[med-svn] r11484 - in trunk/packages/hhsuite/trunk/debian: . patches

Laszlo Kajan lkajan-guest at alioth.debian.org
Wed Jun 27 13:19:09 UTC 2012 

Author: lkajan-guest
Date: 2012-06-27 13:19:09 +0000 (Wed, 27 Jun 2012)
New Revision: 11484

Added:
   trunk/packages/hhsuite/trunk/debian/patches/unnecessary_libz
   trunk/packages/hhsuite/trunk/debian/patches/unused_variables_warning
Modified:
   trunk/packages/hhsuite/trunk/debian/changelog
   trunk/packages/hhsuite/trunk/debian/control
   trunk/packages/hhsuite/trunk/debian/patches/Makefile
   trunk/packages/hhsuite/trunk/debian/patches/help
   trunk/packages/hhsuite/trunk/debian/patches/paths
   trunk/packages/hhsuite/trunk/debian/patches/series
   trunk/packages/hhsuite/trunk/debian/rules
Log:
new upstream release - depends on new ffindex version - awaiting upload of new ffindex; lintian clean, fixed all issues

Modified: trunk/packages/hhsuite/trunk/debian/changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/changelog	2012-06-27 09:52:43 UTC (rev 11483)
+++ trunk/packages/hhsuite/trunk/debian/changelog	2012-06-27 13:19:09 UTC (rev 11484)
@@ -1,3 +1,9 @@
+hhsuite (2.0.15-1) UNRELEASED; urgency=low
+
+  * New upstream release.
+
+ -- Laszlo Kajan <lkajan at rostlab.org>  Wed, 27 Jun 2012 14:17:05 +0200
+
 hhsuite (2.0.14-1) unstable; urgency=low
 
   * [Andreas Tille <tille at debian.org>]

Modified: trunk/packages/hhsuite/trunk/debian/control
===================================================================
--- trunk/packages/hhsuite/trunk/debian/control	2012-06-27 09:52:43 UTC (rev 11483)
+++ trunk/packages/hhsuite/trunk/debian/control	2012-06-27 13:19:09 UTC (rev 11484)
@@ -3,7 +3,7 @@
 Priority: extra
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Laszlo Kajan <lkajan at rostlab.org>
-Build-Depends: debhelper (>= 8.0.0), libffindex0-dev, help2man, libpng12-dev
+Build-Depends: debhelper (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev
 Standards-Version: 3.9.3
 Homepage: http://toolkit.genzentrum.lmu.de/sections/search
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/
@@ -12,7 +12,7 @@
 
 Package: hhsuite
 Architecture: amd64
-Depends: ${shlibs:Depends}, ${misc:Depends}, ffindex, hhsuite-data
+Depends: ${shlibs:Depends}, ${misc:Depends}, ffindex (>= 0.9.6.1), hhsuite-data
 Description: sensitive protein sequence searching based on HMM-HMM alignment
  HH-suite is an open-source software package for sensitive protein sequence
  searching based on the pairwise alignment of hidden Markov models (HMMs).

Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/Makefile	2012-06-27 09:52:43 UTC (rev 11483)
+++ trunk/packages/hhsuite/trunk/debian/patches/Makefile	2012-06-27 13:19:09 UTC (rev 11484)
@@ -27,7 +27,7 @@
 +INSTALL_BDATA_DIR?=$(INSTALL_LIB_DIR)/data
  INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin
  
- dist_name=hhsuite-2.0.14
+ dist_name=hhsuite-2.0.15
  
 -.PHONY: all_static
 -all_static: ffindex_static

Modified: trunk/packages/hhsuite/trunk/debian/patches/help
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/help	2012-06-27 09:52:43 UTC (rev 11483)
+++ trunk/packages/hhsuite/trunk/debian/patches/help	2012-06-27 13:19:09 UTC (rev 11484)
@@ -14,7 +14,7 @@
 +  printf(" -cslib  <file> column state file for fast database prefiltering (default=/usr/lib/hhsuite/data/cs219.lib)\n");
    printf("\n");
    printf("Predict secondary structure\n");
-   printf(" -addss         add 2ndary structure predicted with PSIPRED to output MSA \n");
+   printf(" -addss         add 2ndary structure predicted with PSIPRED to result MSA \n");
 @@ -412,7 +412,12 @@
    printf("An extended list of options can be obtained by calling 'hhblits -help'\n");
    }
@@ -39,7 +39,7 @@
  #include <errno.h>    // perror()
  #include <cassert>
  #include <stdexcept>
-@@ -301,8 +302,8 @@
+@@ -300,8 +301,8 @@
    printf("\n");
    printf("Context-specific pseudo-counts:                                                  \n");
    printf(" -nocontxt      use substitution-matrix instead of context-specific pseudocounts \n");

Modified: trunk/packages/hhsuite/trunk/debian/patches/paths
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/paths	2012-06-27 09:52:43 UTC (rev 11483)
+++ trunk/packages/hhsuite/trunk/debian/patches/paths	2012-06-27 13:19:09 UTC (rev 11484)
@@ -6,7 +6,7 @@
 +++ b/scripts/HHPaths.pm
 @@ -30,7 +30,7 @@
  use Exporter;
- our $VERSION = "version 2.0.14 (Mar 2012)";
+ our $VERSION = "version 2.0.15 (June 2012)";
  our @ISA     = qw(Exporter);
 -our @EXPORT  = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib);
 +our @EXPORT  = qw($VERSION $hhlib $hhshare $hhdata $hhbdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib);
@@ -33,7 +33,7 @@
  our $cs_lib = "$hhdata/cs219.lib";
 --- a/src/hhdecl.C
 +++ b/src/hhdecl.C
-@@ -280,7 +280,7 @@
+@@ -285,7 +285,7 @@
    if(getenv("HHLIB"))
      strcpy(hhlib, getenv("HHLIB"));
    else
@@ -42,7 +42,7 @@
  
    strcat(strcpy(hhdata, hhlib), "/data");
    strcat(strcpy(clusterfile, hhdata), "/context_data.lib");
-@@ -295,7 +295,7 @@
+@@ -300,7 +300,7 @@
        /* we did not find HHLIB, if called with full path or in dist dir, we can try relative to program path */
        if(program_path != NULL)
  	{

Modified: trunk/packages/hhsuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/series	2012-06-27 09:52:43 UTC (rev 11483)
+++ trunk/packages/hhsuite/trunk/debian/patches/series	2012-06-27 13:19:09 UTC (rev 11484)
@@ -3,3 +3,5 @@
 help
 rest1
 hardening
+unused_variables_warning
+unnecessary_libz

Added: trunk/packages/hhsuite/trunk/debian/patches/unnecessary_libz
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/unnecessary_libz	                        (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/patches/unnecessary_libz	2012-06-27 13:19:09 UTC (rev 11484)
@@ -0,0 +1,11 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -46,7 +46,7 @@
+     HHSEARCH_LIBS = -lpthread -lrt
+     HHBLITS_LIBS+=-lrt
+     ifndef NO_PNG
+-      HHALIGN_LIBS = -DNO_FREETYPE -DHH_PNG -lpng -lz
++      HHALIGN_LIBS = -DNO_FREETYPE -DHH_PNG -lpng
+     endif
+   endif
+ endif # ifndef ICC

Added: trunk/packages/hhsuite/trunk/debian/patches/unused_variables_warning
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/unused_variables_warning	                        (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/patches/unused_variables_warning	2012-06-27 13:19:09 UTC (rev 11484)
@@ -0,0 +1,18 @@
+--- a/src/pngwriter.cc
++++ b/src/pngwriter.cc
+@@ -3343,13 +3343,13 @@
+      {
+ 	std::cerr << " PNGwriter::scale_wh - ERROR **: Negative or zero final width or height not allowed." << std::endl;
+      }
+-
++/*
+    double kx;
+    double ky;
+ 
+    kx = ((double)finalwidth)/((double)width_);
+    ky = ((double)finalheight)/((double)height_);
+-
++*/
+    pngwriter temp(finalwidth, finalheight, 0, "temp");
+ 
+    int red, green, blue;

Modified: trunk/packages/hhsuite/trunk/debian/rules
===================================================================
--- trunk/packages/hhsuite/trunk/debian/rules	2012-06-27 09:52:43 UTC (rev 11483)
+++ trunk/packages/hhsuite/trunk/debian/rules	2012-06-27 13:19:09 UTC (rev 11484)
@@ -6,7 +6,7 @@
 export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
 
 # Uncomment this to turn on verbose mode.
-export DH_VERBOSE=1
+#export DH_VERBOSE=1
 
 VERSION=$(shell sed --posix -n -e '/VERSION_AND_DATE/{ s/.*version \([0-9][0-9.]*\).*/\1/; p; }' src/hhdecl.C)
 
@@ -19,12 +19,14 @@
 export n_hhmake=build an HMM from an input alignment or convert between HMMER format and HHsearch format
 export n_hhsearch=search a database of HMMs with a query alignment or query HMM
 
+.PHONY: get-orig-source
+get-orig-source:
+	mkdir -p ../tarballs
+	uscan --verbose --force-download --destdir=../tarballs
+
 .PHONY: hhmanpages
 hhmanpages: $(HHMANPAGES)
 
-%:
-	dh $@ --parallel
-
 .PHONY: override_dh_strip
 override_dh_strip:
 	dh_strip --dbg-package=hhsuite-dbg -Xlibffindex.a -Xlibffindex.so
@@ -34,13 +36,12 @@
 	dh_installman
 
 $(HHMANPAGES): %.1 : debian/tmp/usr/bin/%
-	unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' -o '$@'
+	unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@'
 
 .PHONY: override_dh_clean
 override_dh_clean:
 	rm -f $(HHMANPAGES)
 	dh_clean
 
-get-orig-source:
-	mkdir -p ../tarballs
-	uscan --verbose --force-download --destdir=../tarballs
+%:
+	dh $@ --parallel

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