[med-svn] r7963 - in trunk/packages/infernal/trunk/debian: . patches

Steffen Möller moeller at alioth.debian.org
Tue Sep 27 16:40:05 UTC 2011 

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 <moeller at debian.org>  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 <moeller at debian.org>  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 <moeller at debian.org>,
  Charles Plessy <plessy at debian.org>,
  Andreas Tille <tille at debian.org>
-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 <kolbed at janelia.hhmi.org>
-			Eric Nawrocki <nawrockie at janelia.hhmi.org>
-			Sean Eddy <eddy at janelia.hhmi.org>.
+			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"; \

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