[med-svn] [psortb] 04/04: Use libsquid

[Andreas Tille]

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 <tille at debian.org>
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 <tille at debian.org>  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 <tille at debian.org>
+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 <tille at debian.org>
+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