debian/changelog

+libpsortb (1.0+dfsg-3) unstable; urgency=medium
+
+  * Team upload.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 04 Jan 2019 10:43:39 -0800
+
 libpsortb (1.0+dfsg-2) unstable; urgency=medium
 
   * debhelper 11

debian/control

@@ -6,10 +6,10 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                d-shlibs,
                libsvm-dev,
-               libsquid-dev (>= 1.9g+cvs20050121-9~),
-               libhmmer2-dev (>= 2.3.2+dfsg-2~),
+               libsquid-dev,
+               libhmmer2-dev,
                pkg-config
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/libpsortb
 Vcs-Git: https://salsa.debian.org/med-team/libpsortb.git
 Homepage: http://www.psort.org/
@@ -37,7 +37,6 @@ Package: libmodhmm-dev
 Architecture: any
 Section: libdevel
 Depends: libmodhmm0 (= ${binary:Version}),
-         ${shlibs:Depends},
          ${misc:Depends}
 Description: library for constructing, training and scoring hidden Markov models (dev)
  Library for constructing, training and scoring hidden Markov models.  It
@@ -84,7 +83,6 @@ Architecture: any
 Section: libdevel
 Depends: libsvmloc0 (= ${binary:Version}),
          libsvm-dev,
-         ${shlibs:Depends},
          ${misc:Depends}
 Description: PSORTb adapted library for svm machine-learning library (dev)
  Libsvm is a machine-learning library which is an easy-to-use package

debian/patches/use_debian_packaged_libsvm.patch

@@ -2,22 +2,21 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Fri, 17 Mar 2017 10:23:15 +010
 Description: Use Debian packaged libsvm
 
---- a/svmloc/Makefile.am
-+++ b/svmloc/Makefile.am
-@@ -3,8 +3,8 @@
+--- libpsortb.orig/svmloc/Makefile.am
++++ libpsortb/svmloc/Makefile.am
+@@ -3,8 +3,5 @@
  # svmloc dir
  
  lib_LTLIBRARIES		= libsvmloc.la
 -libsvmloc_la_SOURCES	= binding.cpp libsvm.cpp svmloc.cpp binding.h libsvm.h svmloc.h
-+libsvmloc_la_SOURCES	= binding.cpp svmloc.cpp binding.h svmloc.h
- libsvmloc_la_LDFLAGS	= -version-info 0:0:0
- 
+-libsvmloc_la_LDFLAGS	= -version-info 0:0:0
+-
 -noinst_HEADERS = \
 -COPYRIGHT
-+LDADD = -lsvm
-+
---- a/svmloc/svmloc.h
-+++ b/svmloc/svmloc.h
++libsvmloc_la_SOURCES	= binding.cpp svmloc.cpp binding.h svmloc.h
++libsvmloc_la_LDFLAGS	= -version-info 0:0:0 -lsvm
+--- libpsortb.orig/svmloc/svmloc.h
++++ libpsortb/svmloc/svmloc.h
 @@ -12,7 +12,7 @@
  #include <stdio.h>
  #include <string.h>
@@ -27,9 +26,9 @@ Description: Use Debian packaged libsvm
  
  using namespace std;
  
---- a/svmloc/svmloc.cpp
-+++ b/svmloc/svmloc.cpp
-@@ -166,7 +166,7 @@ int SVM::train(int retrain) {
+--- libpsortb.orig/svmloc/svmloc.cpp
++++ libpsortb/svmloc/svmloc.cpp
+@@ -166,7 +166,7 @@
  
    // Free any old model we have.
    if(model != NULL) {
@@ -38,7 +37,7 @@ Description: Use Debian packaged libsvm
      model = NULL;
    }
  
-@@ -282,7 +282,7 @@ int SVM::loadModel(char *filename) {
+@@ -282,7 +282,7 @@
    }
  
    if(model != NULL) {
@@ -47,7 +46,7 @@ Description: Use Debian packaged libsvm
      model = NULL;
    }
  
-@@ -436,7 +436,7 @@ double SVM::crossValidate(int nfolds) {
+@@ -436,7 +436,7 @@
  	sumyy += y*y;
  	sumvy += v*y;
        }
@@ -56,7 +55,7 @@ Description: Use Debian packaged libsvm
        // cout << "Mean squared error = %g\n", error/(end-begin));
        total_error += error;			
      } else {
-@@ -447,7 +447,7 @@ double SVM::crossValidate(int nfolds) {
+@@ -447,7 +447,7 @@
  	double v = svm_predict(submodel,prob->x[j]);
  	if(v == prob->y[j]) ++correct;
        }
@@ -65,7 +64,7 @@ Description: Use Debian packaged libsvm
        //cout << "Accuracy = " << 100.0*correct/(end-begin) << " (" <<
        //correct << "/" << (end-begin) << endl;
        total_correct += correct;
-@@ -502,6 +502,6 @@ int SVM::checkProbabilityModel() {
+@@ -502,6 +502,6 @@
  
  SVM::~SVM() {
  	if(x_space!=NULL) { free_x_space(); }