This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository psortb.
commit b0700ac63c53b22c10b7772fbb186ce21e6cd223 Author: Andreas Tille <[email protected]> Date: Wed Apr 5 16:34:54 2017 +0200 Use libsquid --- debian/changelog | 2 ++ debian/control | 3 ++- debian/patches/biosquid_includes.patch | 15 +++++++++++++++ debian/patches/series | 2 ++ debian/patches/use_declaration_of_biosquid.patch | 14 ++++++++++++++ 5 files changed, 35 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 43a6aa7..42d36c6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,7 @@ psortb (3.0.4+dfsg-1) UNRELEASED; urgency=medium * Initial release (Closes: #<bug>) + TraceScoreCorrection is part of hmmer2 package. This needs to be + turned into a library -- Andreas Tille <[email protected]> Fri, 17 Mar 2017 10:23:15 +0100 diff --git a/debian/control b/debian/control index f772dad..42f6af6 100644 --- a/debian/control +++ b/debian/control @@ -6,7 +6,8 @@ Priority: optional Build-Depends: debhelper (>= 10), bioperl, ncbi-blast+-legacy, - biosquid-dev + libsquid-dev, + pkg-config Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/psortb.git Vcs-Git: https://anonscm.debian.org/git/debian-med/psortb.git diff --git a/debian/patches/biosquid_includes.patch b/debian/patches/biosquid_includes.patch new file mode 100644 index 0000000..ceb330c --- /dev/null +++ b/debian/patches/biosquid_includes.patch @@ -0,0 +1,15 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Fri, 17 Mar 2017 10:23:15 +010 +Description: Include header files provided by libsquid-dev + +--- a/algorithm-hmm/Makefile.PL ++++ b/algorithm-hmm/Makefile.PL +@@ -33,7 +33,7 @@ WriteMakefile('NAME' => 'Algori + 'LIBS' => $libpath, + 'CC' => $CC, + 'LD' => '$(CC)', +- 'INC' => '-Isrc/include', ++ 'INC' => '-Isrc/include `pkg-config --cflags libsquid`', + 'OBJECT' => "HMM.o hmm-binding.o", + 'XSOPT' => '-C++', + ); diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..1ff75fb --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,2 @@ +biosquid_includes.patch +use_declaration_of_biosquid.patch diff --git a/debian/patches/use_declaration_of_biosquid.patch b/debian/patches/use_declaration_of_biosquid.patch new file mode 100644 index 0000000..24839e6 --- /dev/null +++ b/debian/patches/use_declaration_of_biosquid.patch @@ -0,0 +1,14 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Fri, 17 Mar 2017 10:23:15 +010 +Description: Remove duplicated definition which is provided by libsquid + +--- a/algorithm-hmm/src/include/funcs.h ++++ b/algorithm-hmm/src/include/funcs.h +@@ -170,7 +170,6 @@ 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/psortb.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
