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 <[email protected]> Wed, 27 Jun 2012 14:17:05 +0200 + hhsuite (2.0.14-1) unstable; urgency=low * [Andreas Tille <[email protected]>] 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 <[email protected]> Uploaders: Laszlo Kajan <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
