--- infernal-1.0.2.orig/debian/upstream-metadata.yaml +++ infernal-1.0.2/debian/upstream-metadata.yaml @@ -0,0 +1,14 @@ +DOI: 10.1093/bioinformatics/btp157 +Homepage: http://infernal.janelia.org/ +PMID: 19307242 +Reference: + author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R. + title: Infernal 1.0: inference of RNA alignments + journal: Bioinformatics + volume: 25 + number: 10 + pages: 1335-1337 + doi: 10.1093/bioinformatics/btp157 + year: 2009 + URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/10/1335 + eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/10/1335.pdf --- infernal-1.0.2.orig/debian/control +++ infernal-1.0.2/debian/control @@ -0,0 +1,55 @@ +Source: infernal +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller , + Charles Plessy , + Andreas Tille +Build-Depends: cdbs, debhelper (>= 7), 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/ + +Package: infernal +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: inference of RNA secondary structural alignments + Infernal ("INFERence of RNA ALignment") is for searching DNA sequence + databases for RNA structure and sequence similarities. It is an + implementation of a special case of profile stochastic context-free + grammars called covariance models (CMs). A CM is like a sequence + profile, but it scores a combination of sequence consensus and RNA + secondary structure consensus, so in many cases, it is more capable of + identifying RNA homologs that conserve their secondary structure more + than their primary sequence. + . + The tool is an integral component of the Rfam database. + +Package: infernal-doc +Architecture: all +Section: doc +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: inference of RNA secondary structural alignments – documentation + Infernal ("INFERence of RNA ALignment") is for searching DNA sequence + databases for RNA structure and sequence similarities. It is an + implementation of a special case of profile stochastic context-free + grammars called covariance models (CMs). A CM is like a sequence + profile, but it scores a combination of sequence consensus and RNA + secondary structure consensus, so in many cases, it is more capable of + identifying RNA homologs that conserve their secondary structure more + than their primary sequence. + . + This package provides the documentation which is shipped with the + code of infernal. + +Package: infernal-dbg +Architecture: any +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. --- infernal-1.0.2.orig/debian/compat +++ infernal-1.0.2/debian/compat @@ -0,0 +1 @@ +7 --- infernal-1.0.2.orig/debian/infernal.docs +++ infernal-1.0.2/debian/infernal.docs @@ -0,0 +1,3 @@ +00README +00README-MPI +documentation/release-notes/RELEASE-1.0 --- infernal-1.0.2.orig/debian/changelog +++ infernal-1.0.2/debian/changelog @@ -0,0 +1,67 @@ +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 Tue, 27 Sep 2011 15:48:27 +0200 + +infernal (1.0.2-1) unstable; urgency=low + + * New upstream version + + -- Andreas Tille Tue, 03 Nov 2009 11:15:34 +0100 + +infernal (1.0-2) unstable; urgency=low + + * Switch to CDBS to benefit from automagical config.{sub,guess} + update (debian/rules). Closes: #550253. + * debian/control: + - Depend on cdbs, downgraded requirement on debhelper from 7.1 to 7. + - Transferred bibliographic information from the package description + to debian/upstream-metadata.yaml. + - Clarified the short description of the documentation package. + * Removed debian/infernal.dirs, not needed. + * Edited README.source, removing mention that infernal is in contrib. + * debian/copyright points at the version 3 of the GPL. + + -- Charles Plessy Sat, 10 Oct 2009 11:22:35 +0900 + +infernal (1.0-1) unstable; urgency=low + + [ Charles Plessy ] + * Updated my email address. + + [ Andreas Tille ] + * New upstream version + * debian/control: + - Standards-Version: 3.8.3 (no changes needed) + - Added myself to uploaders + - s/Debian-Med/Debian Med/ + - Build-Depends: debhelper (>= 7.1) autotools-dev + - Package: infernal-doc + * debian/rules rewritten to make use of short dh + * debian/copyright: + - added myself to Copyright holders of debian/* + - squid is not part of the upstream tarball anymore so this + paragraph was deleted + - files/Userguide.pdf: Copied comment about PDF = source from + README.Debian + * debian/infernal-doc.doc-base + * debian/infernal.install: install src/{trcyk,truncyk_check} to + /usr/bin + + * TODO: Convince upstream to release libeazel which is also used in + hmmer as a separate library instead of copying the code into + different projects + + -- Andreas Tille Fri, 25 Sep 2009 15:17:22 +0200 + +infernal (0.81-1) experimental; urgency=low + + * Initial release (Closes: #441840) + + -- Steffen Moeller Mon, 10 Sep 2007 23:15:37 +0200 + --- infernal-1.0.2.orig/debian/infernal.manpages +++ infernal-1.0.2/debian/infernal.manpages @@ -0,0 +1 @@ +documentation/manpages/* --- infernal-1.0.2.orig/debian/rules +++ infernal-1.0.2/debian/rules @@ -0,0 +1,26 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +%: + dh $@ --with quilt + +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 + +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-$${VERSION}.tar.gz"; \ + ln -s infernal-$${VERSION}.tar.gz infernal_$${VERSION}.orig.tar.gz --- infernal-1.0.2.orig/debian/README.source +++ infernal-1.0.2/debian/README.source @@ -0,0 +1,23 @@ +infernal - Changes to upstream source distribution +================================================== + +Upstream provides a readily readable userguide +for Infernal, which is also available online at +ftp://selab.janelia.org/pub/software/infernal/Userguide.pdf +and should better not be distributed with the source to +save disk space. + +The PDFs that are coming with the sources from which +the userguide is built are indeed upstream's original +sources. They are edited with a PDF editor. Upstream, +Dr Eddy, was consulted in this issue. + +Some figures like the sequence alignments could be prepared +with the infrastructure that Debian provides and thus would +not be ultimately required to be shipped as PDFs. This is however +tolerated. + +The redundancy of the squid folder with the Debian package +biosquid needs to remain until upstream resolves the conflicts. + +-- Steffen Moeller Sun, 20 Jan 2008 23:05:22 +0100 --- infernal-1.0.2.orig/debian/infernal.install +++ infernal-1.0.2/debian/infernal.install @@ -0,0 +1,9 @@ +src/cmalign usr/bin +src/cmbuild usr/bin +src/cmcalibrate usr/bin +src/cmemit usr/bin +src/cmscore usr/bin +src/cmsearch usr/bin +src/cmstat usr/bin +src/trcyk usr/bin +src/truncyk_check usr/bin --- infernal-1.0.2.orig/debian/watch +++ infernal-1.0.2/debian/watch @@ -0,0 +1,3 @@ +version=3 +opts="passive,uversionmangle=s/(rc\d+)/~$1/" \ + ftp://infernal.janelia.org/pub/software/infernal/infernal-(.*)\.tar\.gz --- infernal-1.0.2.orig/debian/infernal-doc.install +++ infernal-1.0.2/debian/infernal-doc.install @@ -0,0 +1 @@ +Userguide.pdf usr/share/doc/infernal --- infernal-1.0.2.orig/debian/copyright +++ infernal-1.0.2/debian/copyright @@ -0,0 +1,143 @@ +X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat +X-Debianized-By: Steffen Moeller +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 + Eric Nawrocki + Sean Eddy . + The "rigfilters" code was contributed by Zasha Weinberg + and Larry Ruzzo, University of Washington, Seattle. + + +Files: debian/* +Copyright: © 2007-2008 Steffen Moeller + © 2007-2008 Charles Plessy + © 2009 Andreas Tille +License: Same as infernal + +Files: rigfilters/* +Copyright: © 2004, Zasha Weinberg +License: BSD family + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + . + - Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + - Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + - Neither the name of the University of Washington nor the names of + its contributors may be used to endorse or promote products derived + from this software without specific prior written permission. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT + NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND + FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, + INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES + (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR + SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) + HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, + STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) + ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN + IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +Files: easel/{esl_sse.c,esl_vmx.c} +Copyright: © 2007 Julien Pommier + © 1992 Stephen Moshier +License: BSD + +Files: easel/easel.c::esl_tmpfile() +Copyright: © 1999-2001 David A. Wheeler +License: MIT + +Files: easel/esl_regexp.c +Copyright: © 1986, 1993, 1995 by University of Toronto +License: BSD + +Files: easel/* +Copyright: © 2004-2008 Sean R. Eddy + © 2006-2008 Howard Hughes Medical Institute +License: Easel - a library of C functions for biological sequence analysis + @EASEL_COPYRIGHT@ + . + The Easel library is freely modifiable and redistributable under the + Janelia Farm Software License, a BSD license: + . + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + . + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + . + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the + distribution. + . + 3. Neither the name of the Howard Hughes Medical Institute nor the + names of its contributors may be used to endorse or promote + products derived from this software without specific prior written + permission. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, + NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE + LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF + SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; + REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON + ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR + TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH + DAMAGE. + + +Files: Userguide.pdf +X-Comment: The PDFs that are coming with the sources from which the userguide is + built are indeed upstream's original sources. They are edited with a PDF + editor. Upstream, Dr Eddy, was consulted in this issue. + + +Files: * +Copyright: © 2001-2007 HHMI Janelia Farm + © 1991-2007 Sean R. Eddy + © 2005-2007 Eric P. Nawrocki + © 2005-2007 Diana L. Kolbe + © 2004 Zasha Weinberg + © 1990 Don G. Gilbert + © 1995-2006 Washington University in St. Louis + © 1992-1995 Medical Research Council, UK + © 2004 University of Washington, Seattle + © 1986,1993,1995 University of Toronto + © 1989-2001 Free Software Foundation + © 1991 Massachusetts Institute of Technology +License: GPL-3 + This suite of programs is free software. You can redistribute it + and/or modify it under the terms of the GNU General Public License as + published by the Free Software Foundation; either version 2 of the + License, or (at your option) any later version. + . + In other words, you may modify, copy, or redistribute this source code + and its documentation, but if you do, you must preserve all these + copyrights and distribute all derivative versions as free software + under the GNU General Public License. + . + This software is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this software, in the file LICENSE; if not, write to the + Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, + MA 02110-1301, USA or see http://www.gnu.org/ +X-Comment: On Debian systems, the complete text of the GNU General Public + License version 3 can be found in `/usr/share/common-licenses/GPL-3'. --- infernal-1.0.2.orig/debian/infernal-doc.doc-base +++ infernal-1.0.2/debian/infernal-doc.doc-base @@ -0,0 +1,16 @@ +Document: infernal-doc +Title: INFERNAL User’s Guide +Author: Diana Kolbe, Eric Nawrocki, Sean Eddy +Abstract: Sequence analysis using profiles of RNA secondary structure consensus + Infernal ("INFERence of RNA ALignment") is for searching DNA sequence + databases for RNA structure and sequence similarities. It is an + implementation of a special case of profile stochastic context-free + grammars called covariance models (CMs). A CM is like a sequence + profile, but it scores a combination of sequence consensus and RNA + secondary structure consensus, so in many cases, it is more capable of + identifying RNA homologs that conserve their secondary structure more + than their primary sequence. +Section: Science/Biology + +Format: pdf +Files: /usr/share/doc/infernal/Userguide.pdf --- infernal-1.0.2.orig/debian/README.Debian +++ infernal-1.0.2/debian/README.Debian @@ -0,0 +1,29 @@ +infernal for Debian +------------------- + +The documentation for easel contains many PDFs that are not buildable +from source - although Debian most likely provide the tools at least to +prepare some of the figures, e.g., a sequence alignment. Other figures +would be more difficult to prepare. As an interim solution it was decided +to leave that documentation out and users are requested to address the +web pages of the upstream developers in this matter. + +The directory "squid" that is distributed with the source of infernal +differs slightly from the biosquid Debian package. Upstream was contacted +about this redundancy to his own software and the answer was to please +leave with that situation since the two are not safely substituted for +another. + +Infernal offers to be compiled for LAM-MPI. Please contact us if there is +respective demand. Also, the Large File Support (LFS) was not activated, +which may be of concern for large screening projects on files larger +than 2GB. + +Infernal optionally uses the CFSQP library which is non-free. This is +not supported by this Debian package. Please address the Userguide for +instructions of a manual self-compilation and -installation. + +The packaging has become part of the Debian Med Blend +and everyone interested is invited to join in for maintaining it. + + -- Steffen Moeller Mon, 10 Sep 2007 23:15:37 +0200 --- infernal-1.0.2.orig/debian/patches/series +++ infernal-1.0.2/debian/patches/series @@ -0,0 +1 @@ +format_security.patch --- infernal-1.0.2.orig/debian/patches/format_security.patch +++ infernal-1.0.2/debian/patches/format_security.patch @@ -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);