[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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