[med-svn] [biosquid] 02/05: configure.ac: add EXEC_DEPENDECY macro back in and rework AC_DEFINE
Gert Wollny
gewo at moszumanska.debian.org
Mon Apr 3 18:55:32 UTC 2017
This is an automated email from the git hooks/post-receive script.
gewo pushed a commit to branch master
in repository biosquid.
commit 80f4b3339a2e9faefa91ae44ce6340e98c81ebba
Author: Gert Wollny <gewo at debian.org>
Date: Mon Apr 3 18:08:25 2017 +0000
configure.ac: add EXEC_DEPENDECY macro back in and rework AC_DEFINE
Change all AC_DEFINEs to use three parameters, because otherwise
autoheader returns a nonzero value and package building fails
---
Makefile.in | 67 ++++++++++++-----
Man/afetch.man | 22 ++++--
Man/alistat.man | 20 +++--
Man/compstruct.man | 20 +++--
Man/seqstat.man | 22 ++++--
Man/sfetch.man | 22 ++++--
Man/shuffle.man | 28 ++++---
Man/sindex.man | 22 ++++--
Man/sreformat.man | 24 ++++--
Testsuite/Makefile.in | 1 -
Testsuite/bug-1-sfetch-paths | 1 +
Testsuite/x-base-afetch | 1 +
Testsuite/x-base-alistat | 1 +
Testsuite/x-base-seqstat | 1 +
Testsuite/x-base-sfetch | 1 +
Testsuite/x-base-shuffle | 1 +
Testsuite/x-base-sindex | 1 +
Testsuite/x-base-sreformat | 1 +
configure.ac | 95 +++++++++++-------------
debian/patches/automake.patch | 168 +++++++++++++++++++++++++++++++++++++++++-
getopt.c | 3 +-
21 files changed, 400 insertions(+), 122 deletions(-)
diff --git a/Makefile.in b/Makefile.in
index 5d8c780..7b079f7 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -75,10 +75,12 @@ PROGS = afetch\
MANS = afetch\
alistat\
+ compstruct\
seqstat\
sfetch\
shuffle\
- sreformat\
+ sindex\
+ sreformat
READMES = 00README INSTALL Makefile.in
@@ -103,51 +105,80 @@ HDRS = dirichlet.h\
stopwatch.h\
vectorops.h
-OBJS = a2m.o\
- aligneval.o\
+COMMON_OBJS = \
+ a2m.o\
alignio.o\
clustal.o\
- cluster.o\
- dayhoff.o\
- dirichlet.o\
- eps.o\
file.o\
getopt.o\
gki.o\
hsregex.o\
- iupac.o\
msa.o\
msf.o\
phylip.o\
- revcomp.o\
- rk.o\
selex.o\
- seqencode.o\
- shuffle.o\
sqerror.o\
sqio.o\
squidcore.o\
sre_ctype.o\
- sre_math.o\
sre_random.o\
- sre_stack.o\
sre_string.o\
ssi.o\
stockholm.o\
+ types.o\
+ vectorops.o
+
+OBJS = $(COMMON_OBJS)\
+ aligneval.o\
+ cluster.o\
+ dayhoff.o\
+ dirichlet.o\
+ eps.o\
+ iupac.o\
+ revcomp.o\
+ rk.o\
+ seqencode.o\
+ shuffle.o\
+ sre_math.o\
+ sre_stack.o\
stopwatch.o\
translate.o\
- types.o\
- vectorops.o\
weight.o\
wuss.o
+MAINS = afetch_main.o\
+ alistat_main.o\
+ compalign_main.o\
+ compstruct_main.o\
+ revcomp_main.o\
+ seqsplit_main.o\
+ seqstat_main.o\
+ sfetch_main.o\
+ shuffle_main.o\
+ sindex_main.o\
+ sreformat_main.o\
+ translate_main.o\
+ weight_main.o
+
################################################################
# Targets that actually build the squid executables
all: $(PROGS) libsquid.a
-$(PROGS): @EXEC_DEPENDENCY@ ${OBJS}
- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o $@ $@_main.o ${OBJS} ${PVMLIBS} ${LIBS}
+$(PROGS): @EXEC_DEPENDENCY@ ${OBJS} ${MAINS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o afetch afetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o alistat aligneval.o cluster.o sre_math.o sre_stack.o alistat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compalign aligneval.o compalign_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compstruct sre_math.o sre_stack.o wuss.o compstruct_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o revcomp revcomp.o shuffle.o revcomp_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqsplit seqsplit_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqstat seqstat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sfetch revcomp.o shuffle.o sfetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o shuffle iupac.o shuffle.o shuffle_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sindex sindex_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sreformat eps.o shuffle.o sre_stack.o wuss.o sreformat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o translate iupac.o revcomp.o shuffle.o sre_stack.o translate.o translate_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
+ ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o weight aligneval.o cluster.o iupac.o sre_math.o sre_stack.o weight.o weight_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS}
.c.o:
${CC} ${CFLAGS} ${CPPFLAGS} ${PVMINCDIR} ${DEFS} -c $<
diff --git a/Man/afetch.man b/Man/afetch.man
index dac23ee..5eee8cf 100644
--- a/Man/afetch.man
+++ b/Man/afetch.man
@@ -1,4 +1,4 @@
-.TH "afetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
+.TH "afetch" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
.SH NAME
.TP
@@ -67,15 +67,23 @@ file to prepare it for all future afetch's.
.SH SEE ALSO
-.PP
-Master man page, with full list of and guide to the
-individual man pages for SQUID's auxiliary programs: see
-.B squid(1).
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
.SH AUTHOR
- at PACKAGE@ and its documentation are @COPYRIGHT@
- at LICENSE@
+Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
See COPYING in the source code distribution for more details, or contact me.
.nf
diff --git a/Man/alistat.man b/Man/alistat.man
index 499512a..325cf7c 100644
--- a/Man/alistat.man
+++ b/Man/alistat.man
@@ -1,4 +1,4 @@
-.TH "alistat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
+.TH "alistat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
.SH NAME
.TP
@@ -109,13 +109,23 @@ Babelfish autodetection option.
.SH SEE ALSO
-.PP
- at SEEALSO@
+.BR afetch (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
.SH AUTHOR
- at PACKAGE@ and its documentation are @COPYRIGHT@
- at LICENSE@
+Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
See COPYING in the source code distribution for more details, or contact me.
.nf
diff --git a/Man/compstruct.man b/Man/compstruct.man
index 6ad8691..245c0fa 100644
--- a/Man/compstruct.man
+++ b/Man/compstruct.man
@@ -1,4 +1,4 @@
-.TH "compstruct" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
+.TH "compstruct" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
.SH NAME
.TP
@@ -116,13 +116,23 @@ Don't print any verbose header information.
.SH SEE ALSO
-.PP
- at SEEALSO@
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
.SH AUTHOR
- at PACKAGE@ and its documentation are @COPYRIGHT@
- at LICENSE@
+Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
See COPYING in the source code distribution for more details, or contact me.
.nf
diff --git a/Man/seqstat.man b/Man/seqstat.man
index 8739f00..33bce51 100644
--- a/Man/seqstat.man
+++ b/Man/seqstat.man
@@ -1,4 +1,4 @@
-.TH "seqstat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
+.TH "seqstat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
.SH NAME
.TP
@@ -16,7 +16,7 @@ reads a sequence file
.I seqfile
and shows a number of simple statistics about it.
-.pp
+.PP
The printed statistics include the name of the format, the residue
type of the first sequence (protein, RNA, or DNA), the number of
sequences, the total number of residues, and the average and range of
@@ -69,13 +69,23 @@ and date, the parameters and options in effect).
.SH SEE ALSO
-.PP
- at SEEALSO@
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
.SH AUTHOR
- at PACKAGE@ and its documentation are @COPYRIGHT@
- at LICENSE@
+Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
See COPYING in the source code distribution for more details, or contact me.
.nf
diff --git a/Man/sfetch.man b/Man/sfetch.man
index ca9ffc0..e85ba25 100644
--- a/Man/sfetch.man
+++ b/Man/sfetch.man
@@ -1,4 +1,4 @@
-.TH "sfetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
+.TH "sfetch" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
.SH NAME
.TP
@@ -64,7 +64,7 @@ databases. The program
.B sindex
creates SSI indexes for any sequence file.
-.pp
+.PP
.B sfetch
was originally named
.B getseq,
@@ -191,13 +191,23 @@ Babelfish autodetection option.
.SH SEE ALSO
-.PP
- at SEEALSO@
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
.SH AUTHOR
- at PACKAGE@ and its documentation are @COPYRIGHT@
- at LICENSE@
+Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
See COPYING in the source code distribution for more details, or contact me.
.nf
diff --git a/Man/shuffle.man b/Man/shuffle.man
index 342aa84..8059d22 100644
--- a/Man/shuffle.man
+++ b/Man/shuffle.man
@@ -1,4 +1,4 @@
-.TH "shuffle" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
+.TH "shuffle" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
.SH NAME
.TP
@@ -19,7 +19,7 @@ in FASTA format on standard output. The sequence names
are unchanged; this allows you to track down the source
of each randomized sequence if necessary.
-.pp
+.PP
The default is to simply shuffle each input sequence, preserving
monosymbol composition exactly. To shuffle
each sequence while preserving both its monosymbol and disymbol
@@ -27,7 +27,7 @@ composition exactly, use the
.I -d
option.
-.pp
+.PP
The
.I -0
and
@@ -44,7 +44,7 @@ the generated sequence has the same 1st order
Markov properties as the input sequence (e.g.
the same disymbol frequencies).
-.pp
+.PP
Note that the default and
.I -0,
or
@@ -56,7 +56,7 @@ composition exactly, while the Markov algorithms
only expect to generate a sequence of similar
composition on average.
-.pp
+.PP
Other shuffling algorithms are also available,
as documented below in the options.
@@ -175,13 +175,23 @@ the same output in subsequent runs with the same input.
.SH SEE ALSO
-.PP
- at SEEALSO@
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR sindex (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
.SH AUTHOR
- at PACKAGE@ and its documentation are @COPYRIGHT@
- at LICENSE@
+Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
See COPYING in the source code distribution for more details, or contact me.
.nf
diff --git a/Man/sindex.man b/Man/sindex.man
index 655568c..996fe62 100644
--- a/Man/sindex.man
+++ b/Man/sindex.man
@@ -1,4 +1,4 @@
-.TH "sindex" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
+.TH "sindex" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
.SH NAME
.TP
@@ -67,7 +67,7 @@ Specify that the sequence file is definitely in format
.I <s>;
blocks sequence file format autodetection. This is useful in automated
pipelines, because it improves robustness (autodetection can
-occasionally go wrong on a perversely misformed file). Common examples
+occasionally go wrong on a perversely malformed file). Common examples
include genbank, embl, gcg, pir, stockholm, clustal, msf, or phylip;
see the printed documentation for a complete list of accepted format
names.
@@ -83,12 +83,24 @@ and accession (as a secondary key).
.SH SEE ALSO
.PP
- at SEEALSO@
+
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sreformat (1),
+.BR stranslate (1),
+.BR weight (1).
.SH AUTHOR
- at PACKAGE@ and its documentation are @COPYRIGHT@
- at LICENSE@
+Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
See COPYING in the source code distribution for more details, or contact me.
.nf
diff --git a/Man/sreformat.man b/Man/sreformat.man
index 619bf45..edea0e5 100644
--- a/Man/sreformat.man
+++ b/Man/sreformat.man
@@ -1,4 +1,4 @@
-.TH "sreformat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"
+.TH "sreformat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"
.SH NAME
.TP
@@ -43,7 +43,7 @@ include
.I raw
(raw sequence, no other information).
-.pp
+.PP
The available aligned output file format
codes include
.I stockholm
@@ -59,7 +59,7 @@ codes include
.I selex
(the old SELEX/HMMER/Pfam annotated alignment format);
-.pp
+.PP
All thee codes are interpreted case-insensitively
(e.g. MSF, Msf, or msf all work).
@@ -231,13 +231,23 @@ markup.
.SH SEE ALSO
-.PP
- at SEEALSO@
+.BR afetch (1),
+.BR alistat (1),
+.BR compalign (1),
+.BR compstruct (1),
+.BR revcomp (1),
+.BR seqsplit (1),
+.BR seqstat (1),
+.BR sfetch (1),
+.BR shuffle (1),
+.BR sindex (1),
+.BR stranslate (1),
+.BR weight (1).
.SH AUTHOR
- at PACKAGE@ and its documentation are @COPYRIGHT@
- at LICENSE@
+Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
See COPYING in the source code distribution for more details, or contact me.
.nf
diff --git a/Testsuite/Makefile.in b/Testsuite/Makefile.in
index 055c7b6..773627b 100644
--- a/Testsuite/Makefile.in
+++ b/Testsuite/Makefile.in
@@ -13,7 +13,6 @@
SHELL = /bin/sh
CC = @CC@
-CFLAGS = @CFLAGS@
DEFS = @DEFS@
LIBS = -lsquid @LIBS@ -lm
diff --git a/Testsuite/bug-1-sfetch-paths b/Testsuite/bug-1-sfetch-paths
index 38f5e47..9704bf5 100644
--- a/Testsuite/bug-1-sfetch-paths
+++ b/Testsuite/bug-1-sfetch-paths
@@ -6,6 +6,7 @@
# Reported by Zhirong.
# SRE, Wed Mar 6 21:07:47 2002
+use lib '.';
use testsuite;
testsuite::description("bug-1-sfetch-path", "sfetch/SSI path bug");
diff --git a/Testsuite/x-base-afetch b/Testsuite/x-base-afetch
index 0ed6e9d..032af21 100644
--- a/Testsuite/x-base-afetch
+++ b/Testsuite/x-base-afetch
@@ -1,5 +1,6 @@
#! /usr/bin/perl
+use lib '.';
use testsuite;
testsuite::description("x-base-afetch", "basic tests of afetch");
diff --git a/Testsuite/x-base-alistat b/Testsuite/x-base-alistat
index 6b461f6..bcb7f4c 100644
--- a/Testsuite/x-base-alistat
+++ b/Testsuite/x-base-alistat
@@ -1,5 +1,6 @@
#! /usr/bin/perl
+use lib '.';
use testsuite;
testsuite::description("x-base-alistat", "basic tests of alistat");
diff --git a/Testsuite/x-base-seqstat b/Testsuite/x-base-seqstat
index b7cd7af..6ec9b72 100644
--- a/Testsuite/x-base-seqstat
+++ b/Testsuite/x-base-seqstat
@@ -1,5 +1,6 @@
#! /usr/bin/perl
+use lib '.';
use testsuite;
testsuite::description("x-base-seqstat", "basic tests of seqstat");
diff --git a/Testsuite/x-base-sfetch b/Testsuite/x-base-sfetch
index 73a9a10..d8e2b18 100644
--- a/Testsuite/x-base-sfetch
+++ b/Testsuite/x-base-sfetch
@@ -1,5 +1,6 @@
#! /usr/bin/perl
+use lib '.';
use testsuite;
testsuite::description("x-base-sfetch", "basic tests of sfetch");
diff --git a/Testsuite/x-base-shuffle b/Testsuite/x-base-shuffle
index 4f9b4e2..222ebb2 100644
--- a/Testsuite/x-base-shuffle
+++ b/Testsuite/x-base-shuffle
@@ -1,5 +1,6 @@
#! /usr/bin/perl
+use lib '.';
use testsuite;
testsuite::description("x-base-shuffle", "basic tests of shuffle");
diff --git a/Testsuite/x-base-sindex b/Testsuite/x-base-sindex
index c3d689d..23c9e27 100644
--- a/Testsuite/x-base-sindex
+++ b/Testsuite/x-base-sindex
@@ -1,5 +1,6 @@
#! /usr/bin/perl
+use lib '.';
use testsuite;
testsuite::description("x-base-sindex", "basic tests of sindex");
diff --git a/Testsuite/x-base-sreformat b/Testsuite/x-base-sreformat
index ca4a162..e583298 100644
--- a/Testsuite/x-base-sreformat
+++ b/Testsuite/x-base-sreformat
@@ -1,5 +1,6 @@
#! /usr/bin/perl
+use lib '.';
use testsuite;
testsuite::description("x-base-sreformat", "basic tests of sreformat");
diff --git a/configure.ac b/configure.ac
index 5027a84..48ea01e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -38,6 +38,9 @@ AC_PREREQ(2.57)
AC_INIT(SQUID, 1.9g, eddy at genetics.wustl.edu, squid)
AC_MSG_NOTICE([configuring the SQUID library for your system.])
+# Write out squidconf.h header
+AC_CONFIG_HEADER(squidconf.h)
+
SQUID_RELCODE="squid1_9g"
SQUID_DATE="January 2003"
SQUID_COPYRIGHT="Copyright (C) 1992-2003 HHMI/Washington University School of Medicine"
@@ -53,51 +56,28 @@ AC_SUBST(SQUID_LICENSE)
AC_SUBST(SQUID_LICENSETAG)
AC_SUBST(SQUID_VERSION)
+
# Make preprocessor symbols.
-AC_DEFINE_UNQUOTED(SQUID_DATE, "$SQUID_DATE")
-AC_DEFINE_UNQUOTED(SQUID_COPYRIGHT, "$SQUID_COPYRIGHT")
-AC_DEFINE_UNQUOTED(SQUID_LICENSE, "$SQUID_LICENSE")
-AC_DEFINE_UNQUOTED(SQUID_VERSION, "$SQUID_VERSION")
+AC_DEFINE_UNQUOTED(SQUID_DATE, "$SQUID_DATE", "Release date")
+AC_DEFINE_UNQUOTED(SQUID_COPYRIGHT, "$SQUID_COPYRIGHT", "copyright info")
+AC_DEFINE_UNQUOTED(SQUID_LICENSE, "$SQUID_LICENSE", "Short license info")
+AC_DEFINE_UNQUOTED(SQUID_VERSION, "$SQUID_VERSION", "Version")
+
# Checks for programs.
#
AC_PROG_CC
AC_PROG_RANLIB
+AC_PROG_LIBTOOL
AC_PATH_PROG([AR], [ar], [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin])
-# GNU make check; format of makefile dependency lines for executables.
-# original from John Darrington <j.darrington at elvis.murdoch.edu.au>
-# w/ heavy modifications.
-#
-# We need this because GNU make and SYSV make use different systems
-# specifying variables for dependencies: $$@ in sysv, %: %.o in GNU.
-# Would love to hear a better way of doing this.
-#
-# I use two different conventions in my Makefiles. Sometimes
-# executable "foo" has a file "foo.c" - this is the HMMER convention.
-# Sometimes executable "foo" has a file "foo_main.c" - this is
-# the SQUID convention. The configure script sets the
-# EXEC_DEPENDENCY appropriately: here, HMMER style.
-#
-# This creates a function CHECK_GNU_MAKE, which we immediately call.
-# It sets an output variable EXEC_DEPENDENCY.
-# This is used in the src/Makefile.in.
-#
-AC_DEFUN(CHECK_GNU_MAKE,[
- AC_MSG_CHECKING(whether your make is GNU make)
- foundGNUmake='nope, assuming sysv make.' ;
- EXEC_DEPENDENCY=[\$\$\@_main.o] ;
- if ( make --version nothing 2> /dev/null | grep GNU > /dev/null ) ; then
- foundGNUmake='yes, it is.' ;
- EXEC_DEPENDENCY='%: %_main.o' ;
- fi
- AC_MSG_RESULT($foundGNUmake)
- AC_SUBST(EXEC_DEPENDENCY)
-])
-CHECK_GNU_MAKE
+# We know we use GNU make, but we require this EXEC_DEPENDENCY
+
+EXEC_DEPENDENCY='%: %_main.o'
+AC_SUBST(EXEC_DEPENDENCY)
+
-
# ================================================================
# Provide for unsigned integers of known size
# Sets SQD_UINT16, 32, and 64.
@@ -162,11 +142,14 @@ AC_DEFUN(SQ_ARITHMETIC_FPOS_T, [
fpos_arithmetic="no."
AC_TRY_COMPILE([#include <stdio.h>],
[int main(void) { fpos_t f1, f2; if (f1 == f2) f1 = 0;}],
- [AC_DEFINE(ARITHMETIC_FPOS_T)
- fpos_arithmetic="yes."])
+ [ARITHMETIC_FPOS_T=1
+ fpos_arithmetic="yes."])
AC_MSG_RESULT($fpos_arithmetic)
])
SQ_ARITHMETIC_FPOS_T()
+
+AC_DEFINE(ARITHMETIC_FPOS_T, [], "have fpos_t")
+AC_SUBST(ARITHMETIC_FPOS_T)
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# ================================================================
@@ -177,6 +160,7 @@ AC_CHECK_FUNCS(strtoull)
AC_CHECK_FUNCS(ftello fseeko)
AC_CHECK_FUNCS(ftello64 fseeko64)
AC_CHECK_FUNCS(ftell64 fseek64)
+
AC_CHECK_FUNC(stat64,
[AC_MSG_CHECKING(for struct stat64)
stat64_struct="no!"
@@ -184,10 +168,12 @@ AC_CHECK_FUNC(stat64,
#include <sys/stat.h>
#include <unistd.h>],
[int main(void) { struct stat64 s1;} ],
- [AC_DEFINE(HAVE_STAT64)
+ [HAVE_STAT64=1
stat64_struct="yes."])
AC_MSG_RESULT($stat64_struct)]
)
+AC_DEFINE(HAVE_STAT64, 0, "have struct stat64")
+AC_SUBST(HAVE_STAT64)
AC_CHECK_SIZEOF(off_t)
AC_CHECK_SIZEOF(off64_t)
AC_CHECK_SIZEOF(fpos_t)
@@ -218,6 +204,7 @@ esac])
+AC_DEFINE(DEBUGLEVEL, 0, "Debugging level")
# --enable-debugging=x - set debugging level to <x> (1-3)
#
# At all levels, including 0, replaces CFLAGS w/ "-g -Wall" (so it assumes gcc).
@@ -229,28 +216,28 @@ AC_ARG_ENABLE(debugging,
[ case $enable_debugging in
yes) AC_MSG_NOTICE([enabled debugging diagnostics level 0 (CFLAGS only, no verbosity)])
CFLAGS="-g -Wall"
- AC_DEFINE(DEBUGLEVEL, 0)
+ DEBUGLEVEL=0
;;
1) AC_MSG_NOTICE([enabled debugging diagnostics level 1 (low verbosity)])
CFLAGS="-g -Wall"
- AC_DEFINE(DEBUGLEVEL, 1)
+ DEBUGLEVEL=1
;;
2) AC_MSG_NOTICE([enabled debugging diagnostics level 2 (moderate verbosity)])
CFLAGS="-g -Wall"
- AC_DEFINE(DEBUGLEVEL, 2)
+ DEBUGLEVEL=2
;;
3) AC_MSG_NOTICE([enabled debugging diagnostics level 3 (high verbosity)])
CFLAGS="-g -Wall"
- AC_DEFINE(DEBUGLEVEL, 3)
+ DEBUGLEVEL=3
;;
no) AC_MSG_NOTICE([debugging diagnostics disabled])
- AC_DEFINE(DEBUGLEVEL, 0)
+ DEBUGLEVEL=0
;;
*) echo "Ignoring unknown argument to --enable-debugging: $enable_debugging"
;;
esac])
-
+AC_SUBST(DEBUGLEVEL)
# --enable-lfs Large File Summit (LFS) support for >2GB files
# See: http://ftp.sas.com/standards/large.file/x_open.20Mar96.html
@@ -259,14 +246,22 @@ AC_ARG_ENABLE(lfs,
[ --enable-lfs enable LFS, Large File Support],
[case $enable_lfs in
yes) AC_MSG_NOTICE([configured for optional LFS, large file support])
- AC_DEFINE(_LARGEFILE_SOURCE)
- AC_DEFINE(_LARGEFILE64_SOURCE)
- AC_DEFINE(_FILE_OFFSET_BITS, 64)
+ _LARGEFILE_SOURCE=1
+ _LARGEFILE64_SOURCE=1
+ _FILE_OFFSET_BITS=64
;;
no) ;;
*) echo "Ignoring unknown argument to --enable-lfs: $enable_lfs"
;;
esac])
+AC_DEFINE(_LARGEFILE_SOURCE, 0, "Source supports large files")
+AC_DEFINE(_LARGEFILE64_SOURCE, 0, "Source supports large files")
+AC_DEFINE(_FILE_OFFSET_BITS, 64, "Size of file offset bits)
+AC_SUBST(_LARGEFILE_SOURCE)
+AC_SUBST(_LARGEFILE64_SOURCE)
+AC_SUBST(_FILE_OFFSET_BITS)
+
+
@@ -282,20 +277,20 @@ AC_ARG_ENABLE(pvm,
PVMLIBDIR="-L${PVM_ROOT}/lib/${PVM_ARCH}"
PVMINCDIR="-I${PVM_ROOT}/include"
PVMLIBS="-lpvm3"
- AC_DEFINE(SRE_ENABLE_PVM)
+ SRE_ENABLE_PVM=1
;;
no) AC_MSG_NOTICE([PVM (Parallel Virtual machine) support disabled])
;;
*) echo "Ignoring unknown argument to --enable-pvm: $enable_pvm"
;;
esac])
+AC_DEFINE(SRE_ENABLE_PVM, 0, "Enable PVM")
+AC_SUBST(SRE_ENABLE_PVM)
AC_SUBST(PVMLIBDIR)
AC_SUBST(PVMINCDIR)
AC_SUBST(PVMLIBS)
-# Write out squidconf.h header
-AC_CONFIG_HEADER(squidconf.h)
# Write out Makefiles, and squid.h also has some output variable substitution.
AC_CONFIG_FILES(Makefile)
diff --git a/debian/patches/automake.patch b/debian/patches/automake.patch
index 5210c73..1ef883b 100644
--- a/debian/patches/automake.patch
+++ b/debian/patches/automake.patch
@@ -161,7 +161,34 @@ Last-Update: Thu, 23 Mar 2017 21:55:15 +0100
+
--- a/configure.ac
+++ b/configure.ac
-@@ -64,40 +64,9 @@ AC_DEFINE_UNQUOTED(SQUID_VERSION, "$SQUI
+@@ -38,6 +38,9 @@
+ AC_INIT(SQUID, 1.9g, eddy at genetics.wustl.edu, squid)
+ AC_MSG_NOTICE([configuring the SQUID library for your system.])
+
++# Write out squidconf.h header
++AC_CONFIG_HEADER(squidconf.h)
++
+ SQUID_RELCODE="squid1_9g"
+ SQUID_DATE="January 2003"
+ SQUID_COPYRIGHT="Copyright (C) 1992-2003 HHMI/Washington University School of Medicine"
+@@ -53,51 +56,28 @@
+ AC_SUBST(SQUID_LICENSETAG)
+ AC_SUBST(SQUID_VERSION)
+
++
+ # Make preprocessor symbols.
+-AC_DEFINE_UNQUOTED(SQUID_DATE, "$SQUID_DATE")
+-AC_DEFINE_UNQUOTED(SQUID_COPYRIGHT, "$SQUID_COPYRIGHT")
+-AC_DEFINE_UNQUOTED(SQUID_LICENSE, "$SQUID_LICENSE")
+-AC_DEFINE_UNQUOTED(SQUID_VERSION, "$SQUID_VERSION")
++AC_DEFINE_UNQUOTED(SQUID_DATE, "$SQUID_DATE", "Release date")
++AC_DEFINE_UNQUOTED(SQUID_COPYRIGHT, "$SQUID_COPYRIGHT", "copyright info")
++AC_DEFINE_UNQUOTED(SQUID_LICENSE, "$SQUID_LICENSE", "Short license info")
++AC_DEFINE_UNQUOTED(SQUID_VERSION, "$SQUID_VERSION", "Version")
++
+
+
+ # Checks for programs.
#
AC_PROG_CC
AC_PROG_RANLIB
@@ -198,8 +225,145 @@ Last-Update: Thu, 23 Mar 2017 21:55:15 +0100
- AC_SUBST(EXEC_DEPENDENCY)
-])
-CHECK_GNU_MAKE
--
++# We know we use GNU make, but we require this EXEC_DEPENDENCY
++
++EXEC_DEPENDENCY='%: %_main.o'
++AC_SUBST(EXEC_DEPENDENCY)
++
+
-
# ================================================================
# Provide for unsigned integers of known size
# Sets SQD_UINT16, 32, and 64.
+@@ -162,11 +142,14 @@
+ fpos_arithmetic="no."
+ AC_TRY_COMPILE([#include <stdio.h>],
+ [int main(void) { fpos_t f1, f2; if (f1 == f2) f1 = 0;}],
+- [AC_DEFINE(ARITHMETIC_FPOS_T)
+- fpos_arithmetic="yes."])
++ [ARITHMETIC_FPOS_T=1
++ fpos_arithmetic="yes."])
+ AC_MSG_RESULT($fpos_arithmetic)
+ ])
+ SQ_ARITHMETIC_FPOS_T()
++
++AC_DEFINE(ARITHMETIC_FPOS_T, [], "have fpos_t")
++AC_SUBST(ARITHMETIC_FPOS_T)
+ # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ # ================================================================
+@@ -177,6 +160,7 @@
+ AC_CHECK_FUNCS(ftello fseeko)
+ AC_CHECK_FUNCS(ftello64 fseeko64)
+ AC_CHECK_FUNCS(ftell64 fseek64)
++
+ AC_CHECK_FUNC(stat64,
+ [AC_MSG_CHECKING(for struct stat64)
+ stat64_struct="no!"
+@@ -184,10 +168,12 @@
+ #include <sys/stat.h>
+ #include <unistd.h>],
+ [int main(void) { struct stat64 s1;} ],
+- [AC_DEFINE(HAVE_STAT64)
++ [HAVE_STAT64=1
+ stat64_struct="yes."])
+ AC_MSG_RESULT($stat64_struct)]
+ )
++AC_DEFINE(HAVE_STAT64, 0, "have struct stat64")
++AC_SUBST(HAVE_STAT64)
+ AC_CHECK_SIZEOF(off_t)
+ AC_CHECK_SIZEOF(off64_t)
+ AC_CHECK_SIZEOF(fpos_t)
+@@ -218,6 +204,7 @@
+
+
+
++AC_DEFINE(DEBUGLEVEL, 0, "Debugging level")
+ # --enable-debugging=x - set debugging level to <x> (1-3)
+ #
+ # At all levels, including 0, replaces CFLAGS w/ "-g -Wall" (so it assumes gcc).
+@@ -229,28 +216,28 @@
+ [ case $enable_debugging in
+ yes) AC_MSG_NOTICE([enabled debugging diagnostics level 0 (CFLAGS only, no verbosity)])
+ CFLAGS="-g -Wall"
+- AC_DEFINE(DEBUGLEVEL, 0)
++ DEBUGLEVEL=0
+ ;;
+ 1) AC_MSG_NOTICE([enabled debugging diagnostics level 1 (low verbosity)])
+ CFLAGS="-g -Wall"
+- AC_DEFINE(DEBUGLEVEL, 1)
++ DEBUGLEVEL=1
+ ;;
+ 2) AC_MSG_NOTICE([enabled debugging diagnostics level 2 (moderate verbosity)])
+ CFLAGS="-g -Wall"
+- AC_DEFINE(DEBUGLEVEL, 2)
++ DEBUGLEVEL=2
+ ;;
+ 3) AC_MSG_NOTICE([enabled debugging diagnostics level 3 (high verbosity)])
+ CFLAGS="-g -Wall"
+- AC_DEFINE(DEBUGLEVEL, 3)
++ DEBUGLEVEL=3
+ ;;
+ no) AC_MSG_NOTICE([debugging diagnostics disabled])
+- AC_DEFINE(DEBUGLEVEL, 0)
++ DEBUGLEVEL=0
+ ;;
+ *) echo "Ignoring unknown argument to --enable-debugging: $enable_debugging"
+ ;;
+ esac])
+
+-
++AC_SUBST(DEBUGLEVEL)
+
+ # --enable-lfs Large File Summit (LFS) support for >2GB files
+ # See: http://ftp.sas.com/standards/large.file/x_open.20Mar96.html
+@@ -259,14 +246,22 @@
+ [ --enable-lfs enable LFS, Large File Support],
+ [case $enable_lfs in
+ yes) AC_MSG_NOTICE([configured for optional LFS, large file support])
+- AC_DEFINE(_LARGEFILE_SOURCE)
+- AC_DEFINE(_LARGEFILE64_SOURCE)
+- AC_DEFINE(_FILE_OFFSET_BITS, 64)
++ _LARGEFILE_SOURCE=1
++ _LARGEFILE64_SOURCE=1
++ _FILE_OFFSET_BITS=64
+ ;;
+ no) ;;
+ *) echo "Ignoring unknown argument to --enable-lfs: $enable_lfs"
+ ;;
+ esac])
++AC_DEFINE(_LARGEFILE_SOURCE, 0, "Source supports large files")
++AC_DEFINE(_LARGEFILE64_SOURCE, 0, "Source supports large files")
++AC_DEFINE(_FILE_OFFSET_BITS, 64, "Size of file offset bits)
++AC_SUBST(_LARGEFILE_SOURCE)
++AC_SUBST(_LARGEFILE64_SOURCE)
++AC_SUBST(_FILE_OFFSET_BITS)
++
++
+
+
+
+@@ -282,20 +277,20 @@
+ PVMLIBDIR="-L${PVM_ROOT}/lib/${PVM_ARCH}"
+ PVMINCDIR="-I${PVM_ROOT}/include"
+ PVMLIBS="-lpvm3"
+- AC_DEFINE(SRE_ENABLE_PVM)
++ SRE_ENABLE_PVM=1
+ ;;
+ no) AC_MSG_NOTICE([PVM (Parallel Virtual machine) support disabled])
+ ;;
+ *) echo "Ignoring unknown argument to --enable-pvm: $enable_pvm"
+ ;;
+ esac])
++AC_DEFINE(SRE_ENABLE_PVM, 0, "Enable PVM")
++AC_SUBST(SRE_ENABLE_PVM)
+ AC_SUBST(PVMLIBDIR)
+ AC_SUBST(PVMINCDIR)
+ AC_SUBST(PVMLIBS)
+
+
+-# Write out squidconf.h header
+-AC_CONFIG_HEADER(squidconf.h)
+
+ # Write out Makefiles, and squid.h also has some output variable substitution.
+ AC_CONFIG_FILES(Makefile)
diff --git a/getopt.c b/getopt.c
index 386c352..ee8bea4 100644
--- a/getopt.c
+++ b/getopt.c
@@ -109,7 +109,8 @@ Getopt(int argc, char **argv, struct opt_s *opt, int nopts, char *usage,
opti = i;
if (arglen == strlen(opt[i].name)) break; /* exact match, stop now */
}
- if (nmatch > 1 && arglen != strlen(opt[i].name))
+ if (nmatch > 1 // got several prefix matches
+ && i == nopts) // with none of them being an exact match
Die("Option \"%s\" is ambiguous; please be more specific.\n%s",
argv[optind], usage);
if (nmatch == 0)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/biosquid.git
More information about the debian-med-commit
mailing list