[med-svn] [biosquid] 01/01: Try to use automake to have better control over static and dynamic libs
Andreas Tille
tille at debian.org
Mon Apr 3 14:48:48 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository biosquid.
commit ce3df84c86d78aa0a592ef622abd0b1dc1a8d33d
Author: Andreas Tille <tille at debian.org>
Date: Mon Apr 3 16:48:11 2017 +0200
Try to use automake to have better control over static and dynamic libs
---
debian/changelog | 7 ++
debian/control | 4 +-
debian/patches/automake.patch | 205 ++++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
4 files changed, 215 insertions(+), 2 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index a84ebd9..7bdcf5e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+biosquid (1.9g+cvs20050121-8) UNRELEASED; urgency=medium
+
+ * Moved packaging from SVN to Git
+ * Use automake
+
+ -- Andreas Tille <tille at debian.org> Mon, 03 Apr 2017 16:43:08 +0200
+
biosquid (1.9g+cvs20050121-7) unstable; urgency=medium
* Team upload.
diff --git a/debian/control b/debian/control
index d286e81..8a34606 100644
--- a/debian/control
+++ b/debian/control
@@ -8,8 +8,8 @@ Build-Depends: debhelper (>= 9),
autoconf,
autotools-dev
Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/biosquid/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biosquid/trunk/
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/biosquid.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/biosquid.git
Homepage: http://eddylab.org/software.html
Package: biosquid
diff --git a/debian/patches/automake.patch b/debian/patches/automake.patch
new file mode 100644
index 0000000..5210c73
--- /dev/null
+++ b/debian/patches/automake.patch
@@ -0,0 +1,205 @@
+Description: Use automake
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 23 Mar 2017 21:55:15 +0100
+
+--- /dev/null
++++ b/Makefile.am
+@@ -0,0 +1,154 @@
++lib_LTLIBRARIES = libbiosquid.la
++
++libbiosquiddir=$(includedir)/biosquid
++libbiosquid_HEADERS = dirichlet.h\
++ rk.h\
++ sqfuncs.h\
++ gki.h\
++ msa.h\
++ sre_random.h\
++ sre_stack.h\
++ ssi.h\
++ stopwatch.h\
++ vectorops.h
++
++COMMON_OBJS = \
++ a2m.c\
++ alignio.c\
++ clustal.c\
++ file.c\
++ getopt.c\
++ gki.c\
++ hsregex.c\
++ msa.c\
++ msf.c\
++ phylip.c\
++ selex.c\
++ sqerror.c\
++ sqio.c\
++ squidcore.c\
++ sre_ctype.c\
++ sre_random.c\
++ sre_string.c\
++ ssi.c\
++ stockholm.c\
++ types.c\
++ vectorops.c
++
++libbiosquid_la_SOURCES = $(COMMON_OBJS)\
++ aligneval.c\
++ cluster.c\
++ dayhoff.c\
++ dirichlet.c\
++ eps.c\
++ iupac.c\
++ revcomp.c\
++ rk.c\
++ seqencode.c\
++ shuffle.c\
++ sre_math.c\
++ sre_stack.c\
++ stopwatch.c\
++ translate.c\
++ weight.c\
++ wuss.c
++
++libbiosquid_la_LDFLAGS = -version-info @LIB_VERSION@
++
++libbiosquid_la_CPPFLAGS = $(INCLUDES)
++
++bin_PROGRAMS = afetch\
++ alistat\
++ compalign\
++ compstruct\
++ revcomp\
++ seqsplit\
++ seqstat\
++ sfetch\
++ shuffle\
++ sindex\
++ sreformat\
++ translate\
++ weight
++
++bin_MANS = afetch\
++ alistat\
++ compstruct\
++ seqstat\
++ sfetch\
++ shuffle\
++ sindex\
++ sreformat
++
++READMES = 00README INSTALL
++
++SCRIPTS =
++
++PRECONFHDRS = \
++ squid.h.in\
++ squidconf.h.in
++
++POSTCONFHDRS = \
++ squid.h\
++ squidconf.h
++
++afetch_SOURCES = afetch_main.c
++
++alistat_SOURCES = alistat_main.c\
++ aligneval.c\
++ cluster.c\
++ sre_math.c\
++ sre_stack.c
++
++compalign_SOURCES = compalign_main.c\
++ aligneval.c
++
++compstruct_SOURCES = compstruct_main.c\
++ sre_math.c\
++ sre_stack.c\
++ wuss.c
++
++revcomp_SOURCES = revcomp_main.c\
++ revcomp.c\
++ shuffle.c
++
++seqsplit_SOURCES = seqsplit_main.c
++
++seqstat_SOURCES = seqstat_main.c
++
++sfetch_SOURCES = sfetch_main.c\
++ revcomp.c\
++ shuffle.c
++
++shuffle_SOURCES = shuffle_main.c\
++ iupac.c\
++ shuffle.c
++
++sindex_SOURCES = sindex_main.c
++
++sreformat_SOURCES = sreformat_main.c\
++ eps.c\
++ shuffle.c\
++ sre_stack.c\
++ wuss.c
++
++translate_SOURCES = translate_main.c\
++ iupac.c\
++ revcomp.c\
++ shuffle.c\
++ sre_stack.c\
++ translate.c
++
++weight_SOURCES = weight_main.c\
++ aligneval.c\
++ cluster.c\
++ iupac.c\
++ sre_math.c\
++ sre_stack.c\
++ weight.c
++
++
++check: libsquid.a
++ (cd Testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)")
++ (cd Testsuite; make check)
++
+--- a/configure.ac
++++ b/configure.ac
+@@ -64,40 +64,9 @@ AC_DEFINE_UNQUOTED(SQUID_VERSION, "$SQUI
+ #
+ 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
+-
+-
+ # ================================================================
+ # Provide for unsigned integers of known size
+ # Sets SQD_UINT16, 32, and 64.
diff --git a/debian/patches/series b/debian/patches/series
index 0d525ba..680cb33 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -10,3 +10,4 @@ sreformat.man.patch
getopt-segmentation-fault.patch
reproducible.patch
perl-testsuite-inc.patch
+automake.patch
--
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