[med-svn] [hmmer2] 08/09: Use Debian packaged biosquid

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository hmmer2.

commit 89dd00b0fb85e5e758854ecca1ee8598b263d5f6
Author: Andreas Tille <tille at debian.org>
Date:   Wed Apr 12 13:00:39 2017 +0200

    Use Debian packaged biosquid
---
 debian/control                                    |  4 +-
 debian/patches/series                             |  1 +
 debian/patches/use_debian_packaged_biosquid.patch | 98 +++++++++++++++++++++++
 3 files changed, 102 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 0613f23..7a805da 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,9 @@ Priority: optional
 Build-Depends: debhelper (>= 9),
                pvm-dev,
                autotools-dev,
-               libperl4-corelibs-perl
+               libperl4-corelibs-perl,
+               libsquid-dev,
+               pkg-config
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/git/debian-med/hmmer2.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/hmmer2.git
diff --git a/debian/patches/series b/debian/patches/series
index c3328e9..63460a7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 version2-manpage
 userguidepdf
 spelling.patch
+use_debian_packaged_biosquid.patch
diff --git a/debian/patches/use_debian_packaged_biosquid.patch b/debian/patches/use_debian_packaged_biosquid.patch
new file mode 100644
index 0000000..5536f7f
--- /dev/null
+++ b/debian/patches/use_debian_packaged_biosquid.patch
@@ -0,0 +1,98 @@
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -42,9 +42,9 @@ PVMLIBS   = @PVMLIBS@
+ PVMPROGS  = @PVMPROGS@
+ 
+ SHELL    = /bin/sh
+-MYLIBS   = -lsquid
+-MYLIBDIR = -L../squid
+-MYINCDIR = -I../squid
++MYLIBS   = `pkg-config --libs libsquid`
++MYLIBDIR = 
++MYINCDIR = `pkg-config --cflags libsquid`
+ 
+ PROGS = hmmalign\
+ 	hmmbuild\
+--- a/testsuite/Makefile.in
++++ b/testsuite/Makefile.in
+@@ -17,7 +17,7 @@ CPPFLAGS  = @CPPFLAGS@
+ LDFLAGS   = @LDFLAGS@
+ DEFS      = @DEFS@
+ LIBS      = @LIBS@ -lm
+-MYLIBS    = -lhmmer -lsquid
++MYLIBS    = -lhmmer `pkg-config --libs libsquid`
+ 
+ # Configuration for optional pthreads multiprocessor support
+ #
+@@ -40,12 +40,12 @@ SHIVA = alignalign_test\
+ #######
+ 
+ .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 $<		
+ 
+ all: 	$(SHIVA)
+ 
+ $(SHIVA): @EXEC_DEPENDENCY@
+-	$(CC) $(CFLAGS) $(PTHREAD_CFLAGS) ${LDFLAGS} $(DEFS) -o $@ -L../squid -L../src $@.o $(MYLIBS) $(PTHREAD_LIBS) $(LIBS)
++	$(CC) $(CFLAGS) $(PTHREAD_CFLAGS) ${LDFLAGS} $(DEFS) -o $@ -L../src $@.o $(MYLIBS) $(PTHREAD_LIBS) $(LIBS)
+ 
+ #######
+ ## `make check` actually runs the tests.
+--- a/src/funcs.h
++++ b/src/funcs.h
+@@ -181,7 +181,6 @@ extern void  LogNorm(float *vec, int n);
+ extern float Logp_cvec(float *cvec, int n, float *alpha);
+ extern void  SampleDirichlet(float *alpha, int n, float *p);
+ extern float SampleGamma(float alpha);
+-extern void  SampleCountvector(float *p, int n, int c, float *cvec);
+ extern float P_PvecGivenDirichlet(float *p, int n, float *alpha);
+ 
+ /* from misc.c
+--- a/src/mathsupport.c
++++ b/src/mathsupport.c
+@@ -320,23 +320,6 @@ SampleGamma(float alpha)
+   return 0.0;
+ }
+ 
+-/* Function: SampleCountvector()
+- * 
+- * Purpose:  Given a probability vector p of dimensionality
+- *           n, sample c counts and store them in cvec.
+- *           cvec is n-dimensional and is alloced by the caller.
+- */
+-void
+-SampleCountvector(float *p, int n, int c, float *cvec)
+-{
+-  int i;
+-
+-  FSet(cvec, n, 0.0);
+-  for (i = 0; i < c; i++)
+-    cvec[FChoose(p,n)] += 1.0;
+-}
+-
+-
+ 
+ /* Function: P_PvecGivenDirichlet()
+  * 
+--- a/configure
++++ b/configure
+@@ -2601,7 +2601,7 @@ echo "$as_me: configured for optional LF
+ _ACEOF
+ 
+ 	cat >>confdefs.h <<\_ACEOF
+-#define _LARGEFILE64_SOURCE 1
++#define _LARGEFILE64_SOURCE_defined_in_biosquid 1
+ _ACEOF
+ 
+ 	cat >>confdefs.h <<\_ACEOF
+--- a/src/config.h.in
++++ b/src/config.h.in
+@@ -97,7 +97,6 @@
+ /* --enable-lfs          Large File Summit (LFS) support for >2Gb files
+  */
+ #undef _LARGEFILE_SOURCE
+-#undef _LARGEFILE64_SOURCE
+ #undef _FILE_OFFSET_BITS
+ 
+ /* --enable-pvm          Parallel Virtual Machine (PVM)

-- 
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