debian/0000755000000000000000000000000012265247171007175 5ustar debian/control0000644000000000000000000000317512265240621010577 0ustar Source: libtfbs-perl Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Section: perl Priority: optional Build-Depends: debhelper (>= 9), perl, pdl, bioperl, libwww-perl, libdbi-perl Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libtfbs-perl/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libtfbs-perl/trunk/ Homepage: http://tfbs.genereg.net Package: libtfbs-perl Architecture: any Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, pdl, bioperl, libwww-perl, libdbi-perl Recommends: libgd-gd2-perl | libgd-gd2-noxpm-perl Description: scanning DNA sequence with a position weight matrix The TFBS perl modules comprise a set of routines to interact with the Transfac and Jaspar databases that describe a special family of proteins, the transcription factors. These bind to genomic DNA to initiate (or prevent) the readout of a gene. Once multiple binding sites are known for a transcription factor, these are gathered in a single file and are aligned in order to find position-specific characteristica that might be used to predict such binding events in novel DNA sequences. . If you use TFBS in your work, please cite "Lenhard B., Wasserman W.W. (2002) TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 18:1135-1136". debian/rules0000755000000000000000000000076112265241431010252 0ustar #!/usr/bin/make -f %: dh $@ override_dh_auto_configure: echo "n" | perl Makefile.PL INSTALLDIRS=vendor $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH="" OTHERLDFLAGS="$(LDFLAGS)" # Do not run network test unless in maintainer mode. ifneq (1,$(DEB_MAINTAINER_MODE)) TEST_FILES := $(filter-out t/04_DB_TRANSFAC.t,$(shell echo t/*.t)) else TEST_FILES := $(shell echo t/*.t) endif ifeq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS))) override_dh_auto_test: prove --blib $(TEST_FILES) Ext/t/*.t endif debian/watch0000644000000000000000000000013012265243201010206 0ustar version=3 opts=dversionmangle=s/(\+dfsg)// \ http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz debian/upstream0000644000000000000000000000104012214301056010736 0ustar Contact: Boris.Lenhard at bccs.uib.no Homepage: http://tfbs.genereg.net/ Name: TFBS Reference: DOI: 10.1093/bioinformatics/18.8.1135 PMID: 12176838 Journal: Bioinformatics Title: > TFBS: Computational framework for transcription factor binding site analysis Author: Lenhard, Boris and Wasserman, Wyeth W. Volume: 18 Number: 8 Pages: 1135-1136 Year: 2002 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135 Repository: http://www.ii.uib.no/svn/lenhard/TFBS/ Watch: http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz debian/copyright0000644000000000000000000000255712265244544011142 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://www.ii.uib.no/svn/lenhard/TFBS/ Files-Excluded: .git blib pm_to_blib MYMETA.* Makefile.old Makefile *.BAK *~ Comment: Since the original tarball contains partly totally broken files (like Makefile which will be deleted in clean target anyway) and cruft which makes the original tarball just larger this is deleted here. Files: * Copyright: © 2005-2007 Boris Lenhard , Stephen Montgomery , Leonardo Marino-Ramirez, Wynand Alkema, License: Perl License: Perl This program is free software; you can redistribute it and/or modify it under the terms of either: . a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or . b) the "Artistic License" which comes with Perl. Comment: On Debian GNU/Linux systems, the complete text of the GNU General Public License version 1 can be found in ‘/usr/share/common-licenses/GPL-1’ and the Artistic Licence in ‘/usr/share/common-licenses/Artistic’. Files: debian/* Copyright: © 2008 Steffen Moeller © 2008–11 Charles Plessy License: Perl debian/source/0000755000000000000000000000000012214301056010460 5ustar debian/source/format0000644000000000000000000000001412214301056011666 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000121512214301056011220 0ustar Notes on how this package is tested. ──────────────────────────────────── The regression tests of this Perl module are executed at build time. You can therefore consult the result in the build logs: https://buildd.debian.org/libtfbs-perl Network access is not guaranteed in our auto-builder infrastructure. Tests that depend on the network are therefore disabled. Nevertheless these tests are checked by the package maintainer before upload, by building the package with the DEB_MAINTAINER_MODE=1 option. -- Charles Plessy Sat, 28 Nov 2009 13:52:06 +0900 debian/changelog0000644000000000000000000000654012265247171011054 0ustar libtfbs-perl (0.6.0+dfsg-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * debian/rules: Clean up from get-orig-source since there is a real release * debian/copyright: Exclude several files which are either cruft adding useless bytes to the archive and on the other hand making the build quite complex (Makefile with broken clean target which deletes itself afterwards anyway) all those files are deleted -- Andreas Tille Tue, 14 Jan 2014 14:53:42 +0100 libtfbs-perl (0.5.svn.20100421-2) unstable; urgency=low * debian/upstream: - Single Reference field instead of Reference-* - s/authors/author/ * debian/source/format: 3.0 (quilt) * debian/control: - cme fix dpkg-control - debhelper 9 - canonical Vcs fields * debian/copyright: DEP5 * debian/rules: hardening options * debian/patches/hardening.patch: Enable building with -Wformat-security -- Andreas Tille Sat, 16 Nov 2013 22:02:13 +0100 libtfbs-perl (0.5.svn.20100421-1) unstable; urgency=low * New upstream SVN snapshot fixing issue related to new naming conventions. * Arranged the get-orig-source target of debian/rules to pick the date of the last upstream commit. * Corrected Vcs fields in debian/control. * Conforms with Policy 3.9.2: - Incremented Standards-Version in debian/control. - Mention GPL version 1 in debian/copyright. * Switch to Debhelper 8 and dh rules. * Converted debian/copyright to DEP-5 format. -- Charles Plessy Thu, 25 Aug 2011 13:10:21 +0900 libtfbs-perl (0.5.svn.20091128-1) unstable; urgency=low * New upstream SVN snapshot, adding JASPAR5 support. * Skip test that needs a network connection unless in maintainer mode. (debian/rules). Thanks to Gregor Herrmann (Closes: #533995). * Updated to Policy 3.8.3: - Incremented Standards-Version (debian/control) - Dropped version in build dependency on Perl (debian/control). - Honor the ‘nocheck’ build option (debian/rules). * Documented how this package is tested in debian/README.Debian. * Added meta-information in debian/upstream-metadata.yaml. * Refreshed debian/copyright to latest experimentations on the format. * Debhelper 7: use dh_prep and dh binary-arch in debian/rules. -- Charles Plessy Sat, 28 Nov 2009 14:14:36 +0900 libtfbs-perl (0.5.svn.20080722-2) unstable; urgency=low * debian/control: - Added bioperl to the build dependencies (Closes: #493341). - Dropped quilt build dependency (see below). - Added myself to the Uploaders field. - Added `libgd-gd2-perl | libgd-gd2-noxpm-perl' as recommended package. * debian/compat, debian/control: - Using debhelper 7. * debian/rules: - Refreshed with `dh-make-perl --refresh'. - Removes /usr/lib/perl5/pwm_searchPFF.c and /usr/lib/perl5/pwm_search.h, that should not be installed there. * debian/patches, debian/rules: - Disabling the MySQL tests with `echo "n" |' instead of patches. * debian/copyright: - Converted to machine-readable format. - Added myself to the Hall of Fame. -- Charles Plessy Mon, 11 Aug 2008 13:27:45 +0900 libtfbs-perl (0.5.svn.20080722-1) unstable; urgency=low * Initial release (closes: #491714). -- Steffen Moeller Tue, 22 Jul 2008 00:07:17 +0200 debian/patches/0000755000000000000000000000000012265244722010623 5ustar debian/patches/hardening.patch0000644000000000000000000000051712241765575013616 0ustar Author: Andreas Tille LastChanged: Sat, 16 Nov 2013 22:02:13 +0100 Description: Enable building with -Wformat-security --- a/Ext/lib/pwm_searchPFF.c +++ b/Ext/lib/pwm_searchPFF.c @@ -121,7 +121,7 @@ char *msg; { int retval = 0; - fprintf(stderr,msg); + fprintf(stderr,"%s",msg); return(retval); } debian/patches/series0000644000000000000000000000002012265244720012026 0ustar hardening.patch debian/compat0000644000000000000000000000000212241756361010373 0ustar 9