[med-svn] [Git][med-team/hmmer2][master] 4 commits: Update PKG_CONFIG macro in configure.ac and avoid hard-coding the same to get...
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Mon Mar 25 12:12:34 GMT 2024
Nilesh Patra pushed to branch master at Debian Med / hmmer2
Commits:
ea080a4f by Nilesh Patra at 2024-03-25T17:06:22+05:30
Update PKG_CONFIG macro in configure.ac and avoid hard-coding the same to get package cross-building
- - - - -
7d207224 by Nilesh Patra at 2024-03-25T17:08:11+05:30
Since tests are compiled during build time, cleanup before running dh_installexamples
- - - - -
e02dcb39 by Nilesh Patra at 2024-03-25T17:27:19+05:30
Fixup wrong paths in .pc file
- - - - -
87fe57c5 by Nilesh Patra at 2024-03-25T17:34:53+05:30
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/libhmmer2-dev.install
- debian/missing-sources/configure.ac
- debian/patches/use_debian_packaged_biosquid.patch
- debian/pkgconfig/libhmmer2.pc → debian/pkgconfig/libhmmer2.pc.in
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+hmmer2 (2.3.2+dfsg-10) unstable; urgency=medium
+
+ * Team Upload.
+ * Update PKG_CONFIG macro in configure.ac and avoid
+ hard-coding the same to get package cross-building
+ * Since tests are compiled during build time, cleanup
+ before running dh_installexamples
+ * Fixup wrong paths in .pc file
+
+ -- Nilesh Patra <nilesh at iki.fi> Mon, 25 Mar 2024 17:34:19 +0530
+
hmmer2 (2.3.2+dfsg-9) unstable; urgency=medium
* Team Upload.
=====================================
debian/libhmmer2-dev.install
=====================================
@@ -5,4 +5,4 @@ src/globals.h usr/include/hmmer2
src/postprob.h usr/include/hmmer2
src/structs.h usr/include/hmmer2
src/libhmmer.a usr/lib/${DEB_HOST_MULTIARCH}
-debian/pkgconfig usr/lib/${DEB_HOST_MULTIARCH}
+debian/pkgconfig/libhmmer2.pc usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig/
=====================================
debian/missing-sources/configure.ac
=====================================
@@ -73,6 +73,14 @@ AC_PROG_CC
AC_PROG_RANLIB
AC_PATH_PROG([AR], [ar], [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin])
+dnl directive for enabling PKG_CONFIG
+PKG_PROG_PKG_CONFIG
+AS_IF([test "x$PKG_CONFIG" = "x"],[
+ AC_MSG_ERROR([
+ *** The pkg-config script could not be found. Make sure it is
+ *** in your path, or set the PKG_CONFIG environment variable
+ *** to the full path to pkg-config.])
+ ])
# Figure out what host we're compiling on.
# Three GNU scripts must be included in the distro:
=====================================
debian/patches/use_debian_packaged_biosquid.patch
=====================================
@@ -5,36 +5,45 @@ Description: Link against Debian packaged libsquid and remove
--- a/src/Makefile.in
+++ b/src/Makefile.in
-@@ -42,9 +42,9 @@ PVMLIBS = @PVMLIBS@
+@@ -18,6 +18,7 @@
+ CPPFLAGS = @CPPFLAGS@
+ LDFLAGS = @LDFLAGS@
+ DEFS = @DEFS@
++PKG_CONFIG = @PKG_CONFIG@
+ LIBS = @LIBS@ -lm
+
+ ## archiving command, and ranlib command if you need one.
+@@ -42,9 +43,9 @@
PVMPROGS = @PVMPROGS@
SHELL = /bin/sh
-MYLIBS = -lsquid
-MYLIBDIR = -L../squid
-MYINCDIR = -I../squid
-+MYLIBS = `pkg-config --libs libsquid`
++MYLIBS = `$(PKG_CONFIG) --libs libsquid`
+MYLIBDIR =
-+MYINCDIR = `pkg-config --cflags libsquid`
++MYINCDIR = `$(PKG_CONFIG) --cflags libsquid`
PROGS = hmmalign\
hmmbuild\
--- a/testsuite/Makefile.in
+++ b/testsuite/Makefile.in
-@@ -17,7 +17,7 @@ CPPFLAGS = @CPPFLAGS@
+@@ -17,7 +17,8 @@
LDFLAGS = @LDFLAGS@
DEFS = @DEFS@
LIBS = @LIBS@ -lm
-MYLIBS = -lhmmer -lsquid
-+MYLIBS = -lhmmer `pkg-config --libs libsquid`
++PKG_CONFIG = @PKG_CONFIG@
++MYLIBS = -lhmmer `$(PKG_CONFIG) --libs libsquid`
# Configuration for optional pthreads multiprocessor support
#
-@@ -40,12 +40,12 @@ SHIVA = alignalign_test\
+@@ -40,12 +41,12 @@
#######
.c.o:
- $(CC) $(CFLAGS) $(PTHREAD_CFLAGS) ${CPPFLAGS} $(DEFS) -I../squid -I../src -c $<
-+ $(CC) $(CFLAGS) $(PTHREAD_CFLAGS) ${CPPFLAGS} $(DEFS) `pkg-config --cflags libsquid` -I../src -c $<
++ $(CC) $(CFLAGS) $(PTHREAD_CFLAGS) ${CPPFLAGS} $(DEFS) `$(PKG_CONFIG) --cflags libsquid` -I../src -c $<
all: $(SHIVA)
@@ -46,7 +55,7 @@ Description: Link against Debian packaged libsquid and remove
## `make check` actually runs the tests.
--- a/src/funcs.h
+++ b/src/funcs.h
-@@ -181,7 +181,6 @@ extern void LogNorm(float *vec, int n);
+@@ -181,7 +181,6 @@
extern float Logp_cvec(float *cvec, int n, float *alpha);
extern void SampleDirichlet(float *alpha, int n, float *p);
extern float SampleGamma(float alpha);
@@ -56,7 +65,7 @@ Description: Link against Debian packaged libsquid and remove
/* from misc.c
--- a/src/mathsupport.c
+++ b/src/mathsupport.c
-@@ -320,23 +320,6 @@ SampleGamma(float alpha)
+@@ -320,23 +320,6 @@
return 0.0;
}
@@ -82,7 +91,7 @@ Description: Link against Debian packaged libsquid and remove
*
--- a/configure
+++ b/configure
-@@ -2597,11 +2597,11 @@ if test "${enable_lfs+set}" = set; then
+@@ -2597,11 +2597,11 @@
yes) { echo "$as_me:$LINENO: configured for optional LFS, large file support" >&5
echo "$as_me: configured for optional LFS, large file support" >&6;}
cat >>confdefs.h <<\_ACEOF
@@ -109,7 +118,7 @@ Description: Link against Debian packaged libsquid and remove
/* --enable-pvm Parallel Virtual Machine (PVM)
--- a/Makefile.in
+++ b/Makefile.in
-@@ -87,7 +87,6 @@ all:
+@@ -87,7 +87,6 @@
echo "If you really want to rebuild from source, move or delete the" ;\
echo "binaries/ subdirectory."; \
else\
@@ -117,7 +126,7 @@ Description: Link against Debian packaged libsquid and remove
(cd src; ${MAKE}; ${MAKE} module);\
(cd testsuite; ${MAKE});\
fi
-@@ -98,9 +97,6 @@ all:
+@@ -98,9 +97,6 @@
check:
(cd testsuite; make check)
@@ -127,7 +136,7 @@ Description: Link against Debian packaged libsquid and remove
src/libhmmer.a:
(cd src; make; make module)
-@@ -143,7 +139,6 @@ bindist:
+@@ -143,7 +139,6 @@
#
clean:
(cd src; make clean)
@@ -135,7 +144,7 @@ Description: Link against Debian packaged libsquid and remove
(cd testsuite; make clean)
-rm -f *.o *~ Makefile.bak core TAGS gmon.out
-@@ -156,7 +151,6 @@ distclean:
+@@ -156,7 +151,6 @@
-rm -f *.o *~ Makefile.bak core TAGS gmon.out
-rm Makefile
(cd src; make distclean)
@@ -143,7 +152,7 @@ Description: Link against Debian packaged libsquid and remove
(cd testsuite; make distclean)
-@@ -165,7 +159,6 @@ distclean:
+@@ -165,7 +159,6 @@
#
binclean:
(cd src; make binclean)
=====================================
debian/pkgconfig/libhmmer2.pc → debian/pkgconfig/libhmmer2.pc.in
=====================================
@@ -1,10 +1,10 @@
prefix=/usr
exec_prefix=${prefix}
-libdir=${prefix}/lib/x86_64-linux-gnu
+libdir=${prefix}/lib/@DEB_HOST_MULTIARCH@
includedir=${prefix}/include/hmmer2
Name: libhmmer2
-Version: 2.3.2
+Version: @VERSION@
Description: profile hidden Markov models for protein sequence analysis
Libs: -L${libdir} -lhmmer
Cflags: -I${includedir}
=====================================
debian/rules
=====================================
@@ -8,6 +8,8 @@ endif
pkgdata:=hmmer2
sampledir:=$(CURDIR)/debian/$(pkgdata)/usr/share/doc/$(pkgdata)/examples
+include /usr/share/dpkg/pkg-info.mk
+UPSTREAM_VERSION := $(shell echo $(DEB_VERSION_UPSTREAM) | sed -e 's,+dfsg,,g')
export AUTOHEADER = 'true'
@@ -66,7 +68,14 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
cd testsuite && make clean
endif
+override_dh_install:
+ sed -e "s/@DEB_HOST_MULTIARCH@/$(DEB_HOST_MULTIARCH)/" \
+ -e "s/@VERSION@/$(UPSTREAM_VERSION)/" debian/pkgconfig/libhmmer2.pc.in > debian/pkgconfig/libhmmer2.pc
+ dh_install
+ rm -f debian/pkgconfig/libhmmer2.pc
+
override_dh_installexamples:
+ cd testsuite && make clean && cd ..
dh_installexamples
mkdir -p $(sampledir);
cp -a testsuite/* $(sampledir)/;
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/04766961c8a832c97312b22a09f0dd61bc098504...87fe57c5b4ae62513d77aba56d942914ca93c48d
--
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/04766961c8a832c97312b22a09f0dd61bc098504...87fe57c5b4ae62513d77aba56d942914ca93c48d
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