,7 +44,7 @@ int main(int argc, char *argv[])
cerr << "fq2fa - Filter out fasta sequence containing N." << endl;
cerr << "Usage: filterfa tmp.fa out.fa " << endl;
cerr << " filterfa --paired tmp.fa out.fa" << endl;
- cerr << " filterfa --merged tmp_1.fa tmp_2.fa out.fa" << endl;
+ cerr << " filterfa --merge tmp_1.fa tmp_2.fa out.fa" << endl;
cerr << "Allowed Options: " << endl;
cerr << desc << endl;
exit(1);
diff --git a/src/release/idba_tran.cpp b/src/release/idba_tran.cpp
index ca45424..214ec80 100644
--- a/src/release/idba_tran.cpp
+++ b/src/release/idba_tran.cpp
@@ -49,6 +49,7 @@ struct IDBAOption
int min_count;
int min_support;
int min_contig;
+ int min_transcript;
double similar;
int max_mismatch;
int seed_kmer_size;
@@ -75,6 +76,7 @@ struct IDBAOption
min_count = 2;
min_support = 1;
min_contig = 200;
+ min_transcript = 300;
similar = 0.95;
max_mismatch = 3;
seed_kmer_size = 30;
@@ -236,7 +238,7 @@ void FindIsoforms(ContigGraphPath &path, deque<ContigGraphPath> &isoforms, Conti
{
bool flag = true;
- if (flag && path.size() > 300)
+ if (flag && path.size() > option.min_transcript)
{
isoforms.push_back(path);
}
@@ -300,6 +302,7 @@ int main(int argc, char *argv[])
desc.AddOption("num_threads", "", option.num_threads, "number of threads");
desc.AddOption("seed_kmer", "", option.seed_kmer_size, "seed kmer size for alignment");
desc.AddOption("min_contig", "", option.min_contig, "minimum size of contig");
+ desc.AddOption("min_transcript", "", option.min_transcript, "minimum size of transcript");
desc.AddOption("similar", "", option.similar, "similarity for alignment");
desc.AddOption("max_mismatch", "", option.max_mismatch, "max mismatch of error correction");
//desc.AddOption("min_pairs", "", option.min_pairs, "minimum number of pairs");
@@ -517,7 +520,7 @@ void Assemble(HashGraph &hash_graph)
int index = 0;
for (unsigned i = 0; i < transcripts.size(); ++i)
{
- if (transcripts[i].size() >= 300)
+ if (transcripts[i].size() >= option.min_transcript)
{
transcript_paths[index] = transcript_paths[i];
transcripts[index++] = transcripts[i];
diff --git a/src/sequence/sequence_reader.cpp b/src/sequence/sequence_reader.cpp
index bc881fd..4687dd1 100644
--- a/src/sequence/sequence_reader.cpp
+++ b/src/sequence/sequence_reader.cpp
@@ -47,11 +47,11 @@ bool SequenceReader::Read(Sequence &seq, string &comment, string &quality)
bool FastaReader::ReadRecord(Sequence &seq, string &comment, string &quality)
{
- return ReadFasta(*is_, seq, comment);
+ return ReadFasta(*is_, seq, comment).good();
}
bool FastqReader::ReadRecord(Sequence &seq, string &comment, string &quality)
{
- return ReadFastq(*is_, seq, comment, quality);
+ return ReadFastq(*is_, seq, comment, quality).good();
}
diff --git a/src/sequence/sequence_writer.cpp b/src/sequence/sequence_writer.cpp
index febf1af..c9544dd 100644
--- a/src/sequence/sequence_writer.cpp
+++ b/src/sequence/sequence_writer.cpp
@@ -46,11 +46,11 @@ bool SequenceWriter::Write(const Sequence &seq, const string &comment, const str
bool FastaWriter::WriteRecord(const Sequence &seq, const string &comment, const string &quality)
{
- return WriteFasta(*os_, seq, comment);
+ return WriteFasta(*os_, seq, comment).good();
}
bool FastqWriter::WriteRecord(const Sequence &seq, const string &comment, const string &quality)
{
- return WriteFastq(*os_, seq, comment, quality);
+ return WriteFastq(*os_, seq, comment, quality).good();
}
diff --git a/test-driver b/test-driver
new file mode 100755
index 0000000..d306056
--- /dev/null
+++ b/test-driver
@@ -0,0 +1,139 @@
+#! /bin/sh
+# test-driver - basic testsuite driver script.
+
+scriptversion=2013-07-13.22; # UTC
+
+# Copyright (C) 2011-2013 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
+ estatus=1
+fi
+
+case $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 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/test/Makefile.am b/test/Makefile.am
index 3639a90..9fa2297 100644
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -16,7 +16,7 @@ sequence_unittest_SOURCES = $(top_srcdir)/src/test/sequence_unittest.cpp
short_sequence_unittest_SOURCES = $(top_srcdir)/src/test/short_sequence_unittest.cpp
hash_map_unittest_SOURCES = $(top_srcdir)/src/test/hash_map_unittest.cpp
-noinst_PROGRAMS = \
+check_PROGRAMS = \
compact_sequence_unittest \
hash_table_unittest \
bit_edges_unittest \
@@ -30,3 +30,4 @@ noinst_PROGRAMS = \
short_sequence_unittest \
hash_map_unittest
+TESTS=$(check_PROGRAMS)
diff --git a/test/Makefile.in b/test/Makefile.in
index fea46f0..13f3d6b 100644
--- a/test/Makefile.in
+++ b/test/Makefile.in
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.11.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 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.
@@ -14,8 +13,52 @@
# PARTICULAR PURPOSE.
@SET_MAKE@
-
VPATH = @srcdir@
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+ case $${target_option-} in \
+ ?) ;; \
+ *) echo "am__make_running_with_option: internal error: invalid" \
+ "target option '$${target_option-}' specified" >&2; \
+ exit 1;; \
+ esac; \
+ has_opt=no; \
+ sane_makeflags=$$MAKEFLAGS; \
+ if $(am__is_gnu_make); then \
+ sane_makeflags=$$MFLAGS; \
+ else \
+ case $$MAKEFLAGS in \
+ *\\[\ \ ]*) \
+ bs=\\; \
+ sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+ | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
+ esac; \
+ fi; \
+ skip_next=no; \
+ strip_trailopt () \
+ { \
+ flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+ }; \
+ for flg in $$sane_makeflags; do \
+ test $$skip_next = yes && { skip_next=no; continue; }; \
+ case $$flg in \
+ *=*|--*) continue;; \
+ -*I) strip_trailopt 'I'; skip_next=yes;; \
+ -*I?*) strip_trailopt 'I';; \
+ -*O) strip_trailopt 'O'; skip_next=yes;; \
+ -*O?*) strip_trailopt 'O';; \
+ -*l) strip_trailopt 'l'; skip_next=yes;; \
+ -*l?*) strip_trailopt 'l';; \
+ -[dEDm]) skip_next=yes;; \
+ -[JT]) skip_next=yes;; \
+ esac; \
+ case $$flg in \
+ *$$target_option*) has_opt=yes; break;; \
+ esac; \
+ done; \
+ test $$has_opt = yes
+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 = $(libdir)/@PACKAGE@
@@ -32,7 +75,7 @@ POST_INSTALL = :
NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
-noinst_PROGRAMS = compact_sequence_unittest$(EXEEXT) \
+check_PROGRAMS = compact_sequence_unittest$(EXEEXT) \
hash_table_unittest$(EXEEXT) bit_edges_unittest$(EXEEXT) \
kmer_unittest$(EXEEXT) hash_set_unittest$(EXEEXT) \
atomic_integer_unittest$(EXEEXT) \
@@ -40,7 +83,8 @@ noinst_PROGRAMS = compact_sequence_unittest$(EXEEXT) \
managed_list_unittest$(EXEEXT) sequence_unittest$(EXEEXT) \
short_sequence_unittest$(EXEEXT) hash_map_unittest$(EXEEXT)
subdir = test
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+ $(top_srcdir)/depcomp $(top_srcdir)/test-driver
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -49,7 +93,6 @@ mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
-PROGRAMS = $(noinst_PROGRAMS)
am_atomic_integer_unittest_OBJECTS = \
atomic_integer_unittest.$(OBJEXT)
atomic_integer_unittest_OBJECTS = \
@@ -92,15 +135,39 @@ short_sequence_unittest_LDADD = $(LDADD)
am_vertex_status_unittest_OBJECTS = vertex_status_unittest.$(OBJEXT)
vertex_status_unittest_OBJECTS = $(am_vertex_status_unittest_OBJECTS)
vertex_status_unittest_LDADD = $(LDADD)
+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 =
+AM_V_at = $(am__v_at_ at AM_V@)
+am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 =
DEFAULT_INCLUDES = -I. at am__isrc@ -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/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 =
SOURCES = $(atomic_integer_unittest_SOURCES) \
$(bit_edges_unittest_SOURCES) \
$(compact_sequence_unittest_SOURCES) \
@@ -119,11 +186,238 @@ DIST_SOURCES = $(atomic_integer_unittest_SOURCES) \
$(sequence_unittest_SOURCES) \
$(short_sequence_unittest_SOURCES) \
$(vertex_status_unittest_SOURCES)
+am__can_run_installinfo = \
+ case $$AM_UPDATE_INFO_DIR in \
+ n|no|NO) false;; \
+ *) (install-info --version) >/dev/null 2>&1;; \
+ esac
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates. Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+ BEGIN { nonempty = 0; } \
+ { items[$$0] = 1; nonempty = 1; } \
+ END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique. This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+ list='$(am__tagged_files)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
+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'; \
+ blu='[1;34m'; \
+ mgn='[0;35m'; \
+ brg='[1m'; \
+ std='[m'; \
+ fi; \
+}
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+ *) f=$$p;; \
+ esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+ for p in $$list; do echo "$$p $$p"; done | \
+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+ if (++n[$$2] == $(am__install_max)) \
+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+ END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+ sed '$$!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; }; \
+ }
+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
+# standard input, print the name of the tests that are to be re-run
+# upon "make recheck".
+am__list_recheck_tests = $(AWK) '{ \
+ recheck = 1; \
+ while ((rc = (getline line < ($$0 ".trs"))) != 0) \
+ { \
+ if (rc < 0) \
+ { \
+ if ((getline line2 < ($$0 ".log")) < 0) \
+ recheck = 0; \
+ break; \
+ } \
+ else if (line ~ /$(am__recheck_rx)[nN][Oo]/) \
+ { \
+ recheck = 0; \
+ break; \
+ } \
+ else if (line ~ /$(am__recheck_rx)[yY][eE][sS]/) \
+ { \
+ break; \
+ } \
+ }; \
+ if (recheck) \
+ print $$0; \
+ close ($$0 ".trs"); \
+ close ($$0 ".log"); \
+}'
+# A command that, given a newline-separated list of test names on the
+# standard input, create the global log from their .trs and .log files.
+am__create_global_log = $(AWK) ' \
+function fatal(msg) \
+{ \
+ print "fatal: making $@: " msg | "cat >&2"; \
+ exit 1; \
+} \
+function rst_section(header) \
+{ \
+ print header; \
+ len = length(header); \
+ for (i = 1; i <= len; i = i + 1) \
+ printf "="; \
+ printf "\n\n"; \
+} \
+{ \
+ copy_in_global_log = 1; \
+ global_test_result = "RUN"; \
+ while ((rc = (getline line < ($$0 ".trs"))) != 0) \
+ { \
+ if (rc < 0) \
+ fatal("failed to read from " $$0 ".trs"); \
+ if (line ~ /$(am__global_test_result_rx)/) \
+ { \
+ sub("$(am__global_test_result_rx)", "", line); \
+ sub("[ ]*$$", "", line); \
+ global_test_result = line; \
+ } \
+ else if (line ~ /$(am__copy_in_global_log_rx)[nN][oO]/) \
+ copy_in_global_log = 0; \
+ }; \
+ if (copy_in_global_log) \
+ { \
+ rst_section(global_test_result ": " $$0); \
+ while ((rc = (getline line < ($$0 ".log"))) != 0) \
+ { \
+ if (rc < 0) \
+ fatal("failed to read from " $$0 ".log"); \
+ print line; \
+ }; \
+ printf "\n"; \
+ }; \
+ close ($$0 ".trs"); \
+ close ($$0 ".log"); \
+}'
+# Restructured Text title.
+am__rst_title = { sed 's/.*/ & /;h;s/./=/g;p;x;s/ *$$//;p;g' && echo; }
+# Solaris 10 'make', and several other traditional 'make' implementations,
+# pass "-e" to $(SHELL), and POSIX 2008 even requires this. Work around it
+# by disabling -e (using the XSI extension "set +e") if it's set.
+am__sh_e_setup = case $$- in *e*) set +e;; esac
+# Default flags passed to test drivers.
+am__common_driver_flags = \
+ --color-tests "$$am__color_tests" \
+ --enable-hard-errors "$$am__enable_hard_errors" \
+ --expect-failure "$$am__expect_failure"
+# To be inserted before the command running the test. Creates the
+# directory for the log if needed. Stores in $dir the directory
+# containing $f, in $tst the test, in $log the log. Executes the
+# developer- defined test setup AM_TESTS_ENVIRONMENT (if any), and
+# passes TESTS_ENVIRONMENT. Set up options for the wrapper that
+# will run the test scripts (or their associated LOG_COMPILER, if
+# thy have one).
+am__check_pre = \
+$(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 $$?; \
+if test -f "./$$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`
+RECHECK_LOGS = $(TEST_LOGS)
+AM_RECURSIVE_TARGETS = check recheck
+TEST_SUITE_LOG = test-suite.log
+TEST_EXTENSIONS = @EXEEXT@ .test
+LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver
+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)/test-driver
+TEST_LOG_COMPILE = $(TEST_LOG_COMPILER) $(AM_TEST_LOG_FLAGS) \
+ $(TEST_LOG_FLAGS)
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = @ACLOCAL@
AMTAR = @AMTAR@
+AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
@@ -228,10 +522,11 @@ managed_list_unittest_SOURCES = $(top_srcdir)/src/test/managed_list_unittest.cpp
sequence_unittest_SOURCES = $(top_srcdir)/src/test/sequence_unittest.cpp
short_sequence_unittest_SOURCES = $(top_srcdir)/src/test/short_sequence_unittest.cpp
hash_map_unittest_SOURCES = $(top_srcdir)/src/test/hash_map_unittest.cpp
+TESTS = $(check_PROGRAMS)
all: all-am
.SUFFIXES:
-.SUFFIXES: .cpp .o .obj
+.SUFFIXES: .cpp .log .o .obj .test .test$(EXEEXT) .trs
$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
@for dep in $?; do \
case '$(am__configure_deps)' in \
@@ -263,44 +558,56 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(am__aclocal_m4_deps):
-clean-noinstPROGRAMS:
- -test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
+clean-checkPROGRAMS:
+ -test -z "$(check_PROGRAMS)" || rm -f $(check_PROGRAMS)
+
atomic_integer_unittest$(EXEEXT): $(atomic_integer_unittest_OBJECTS) $(atomic_integer_unittest_DEPENDENCIES) $(EXTRA_atomic_integer_unittest_DEPENDENCIES)
@rm -f atomic_integer_unittest$(EXEEXT)
- $(CXXLINK) $(atomic_integer_unittest_OBJECTS) $(atomic_integer_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(atomic_integer_unittest_OBJECTS) $(atomic_integer_unittest_LDADD) $(LIBS)
+
bit_edges_unittest$(EXEEXT): $(bit_edges_unittest_OBJECTS) $(bit_edges_unittest_DEPENDENCIES) $(EXTRA_bit_edges_unittest_DEPENDENCIES)
@rm -f bit_edges_unittest$(EXEEXT)
- $(CXXLINK) $(bit_edges_unittest_OBJECTS) $(bit_edges_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(bit_edges_unittest_OBJECTS) $(bit_edges_unittest_LDADD) $(LIBS)
+
compact_sequence_unittest$(EXEEXT): $(compact_sequence_unittest_OBJECTS) $(compact_sequence_unittest_DEPENDENCIES) $(EXTRA_compact_sequence_unittest_DEPENDENCIES)
@rm -f compact_sequence_unittest$(EXEEXT)
- $(CXXLINK) $(compact_sequence_unittest_OBJECTS) $(compact_sequence_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(compact_sequence_unittest_OBJECTS) $(compact_sequence_unittest_LDADD) $(LIBS)
+
hash_map_unittest$(EXEEXT): $(hash_map_unittest_OBJECTS) $(hash_map_unittest_DEPENDENCIES) $(EXTRA_hash_map_unittest_DEPENDENCIES)
@rm -f hash_map_unittest$(EXEEXT)
- $(CXXLINK) $(hash_map_unittest_OBJECTS) $(hash_map_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(hash_map_unittest_OBJECTS) $(hash_map_unittest_LDADD) $(LIBS)
+
hash_set_unittest$(EXEEXT): $(hash_set_unittest_OBJECTS) $(hash_set_unittest_DEPENDENCIES) $(EXTRA_hash_set_unittest_DEPENDENCIES)
@rm -f hash_set_unittest$(EXEEXT)
- $(CXXLINK) $(hash_set_unittest_OBJECTS) $(hash_set_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(hash_set_unittest_OBJECTS) $(hash_set_unittest_LDADD) $(LIBS)
+
hash_table_unittest$(EXEEXT): $(hash_table_unittest_OBJECTS) $(hash_table_unittest_DEPENDENCIES) $(EXTRA_hash_table_unittest_DEPENDENCIES)
@rm -f hash_table_unittest$(EXEEXT)
- $(CXXLINK) $(hash_table_unittest_OBJECTS) $(hash_table_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(hash_table_unittest_OBJECTS) $(hash_table_unittest_LDADD) $(LIBS)
+
histgram_unittest$(EXEEXT): $(histgram_unittest_OBJECTS) $(histgram_unittest_DEPENDENCIES) $(EXTRA_histgram_unittest_DEPENDENCIES)
@rm -f histgram_unittest$(EXEEXT)
- $(CXXLINK) $(histgram_unittest_OBJECTS) $(histgram_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(histgram_unittest_OBJECTS) $(histgram_unittest_LDADD) $(LIBS)
+
kmer_unittest$(EXEEXT): $(kmer_unittest_OBJECTS) $(kmer_unittest_DEPENDENCIES) $(EXTRA_kmer_unittest_DEPENDENCIES)
@rm -f kmer_unittest$(EXEEXT)
- $(CXXLINK) $(kmer_unittest_OBJECTS) $(kmer_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(kmer_unittest_OBJECTS) $(kmer_unittest_LDADD) $(LIBS)
+
managed_list_unittest$(EXEEXT): $(managed_list_unittest_OBJECTS) $(managed_list_unittest_DEPENDENCIES) $(EXTRA_managed_list_unittest_DEPENDENCIES)
@rm -f managed_list_unittest$(EXEEXT)
- $(CXXLINK) $(managed_list_unittest_OBJECTS) $(managed_list_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(managed_list_unittest_OBJECTS) $(managed_list_unittest_LDADD) $(LIBS)
+
sequence_unittest$(EXEEXT): $(sequence_unittest_OBJECTS) $(sequence_unittest_DEPENDENCIES) $(EXTRA_sequence_unittest_DEPENDENCIES)
@rm -f sequence_unittest$(EXEEXT)
- $(CXXLINK) $(sequence_unittest_OBJECTS) $(sequence_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(sequence_unittest_OBJECTS) $(sequence_unittest_LDADD) $(LIBS)
+
short_sequence_unittest$(EXEEXT): $(short_sequence_unittest_OBJECTS) $(short_sequence_unittest_DEPENDENCIES) $(EXTRA_short_sequence_unittest_DEPENDENCIES)
@rm -f short_sequence_unittest$(EXEEXT)
- $(CXXLINK) $(short_sequence_unittest_OBJECTS) $(short_sequence_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(short_sequence_unittest_OBJECTS) $(short_sequence_unittest_LDADD) $(LIBS)
+
vertex_status_unittest$(EXEEXT): $(vertex_status_unittest_OBJECTS) $(vertex_status_unittest_DEPENDENCIES) $(EXTRA_vertex_status_unittest_DEPENDENCIES)
@rm -f vertex_status_unittest$(EXEEXT)
- $(CXXLINK) $(vertex_status_unittest_OBJECTS) $(vertex_status_unittest_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(vertex_status_unittest_OBJECTS) $(vertex_status_unittest_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
@@ -322,207 +629,196 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/vertex_status_unittest.Po at am__quote@
.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
atomic_integer_unittest.o: $(top_srcdir)/src/test/atomic_integer_unittest.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT atomic_integer_unittest.o -MD -MP -MF $(DEPDIR)/atomic_integer_unittest.Tpo -c -o atomic_integer_unittest.o `test -f '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' || echo '$(srcdir)/'`$(top_srcdir)/src/test/atomic_integer_unittest.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/atomic_integer_unittest.Tpo $(DEPDIR)/atomic_integer_unittest.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$(top_srcdir)/src/test/atomic_integer_unittest.cpp' object='atomic_integer_unittest.o' libtool=no @AMDEPBACKSLASH@
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT atomic_integer_unittest.o -MD -MP -MF $(DEPDIR)/atomic_integer_unittest.Tpo -c -o atomic_integer_unittest.o `test -f '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' || echo '$(srcdir)/'`$(top_srcdir)/src/test/atomic_integer_unittest.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/atomic_integer_unittest.Tpo $(DEPDIR)/atomic_integer_unittest.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='$(top_srcdir)/src/test/atomic_integer_unittest.cpp' object='atomic_integer_unittest.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o atomic_integer_unittest.o `test -f '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' || echo '$(srcdir)/'`$(top_srcdir)/src/test/atomic_integer_unittest.cpp
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distclean-tags:
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+ $(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) TEST_LOGS="$$log_list"; \
+ exit $$?;
+recheck: all $(check_PROGRAMS)
+ @test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
+ @set +e; $(am__set_TESTS_bases); \
+ bases=`for i in $$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="$$log_list"; \
+ exit $$?
+compact_sequence_unittest.log: compact_sequence_unittest$(EXEEXT)
+ @p='compact_sequence_unittest$(EXEEXT)'; \
+ b='compact_sequence_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+hash_table_unittest.log: hash_table_unittest$(EXEEXT)
+ @p='hash_table_unittest$(EXEEXT)'; \
+ b='hash_table_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+bit_edges_unittest.log: bit_edges_unittest$(EXEEXT)
+ @p='bit_edges_unittest$(EXEEXT)'; \
+ b='bit_edges_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+kmer_unittest.log: kmer_unittest$(EXEEXT)
+ @p='kmer_unittest$(EXEEXT)'; \
+ b='kmer_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+hash_set_unittest.log: hash_set_unittest$(EXEEXT)
+ @p='hash_set_unittest$(EXEEXT)'; \
+ b='hash_set_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+atomic_integer_unittest.log: atomic_integer_unittest$(EXEEXT)
+ @p='atomic_integer_unittest$(EXEEXT)'; \
+ b='atomic_integer_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+vertex_status_unittest.log: vertex_status_unittest$(EXEEXT)
+ @p='vertex_status_unittest$(EXEEXT)'; \
+ b='vertex_status_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+histgram_unittest.log: histgram_unittest$(EXEEXT)
+ @p='histgram_unittest$(EXEEXT)'; \
+ b='histgram_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+managed_list_unittest.log: managed_list_unittest$(EXEEXT)
+ @p='managed_list_unittest$(EXEEXT)'; \
+ b='managed_list_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+sequence_unittest.log: sequence_unittest$(EXEEXT)
+ @p='sequence_unittest$(EXEEXT)'; \
+ b='sequence_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+short_sequence_unittest.log: short_sequence_unittest$(EXEEXT)
+ @p='short_sequence_unittest$(EXEEXT)'; \
+ b='short_sequence_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+hash_map_unittest.log: hash_map_unittest$(EXEEXT)
+ @p='hash_map_unittest$(EXEEXT)'; \
+ b='hash_map_unittest'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+.test.log:
+ @p='$<'; \
+ $(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" $(AM_TESTS_FD_REDIRECT)
+ at am__EXEEXT_TRUE@.test$(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)
+
distdir: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
@@ -586,8 +1133,10 @@ distdir: $(DISTFILES)
fi; \
done
check-am: all-am
+ $(MAKE) $(AM_MAKEFLAGS) $(check_PROGRAMS)
+ $(MAKE) $(AM_MAKEFLAGS) check-TESTS
check: check-am
-all-am: Makefile $(PROGRAMS)
+all-am: Makefile
installdirs:
install: install-am
install-exec: install-exec-am
@@ -609,6 +1158,9 @@ install-strip:
"INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
fi
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_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG)
clean-generic:
@@ -621,7 +1173,7 @@ maintainer-clean-generic:
@echo "it deletes files that may require special tools to rebuild."
clean: clean-am
-clean-am: clean-generic clean-noinstPROGRAMS mostlyclean-am
+clean-am: clean-checkPROGRAMS clean-generic mostlyclean-am
distclean: distclean-am
-rm -rf ./$(DEPDIR)
@@ -688,20 +1240,20 @@ ps-am:
uninstall-am:
-.MAKE: install-am install-strip
-
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
- clean-noinstPROGRAMS ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-data \
- install-data-am install-dvi install-dvi-am install-exec \
- install-exec-am install-html install-html-am install-info \
- install-info-am install-man install-pdf install-pdf-am \
- install-ps install-ps-am install-strip installcheck \
- installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am
+.MAKE: check-am install-am install-strip
+
+.PHONY: CTAGS GTAGS TAGS all all-am check check-TESTS check-am clean \
+ clean-checkPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-data install-data-am install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
+ install-html-am install-info install-info-am install-man \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
+ recheck tags tags-am uninstall uninstall-am
# Tell versions [3.59,3.63) of GNU make to not export all variables.
--
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