Author: lkajan-guest Date: 2012-10-08 16:29:06 +0000 (Mon, 08 Oct 2012) New Revision: 12342
Added: trunk/packages/sift/trunk/debian/patches/jarfile Modified: trunk/packages/sift/trunk/debian/ trunk/packages/sift/trunk/debian/changelog trunk/packages/sift/trunk/debian/patches/ld-as-needed trunk/packages/sift/trunk/debian/patches/series trunk/packages/sift/trunk/debian/rules Log: merged changes from Ubuntu, fixed the .jar lintian warning, patched (unused) script to find .jar file in /usr/share Property changes on: trunk/packages/sift/trunk/debian ___________________________________________________________________ Modified: svn:ignore - *.substvars files *.debhelper.log + sift *.substvars files *.debhelper.log Modified: trunk/packages/sift/trunk/debian/changelog =================================================================== --- trunk/packages/sift/trunk/debian/changelog 2012-10-08 15:34:46 UTC (rev 12341) +++ trunk/packages/sift/trunk/debian/changelog 2012-10-08 16:29:06 UTC (rev 12342) @@ -1,9 +1,21 @@ -sift (4.0.3b-4) UNRELEASED; urgency=low +sift (4.0.3b-4) unstable; urgency=low + [ Andreas Tille ] * debian/upstream: Add citations - -- Andreas Tille <ti...@debian.org> Fri, 25 May 2012 10:45:33 +0200 + [ Laszlo Kajan ] + * Merge updates from Ubuntu 4.0.3b-3ubuntu1. + -- Laszlo Kajan <lka...@rostlab.org> Mon, 08 Oct 2012 16:41:15 +0200 + +sift (4.0.3b-3ubuntu1) quantal; urgency=low + + * Merge with Debian unstable. Remaining changes: + - Update patches/debian/ld-as-needed: + Move libs from LDFLAGS to LIBS. + + -- Michael Bienia <ge...@ubuntu.com> Sat, 26 May 2012 11:38:24 +0200 + sift (4.0.3b-3) unstable; urgency=low * Added patches from Michael Bienia <ge...@ubuntu.com>. Added: trunk/packages/sift/trunk/debian/patches/jarfile =================================================================== --- trunk/packages/sift/trunk/debian/patches/jarfile (rev 0) +++ trunk/packages/sift/trunk/debian/patches/jarfile 2012-10-08 16:29:06 UTC (rev 12342) @@ -0,0 +1,10 @@ +Author: Laszlo Kajan <lka...@rostlab.org> +Description: path to IntersectFeatures.jar + IntersectFeatures.jar file now in /usr/share, patch for calling script. +--- a/bin/IntersectLocations.sh ++++ b/bin/IntersectLocations.sh +@@ -1,3 +1,3 @@ + #!/bin/sh +-bin="/usr/local/projects/SIFT/sift4.0/bin/" ++bin="/usr/share/sift" + java -Xmx500m -jar $bin/IntersectFeatures.jar $1 $2 $3 $4 $5 Modified: trunk/packages/sift/trunk/debian/patches/ld-as-needed =================================================================== --- trunk/packages/sift/trunk/debian/patches/ld-as-needed 2012-10-08 15:34:46 UTC (rev 12341) +++ trunk/packages/sift/trunk/debian/patches/ld-as-needed 2012-10-08 16:29:06 UTC (rev 12342) @@ -5,11 +5,14 @@ use in CFLAGS and LDFLAGS. [Laszlo Kajan] Added dpkg-buildflags to CPPFLAGS. + Michael's explicit $(BIN) rule is made unnecessary by using LDLIBS instead + of his LIBS, as LDLIBS get used by the implicit make rules and achieves the + same result. Author: Michael Bienia <ge...@ubuntu.com> Author: Laszlo Kajan <lka...@rostlab.org> --- a/src/Makefile +++ b/src/Makefile -@@ -9,8 +9,9 @@ +@@ -9,8 +9,10 @@ seqs_from_psiblast_res CC := gcc @@ -17,7 +20,8 @@ -LDFLAGS := -L$(lib-prefix)/lib -lblimps $(LDFLAGS) +CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS) +CFLAGS := $(shell dpkg-buildflags --get CFLAGS) -Wno-unused-result -I$(include-prefix)/include/blimps -O2 -D__MAKE_PREFIX__=\"$(prefix)\" -+LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -L$(lib-prefix)/lib -lblimps -lm ++LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -L$(lib-prefix)/lib ++LDLIBS := -lblimps -lm all: bin Modified: trunk/packages/sift/trunk/debian/patches/series =================================================================== --- trunk/packages/sift/trunk/debian/patches/series 2012-10-08 15:34:46 UTC (rev 12341) +++ trunk/packages/sift/trunk/debian/patches/series 2012-10-08 16:29:06 UTC (rev 12342) @@ -1,3 +1,4 @@ fix_perl_interpreter_and_lib_path ld-as-needed fix_gcc_warnings +jarfile Modified: trunk/packages/sift/trunk/debian/rules =================================================================== --- trunk/packages/sift/trunk/debian/rules 2012-10-08 15:34:46 UTC (rev 12341) +++ trunk/packages/sift/trunk/debian/rules 2012-10-08 16:29:06 UTC (rev 12342) @@ -1,11 +1,13 @@ #!/usr/bin/make -f # Uncomment this to turn on verbose mode. -export DH_VERBOSE=1 +#export DH_VERBOSE=1 -DESTDIR:=$(CURDIR)/debian/sift +PACKAGE:=sift +DESTDIR:=$(CURDIR)/debian/$(PACKAGE) VERSION:=4.0.3b prefix:=/usr +pkgdatadir:=$(prefix)/share/$(PACKAGE) SIFT_BINDIR := $(prefix)/lib/sift/bin SIFT_SCRIPTDIR := $(prefix)/lib/sift/bin @@ -46,7 +48,8 @@ override_dh_install: # lkajan: fastaseqs comes from the blimps package, this source does not have rules for creating it - dh_install -X.svn -X.swp -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/ + dh_install -X.svn -X.swp -XIntersectFeatures.jar -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/ + dh_install bin/IntersectFeatures.jar $(pkgdatadir)/ dh_install -X.svn -X.swp blimps/docs $(prefix)/share/sift/blimps/ #Links are created by debian/links for f in SIFT_for_submitting_fasta_seq.csh SIFT_for_submitting_NCBI_gi_id.csh; do \ @@ -57,9 +60,12 @@ done; chmod +x $(DESTDIR)$(prefix)/lib/sift/bin/perlscripts/separate_query_from_rest_of_seqs.pl # look out: DNA_PROT_SUBROUTINES.pl is really a module (should be pm)! - for f in IntersectFeatures.jar SIFT_subroutines.pm DNA_PROT_SUBROUTINES.pl; do \ + for f in SIFT_subroutines.pm DNA_PROT_SUBROUTINES.pl; do \ chmod -x $(DESTDIR)$(prefix)/lib/sift/bin/$$f; \ done; + for f in IntersectFeatures.jar; do \ + chmod -x $(DESTDIR)$(pkgdatadir)/$$f; \ + done; get-orig-source: mkdir -p ../tarballs _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit