Author: moeller Date: 2011-09-27 16:40:05 +0000 (Tue, 27 Sep 2011) New Revision: 7963
Added: trunk/packages/infernal/trunk/debian/patches/ trunk/packages/infernal/trunk/debian/patches/format_security.patch trunk/packages/infernal/trunk/debian/patches/series trunk/packages/infernal/trunk/debian/source/ Modified: trunk/packages/infernal/trunk/debian/changelog trunk/packages/infernal/trunk/debian/control trunk/packages/infernal/trunk/debian/copyright trunk/packages/infernal/trunk/debian/rules Log: Some bit of an overhaul of the Infernal package. Modified: trunk/packages/infernal/trunk/debian/changelog =================================================================== --- trunk/packages/infernal/trunk/debian/changelog 2011-09-27 16:21:53 UTC (rev 7962) +++ trunk/packages/infernal/trunk/debian/changelog 2011-09-27 16:40:05 UTC (rev 7963) @@ -1,3 +1,19 @@ +infernal (1.0.2-3) UNRELEASED; urgency=low + + * Extra fixed for lintian cleanliness (Steffen) + + -- Steffen Moeller <[email protected]> Tue, 27 Sep 2011 18:39:31 +0200 + +infernal (1.0.2-2) unstable; urgency=low + + * Series of mall fixes (Closes: #643407). + * source/format 3.0 + * Policy to 3.9.2 + * added infernal-dbg + * corrected upstream's email address + + -- Steffen Moeller <[email protected]> Tue, 27 Sep 2011 15:48:27 +0200 + infernal (1.0.2-1) unstable; urgency=low * New upstream version Modified: trunk/packages/infernal/trunk/debian/control =================================================================== --- trunk/packages/infernal/trunk/debian/control 2011-09-27 16:21:53 UTC (rev 7962) +++ trunk/packages/infernal/trunk/debian/control 2011-09-27 16:40:05 UTC (rev 7963) @@ -6,9 +6,9 @@ Uploaders: Steffen Moeller <[email protected]>, Charles Plessy <[email protected]>, Andreas Tille <[email protected]> -Build-Depends: cdbs, debhelper (>= 7), autotools-dev -Standards-Version: 3.8.3 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/infernal/trunk/?rev=0&sc=0 +Build-Depends: debhelper (>= 7.0.50~), autotools-dev, quilt +Standards-Version: 3.9.2 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/infernal/trunk/ Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/infernal/trunk/ Homepage: http://infernal.janelia.org/ @@ -43,3 +43,14 @@ . This package provides the documentation which is shipped with the code of infernal. + +Package: infernal-dbg +Architecture: any +Priority: extra +Section: debug +Depends: ${misc:Depends}, infernal (= ${binary:Version}) +Description: debug information for infernal + This package contains extra information to help the debugging of the + infernal suite. The package is auto-generated. You may be asked + by the upstream developer to install it to help the identification + of a technical problem. Modified: trunk/packages/infernal/trunk/debian/copyright =================================================================== --- trunk/packages/infernal/trunk/debian/copyright 2011-09-27 16:21:53 UTC (rev 7962) +++ trunk/packages/infernal/trunk/debian/copyright 2011-09-27 16:40:05 UTC (rev 7963) @@ -3,9 +3,9 @@ X-Debianized-Date: Mon, 10 Sep 2007 23:15:37 +0200 X-Source-Downloaded-From: ftp://infernal.janelia.org/pub/software/infernal X-Upstream-Author: Infernal developer team at HHMI Janelia Farm: - Diana Kolbe <[email protected]> - Eric Nawrocki <[email protected]> - Sean Eddy <[email protected]>. + Diana Kolbe <kolbed janelia.hhmi.org> + Eric Nawrocki <nawrockie janelia.hhmi.org> + Sean Eddy <eddys janelia.hhmi.org>. The "rigfilters" code was contributed by Zasha Weinberg and Larry Ruzzo, University of Washington, Seattle. Added: trunk/packages/infernal/trunk/debian/patches/format_security.patch =================================================================== --- trunk/packages/infernal/trunk/debian/patches/format_security.patch (rev 0) +++ trunk/packages/infernal/trunk/debian/patches/format_security.patch 2011-09-27 16:40:05 UTC (rev 7963) @@ -0,0 +1,41 @@ +Index: infernal-1.0.2/easel/esl_getopts.c +=================================================================== +--- infernal-1.0.2.orig/easel/esl_getopts.c 2009-10-30 18:30:58.000000000 +0100 ++++ infernal-1.0.2/easel/esl_getopts.c 2011-09-27 15:52:41.490289335 +0200 +@@ -1270,7 +1270,7 @@ + "Arg looks like option? Use %.24s%.24s if you really mean it.", + g->opt[opti].name, *ret_optarg); + } else +- ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name); ++ ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name); + + g->optstring = NULL; /* An optchar that takes an arg must terminate an optstring. */ + } +Index: infernal-1.0.2/easel/esl_msa.c +=================================================================== +--- infernal-1.0.2.orig/easel/esl_msa.c 2009-10-30 18:30:55.000000000 +0100 ++++ infernal-1.0.2/easel/esl_msa.c 2011-09-27 15:57:44.961318373 +0200 +@@ -3614,7 +3614,8 @@ + ESL_MSA *msa = NULL; + + if (esl_tmpfile_named(tmpfile, &fp) != eslOK) goto ERROR; +- fprintf(fp, s); ++ //fprintf(fp, s); // provokes error: format not a string literal and no format arguments [-Werror=format-security] ++ fputs(s,fp); + fclose(fp); + fp = NULL; + if (esl_msafile_Open(tmpfile, fmt, NULL, &mfp) != eslOK) goto ERROR; +Index: infernal-1.0.2/easel/esl_tree.c +=================================================================== +--- infernal-1.0.2.orig/easel/esl_tree.c 2009-10-30 18:30:58.000000000 +0100 ++++ infernal-1.0.2/easel/esl_tree.c 2011-09-27 15:59:14.101032221 +0200 +@@ -149,7 +149,8 @@ + ESL_TREE *T = NULL; + + if (esl_tmpfile(tmpfile, &fp) != eslOK) goto ERROR; +- fprintf(fp, s); ++ //fprintf(fp, s); // provokes error: format not a string literal and no format arguments [-Werror=format-security] ++ fputs(s,fp); + rewind(fp); + if (esl_tree_ReadNewick(fp, NULL, &T) != eslOK) goto ERROR; + fclose(fp); Added: trunk/packages/infernal/trunk/debian/patches/series =================================================================== --- trunk/packages/infernal/trunk/debian/patches/series (rev 0) +++ trunk/packages/infernal/trunk/debian/patches/series 2011-09-27 16:40:05 UTC (rev 7963) @@ -0,0 +1 @@ +format_security.patch Modified: trunk/packages/infernal/trunk/debian/rules =================================================================== --- trunk/packages/infernal/trunk/debian/rules 2011-09-27 16:21:53 UTC (rev 7962) +++ trunk/packages/infernal/trunk/debian/rules 2011-09-27 16:40:05 UTC (rev 7963) @@ -1,19 +1,25 @@ #!/usr/bin/make -f # -*- makefile -*- -include /usr/share/cdbs/1/class/autotools.mk -include /usr/share/cdbs/1/rules/debhelper.mk +%: + dh $@ --with quilt -DEB_COMPRESS_EXCLUDE = .pdf - -clean:: +override_dh_auto_clean: if [ -r Makefile ]; then $(MAKE) distclean; fi cd documentation/userguide; make distclean cd easel/documentation; make distclean dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1 -DEB_MAKE_INSTALL_TARGET = install prefix=$(CURDIR)/debian/tmp +override_dh_compress : + dh_compress -X.pdf +override_dh_strip: + dh_strip --dbg-package=infernal-dbg + + +override_dh_auto_install: + $(MAKE) install prefix=$(CURDIR)/debian/tmp + get-orig-source: VERSION=`dpkg-parsechangelog | grep Ver | cut -d' ' -f2 | cut -d- -f1` ; \ URL="ftp://selab.janelia.org/pub/software/infernal/infernal-$${VERSION}.tar.gz";; \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
