[med-svn] [Git][med-team/infernal][upstream] 45 commits: SVN-Git conversion failed - just commit status of 1.0.2 (oldstable at the time of conversion)
Michael R. Crusoe
gitlab at salsa.debian.org
Sun Dec 1 15:44:48 GMT 2019
Michael R. Crusoe pushed to branch upstream at Debian Med / infernal
Commits:
d0c0d54a by Andreas Tille at 2016-06-21T09:19:17Z
SVN-Git conversion failed - just commit status of 1.0.2 (oldstable at the time of conversion)
- - - - -
1166e414 by Andreas Tille at 2016-06-21T09:20:24Z
Merge tag 'upstream/1.1.1'
Upstream version 1.1.1
- - - - -
280ba637 by Andreas Tille at 2016-06-21T09:21:59Z
Commit status of 1.1.1-2 (stable at the time when moving from svn to git)
- - - - -
c9c9685b by Andreas Tille at 2016-06-21T09:23:47Z
Commit status as uploaded at time of svn-git conversion
- - - - -
74a32960 by Andreas Tille at 2016-06-21T09:26:16Z
Move packaging from SVN to Git
- - - - -
dc788b20 by Andreas Tille at 2016-06-21T09:27:12Z
cme fix dpkg-control
- - - - -
6adbb898 by cbk-guest at 2016-06-22T02:39:11Z
Autopkgtests added
- - - - -
a61b4c9d by Andreas Tille at 2016-06-22T06:13:38Z
Fix changelog
- - - - -
0afabb23 by Andreas Tille at 2016-06-22T06:29:57Z
Better hardening, upload to unstable
- - - - -
1fbf0cb0 by Sascha Steinbiss at 2016-08-06T00:01:26Z
fix watchfile
- - - - -
e5b003ec by Sascha Steinbiss at 2016-08-06T00:01:52Z
Merge tag 'upstream/1.1.2'
Upstream version 1.1.2
- - - - -
5c8e52f5 by Sascha Steinbiss at 2016-08-06T01:06:45Z
make build reproducible
- - - - -
25d0decf by Sascha Steinbiss at 2016-08-11T21:44:44Z
SOURCE_DATE_EPOCH support accepted upstream
- - - - -
c1bd0140 by Andreas Tille at 2017-01-18T11:57:11Z
Fix homepage
- - - - -
15c9f904 by Andreas Tille at 2017-01-18T12:00:54Z
TODO: remove code copy of hmmer ... after stretch release
- - - - -
2ea2d3e0 by Andreas Tille at 2017-01-18T12:01:31Z
debhelper 10
- - - - -
0c282646 by Andreas Tille at 2017-01-18T12:02:02Z
d/watch: version=4
- - - - -
25e1072b by Steffen Moeller at 2017-09-01T14:10:01Z
Added references to registries.
- - - - -
0c050e21 by Andreas Tille at 2018-04-09T12:22:48Z
Remove invalid fields from debian/upstream/metadata
- - - - -
4058f0e4 by Steffen Möller at 2018-05-11T22:50:02Z
RRID -> SciCrunch
- - - - -
9124281e by Andreas Tille at 2018-07-15T18:57:24Z
debhelper 11
- - - - -
0b271fb2 by Andreas Tille at 2018-07-15T18:57:27Z
Point Vcs fields to salsa.debian.org
- - - - -
b49cdc0d by Andreas Tille at 2018-07-15T18:57:27Z
Standards-Version: 4.1.5
- - - - -
666df109 by Andreas Tille at 2018-07-15T19:03:41Z
DEP3
- - - - -
cd5470b8 by Andreas Tille at 2018-07-15T19:12:16Z
Obtain source package name
- - - - -
a9a0482f by Andreas Tille at 2018-07-16T06:34:30Z
Fix configure.ac to enable autoreconf
- - - - -
3fce8ef5 by Andreas Tille at 2018-07-16T09:59:33Z
Thanks again to Yavor Doganov <yavor at gnu.org> for another very helpful hint
- - - - -
421b9827 by Andreas Tille at 2018-07-16T10:20:19Z
Fix spelling
- - - - -
3cc895af by Andreas Tille at 2018-07-16T10:30:40Z
Upload to unstable
- - - - -
d757f80d by Steffen Möller at 2019-09-21T12:24:19Z
Added ref to conda
- - - - -
729095a6 by Steffen Moeller at 2019-11-29T23:03:03Z
New upstream version
- - - - -
dfa5dd7a by Steffen Moeller at 2019-11-29T23:04:30Z
Update upstream source from tag 'upstream/1.1.3'
Update to upstream version '1.1.3'
with Debian dir 9aea7cbf3c9d273ac6f787d461b2957b09f60a03
- - - - -
61023036 by Steffen Moeller at 2019-11-29T23:04:30Z
debhelper-compat 12
- - - - -
1f738b7d by Steffen Moeller at 2019-11-29T23:04:34Z
Standards-Version: 4.4.1
- - - - -
a5757fc8 by Steffen Moeller at 2019-11-29T23:21:22Z
New upstream version
- - - - -
f40a6f6d by Michael R. Crusoe at 2019-11-30T10:06:29Z
Add python3 build-dep for 'make check'
- - - - -
7e3cc6e2 by Michael R. Crusoe at 2019-11-30T10:06:32Z
Secure URI in copyright format
- - - - -
ab53cb95 by Michael R. Crusoe at 2019-11-30T10:06:33Z
Remove trailing whitespace in debian/changelog
- - - - -
3e4182b3 by Michael R. Crusoe at 2019-11-30T10:06:33Z
Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
- - - - -
21c20708 by Michael R. Crusoe at 2019-11-30T10:06:33Z
Set upstream metadata fields: Bug-Submit.
- - - - -
c763413a by Michael R. Crusoe at 2019-11-30T11:45:27Z
Enable a verbose build log
- - - - -
f80d3b0e by Michael R. Crusoe at 2019-11-30T11:47:10Z
infernal-doc: mark Multi-Arch: foreign
- - - - -
aca65ff9 by Michael R. Crusoe at 2019-11-30T12:31:00Z
CPPFLAGS for easel
- - - - -
4bc3f382 by Michael R. Crusoe at 2019-12-01T12:25:37Z
Install example binaries into /usr/lib/
- - - - -
847ca321 by Michael R. Crusoe at 2019-12-01T15:35:55Z
upload to unstable
- - - - -
23 changed files:
- + debian/README.Debian
- + debian/README.source
- + debian/TODO
- + debian/bin/cmalign
- + debian/changelog
- + debian/control
- + debian/copyright
- + debian/infernal-doc.doc-base
- + debian/infernal-doc.install
- + debian/infernal.docs
- + debian/infernal.install
- + debian/infernal.manpages
- + debian/patches/autoreconf.patch
- + debian/patches/format_security.patch
- + debian/patches/hardening
- + debian/patches/series
- + debian/patches/spelling.patch
- + debian/rules
- + debian/source/format
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/upstream/metadata
- + debian/watch
Changes:
=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,23 @@
+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.
+
+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 <moeller at debian.org> Mon, 10 Sep 2007 23:15:37 +0200
=====================================
debian/README.source
=====================================
@@ -0,0 +1,20 @@
+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.
+
+-- Steffen Moeller Sun, 20 Jan 2008 23:05:22 +0100
=====================================
debian/TODO
=====================================
@@ -0,0 +1 @@
+Remove code copy of hmmer
=====================================
debian/bin/cmalign
=====================================
@@ -0,0 +1,12 @@
+#!/bin/sh
+BINNAME=`basename $0`
+
+if grep -q '^flags[[:space:]]*:.* sse2 ' /proc/cpuinfo ; then
+ /usr/lib/infernal/$BINNAME $@
+else
+cat <<EOT
+To run $BINNAME from infernal package your proccessor needs SSE2 which is not
+available on this machine.
+ ... Exiting
+EOT
+fi
=====================================
debian/changelog
=====================================
@@ -0,0 +1,235 @@
+infernal (1.1.3-2) unstable; urgency=medium
+
+ * Team upload.
+ * Add python3 build-dep for `make check`
+ * Secure URI in copyright format
+ * Remove trailing whitespace in debian/changelog
+ * Trim trailing whitespace.
+ * Set upstream metadata fields: Bug-Submit.
+ * Enable a verbose build log
+ * infernal-doc: mark Multi-Arch: foreign (thanks Multiarch hinter!)
+ * debian/patches/hardening: added CPPFLAGS to easel, rmark, and hmmer/profmark
+ * Install example binaries into /usr/lib/ and symlink them into the
+ doc/infernal/examples directory (fixes a FHS violation)
+ * Added missing autopkgtest dependency on python3
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sun, 01 Dec 2019 16:35:34 +0100
+
+infernal (1.1.3-1) unstable; urgency=medium
+
+ * New upstream version
+ - Upstream accepted patch for reproducible builds
+ - autoreconf now works without respective non-applicable patch
+ * Still debian/TODO: remove code copy of hmmer
+ * debhelper-compat 12
+ * Standards-Version: 4.4.1
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 30 Nov 2019 00:03:03 +0100
+
+infernal (1.1.2-2) unstable; urgency=medium
+
+ * Fix homepage
+ * Add debian/TODO: remove code copy of hmmer
+ * debhelper 10
+ * d/watch: version=4
+ * Added references to RRID and OMICtools registries (Steffen Moeller)
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.1.5
+ * Fix configure.ac to enable autoreconf
+ * Fix spelling
+
+ -- Andreas Tille <tille at debian.org> Mon, 16 Jul 2018 12:20:32 +0200
+
+infernal (1.1.2-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream release.
+ * Fix watchfile.
+ * Make build reproducible.
+
+ -- Sascha Steinbiss <satta at debian.org> Sat, 06 Aug 2016 00:00:56 +0000
+
+infernal (1.1.1-5) unstable; urgency=medium
+
+ * Team upload.
+ [Canberk Koç]
+ * Added Autopkgtest suite
+ * debian/rules file changed
+ * debian/tests directory added
+
+ [ Andreas Tille ]
+ * Move packaging from SVN to Git
+ * cme fix dpkg-control
+ * Better hardening
+
+ -- Canberk Koç <canberkkoc at gmail.com> Wed, 22 Jun 2016 05:35:41 +0300
+
+infernal (1.1.1-4) unstable; urgency=medium
+
+ * Architecture: any-amd64 any-i386
+ Closes: #815310
+ * cme fix dpkg-control
+ * Secure Vcs-Browser
+
+ -- Andreas Tille <tille at debian.org> Sat, 20 Feb 2016 23:07:53 +0100
+
+infernal (1.1.1-3) unstable; urgency=medium
+
+ * cme fix dpkg-control
+ * drop dpg package at all since it is auto-generated by dpkg now
+ Closes: #766309
+
+ -- Andreas Tille <tille at debian.org> Mon, 21 Dec 2015 09:35:57 +0100
+
+infernal (1.1.1-2) unstable; urgency=medium
+
+ * Re-enable i386 by checking availability of sse2
+ * d/copyright: Deleted unneeded paragraphs
+ * d/rules: drop redundant targets
+ * d/README*: drop pararaphs about squid which is not part of the
+ source any more
+
+ -- Andreas Tille <tille at debian.org> Thu, 18 Sep 2014 10:00:12 +0200
+
+infernal (1.1.1-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream release.
+
+ -- Charles Plessy <plessy at debian.org> Fri, 08 Aug 2014 21:45:26 +0900
+
+infernal (1.1-1) unstable; urgency=low
+
+ * Team upload.
+ * New upstream release.
+ * Removed i386 architecture as some processors do not provide SSE2.
+ * Conforms with Policy 3.9.5.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 01 Dec 2013 10:30:00 +0900
+
+infernal (1.1~rc4-2) unstable; urgency=low
+
+ * Team upload.
+ * Build-depends on libperl4-corelibs-perl (Closes: #724119).
+ * debian/control: removed myself from Uploaders.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 23 Sep 2013 10:57:17 +0900
+
+infernal (1.1~rc4-1) unstable; urgency=low
+
+ * New upstream source
+ * debian/source/format: 3.0 (quilt)
+ * debian/control:
+ - cme fix dpkg-control
+ - debhelper 9
+ - do not Build-Depend: quilt since source format implies this
+ - The package builds only on architectures with SSE instructions.
+ Quoting from build log on armel:
+ configure: WARNING: Infernal 1.1 requires VMX or SSE capability for
+ parallel instructions.
+ configure: error: It appears your platform has neither and will not
+ support Infernal.
+ So all non i386/amd64 architectures were excluded
+ Closes: #718742
+ - use anonscm in Vcs fields
+ * debian/rules:
+ - remove redundant setting for flags which is handled by debhelper 9
+ automatically
+ - use xz compression
+ * debian/copyright: DEP5
+
+ -- Andreas Tille <tille at debian.org> Mon, 05 Aug 2013 12:06:12 +0200
+
+infernal (1.1~rc2-1) unstable; urgency=low
+
+ * New upstream version - aiming to support RNAWorld BOINC project,
+ with many thanks and regards to Yoyo!
+ - cmscore no longer available
+ * Bumped policy to 3.9.4 (no changes needed)
+ - introduced hardening, with it build dep on
+ dpkg-dev (>= 1.16.1~)
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 01 May 2013 20:24:17 +0200
+
+infernal (1.0.2-3) UNRELEASED; urgency=low
+
+ [ Steffen Moeller ]
+ * Extra fixed for lintian cleanliness (Steffen)
+
+ [ Andreas Tille ]
+ * debian/upstream:
+ - do not specify DOI twice
+ - Moved PMID to references
+ * debian/control:
+ - Fixed Vcs-Svn field
+ - Standards-Version: 3.9.3 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Thu, 08 Mar 2012 11:44:54 +0100
+
+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
+
+ -- Andreas Tille <tille at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> Fri, 25 Sep 2009 15:17:22 +0200
+
+infernal (0.81-1) experimental; urgency=low
+
+ * Initial release (Closes: #441840)
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 10 Sep 2007 23:15:37 +0200
=====================================
debian/control
=====================================
@@ -0,0 +1,48 @@
+Source: infernal
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper-compat (= 12),
+ libperl4-corelibs-perl,
+ python3
+Standards-Version: 4.4.1
+Vcs-Browser: https://salsa.debian.org/med-team/infernal
+Vcs-Git: https://salsa.debian.org/med-team/infernal.git
+Homepage: http://eddylab.org/infernal/
+
+Package: infernal
+Architecture: any-amd64 any-i386
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: inference of RNA secondary structural alignments
+ Infernal ("INFERence of RNA ALignment") searches DNA sequence
+ databases for RNA structure and sequence similarities. It provides an
+ implementation of a special variant 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
+Multi-Arch: foreign
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: inference of RNA secondary structural alignments – documentation
+ Infernal ("INFERence of RNA ALignment") searches DNA sequence
+ databases for RNA structure and sequence similarities. It provides 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.
=====================================
debian/copyright
=====================================
@@ -0,0 +1,114 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Infernal developer team at HHMI Janelia Farm:
+ Diana Kolbe <kolbed janelia.hhmi.org>
+ Eric Nawrocki <nawrockie janelia.hhmi.org>
+ Sean Eddy <eddys janelia.hhmi.org>.
+Source: ftp://infernal.janelia.org/pub/software/infernal/infernal-1.1.1.tar.gz
+
+Files: *
+Copyright: © 2001-2014 HHMI Janelia Farm
+ © 1991-2013 Sean R. Eddy
+ © 2005-2013 Eric P. Nawrocki
+ © 2005-2011 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
+
+Files: debian/*
+Copyright: © 2007-2008 Steffen Moeller <moeller at debian.org>
+ © 2009-2014 Andreas Tille <tille at debian.org>
+License: GPL-3
+
+Files: easel/*
+Copyright: © 2004-2014 Sean R. Eddy
+ © 2006-2008 Howard Hughes Medical Institute
+License: BSD-Easel
+
+Files: easel/esl_sse.c easel/esl_vmx.c
+Copyright: © 2007 Julien Pommier
+ © 1992 Stephen Moshier
+License: BSD-Easel
+
+Files: easel/easel.c
+Copyright: © 1999-2001 David A. Wheeler
+License: BSD-Easel
+Comment: This only concerns esl_tmpfile()
+
+Files: easel/esl_regexp.c
+Copyright: © 1986, 1993, 1995 by University of Toronto
+License: BSD-Easel
+
+License: BSD-Easel
+ @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
+Copyright: Sean R. Eddy
+License: GPL-3
+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.
+
+
+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/
+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'.
=====================================
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
=====================================
debian/infernal-doc.install
=====================================
@@ -0,0 +1 @@
+Userguide.pdf usr/share/doc/infernal
=====================================
debian/infernal.docs
=====================================
@@ -0,0 +1,2 @@
+README
+RELEASE-*.md
=====================================
debian/infernal.install
=====================================
@@ -0,0 +1,2 @@
+bin/* usr/lib/infernal
+debian/bin/* usr/bin
=====================================
debian/infernal.manpages
=====================================
@@ -0,0 +1,3 @@
+#documentation/manpages/*
+#share/man/man1/*.1
+debian/tmp/share/man/man1/*.1
=====================================
debian/patches/autoreconf.patch
=====================================
@@ -0,0 +1,171 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 16 Jul 2018 07:59:38 +0200
+Origin: https://lists.debian.org/debian-mentors/2018/07/msg00193.html
+Description: Fix configure.ac to enable autoreconf
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -121,24 +121,24 @@ AC_SUBST(EASEL_VERSION)
+ AC_SUBST(EASEL_URL)
+
+ # Preprocessor symbols (replace #undefs in hmmer/src/p7_config.h and src/config.h)
+-AC_DEFINE_UNQUOTED(INFERNAL_DATE, "$INFERNAL_DATE")
+-AC_DEFINE_UNQUOTED(INFERNAL_COPYRIGHT, "$INFERNAL_COPYRIGHT")
+-AC_DEFINE_UNQUOTED(INFERNAL_LICENSE, "$INFERNAL_LICENSE")
+-AC_DEFINE_UNQUOTED(INFERNAL_VERSION, "$INFERNAL_VERSION")
+-AC_DEFINE_UNQUOTED(INFERNAL_URL, "$INFERNAL_URL")
+-
+-AC_DEFINE_UNQUOTED(HMMER_DATE, "$HMMER_DATE")
+-AC_DEFINE_UNQUOTED(HMMER_COPYRIGHT, "$HMMER_COPYRIGHT")
+-AC_DEFINE_UNQUOTED(HMMER_LICENSE, "$HMMER_LICENSE")
+-AC_DEFINE_UNQUOTED(HMMER_VERSION, "$HMMER_VERSION")
+-AC_DEFINE_UNQUOTED(HMMER_URL, "$HMMER_URL")
+-
+-AC_DEFINE_UNQUOTED(EASEL_DATE, "$EASEL_DATE")
+-AC_DEFINE_UNQUOTED(EASEL_COPYRIGHT, "$EASEL_COPYRIGHT")
+-AC_DEFINE_UNQUOTED(EASEL_LICENSE, "$EASEL_LICENSE")
+-AC_DEFINE_UNQUOTED(EASEL_VERSION, "$EASEL_VERSION")
++AC_DEFINE_UNQUOTED([INFERNAL_DATE], ["$INFERNAL_DATE"], [Timestamp of infernal code])
++AC_DEFINE_UNQUOTED([INFERNAL_COPYRIGHT], ["$INFERNAL_COPYRIGHT"], [Infernal copyright information])
++AC_DEFINE_UNQUOTED([INFERNAL_LICENSE], ["$INFERNAL_LICENSE"], [Infernal license])
++AC_DEFINE_UNQUOTED([INFERNAL_VERSION], ["$INFERNAL_VERSION"], [Invernal version])
++AC_DEFINE_UNQUOTED([INFERNAL_URL], ["$INFERNAL_URL"], [Link to infernal homepage])
++
++AC_DEFINE_UNQUOTED([HMMER_DATE], ["$HMMER_DATE"], [Timestamp of hmmer code])
++AC_DEFINE_UNQUOTED([HMMER_COPYRIGHT], ["$HMMER_COPYRIGHT"], [Hmmer copyright information])
++AC_DEFINE_UNQUOTED([HMMER_LICENSE], ["$HMMER_LICENSE"], [Hmmer license])
++AC_DEFINE_UNQUOTED([HMMER_VERSION], ["$HMMER_VERSION"], [Hmmer version])
++AC_DEFINE_UNQUOTED([HMMER_URL], ["$HMMER_URL"], [Link to hmmer homepage])
++
++AC_DEFINE_UNQUOTED([EASEL_DATE], ["$EASEL_DATE"], [Timestamp of easel code])
++AC_DEFINE_UNQUOTED([EASEL_COPYRIGHT], ["$EASEL_COPYRIGHT"], [Easel copyright information])
++AC_DEFINE_UNQUOTED([EASEL_LICENSE], ["$EASEL_LICENSE"], [Easel license])
++AC_DEFINE_UNQUOTED([EASEL_VERSION], ["$EASEL_VERSION"], [Easel version])
+
+-AC_DEFINE(eslLIBRARY)
++AC_DEFINE(eslLIBRARY, [], [esl library])
+ #AC_DEFINE(hmmerLIBRARY)
+
+ # Figure out what host we're compiling on.
+@@ -182,11 +182,11 @@ AS_HELP_STRING([--enable-debugging=x],[a
+ enable_debugging=$enableval, enable_debugging=no)
+
+ case $enable_debugging in
+- yes) AC_DEFINE(eslDEBUGLEVEL, 0);;
+- 1) AC_DEFINE(eslDEBUGLEVEL, 1);;
+- 2) AC_DEFINE(eslDEBUGLEVEL, 2);;
+- 3) AC_DEFINE(eslDEBUGLEVEL, 3);;
+- no) AC_DEFINE(eslDEBUGLEVEL, 0);;
++ yes) AC_DEFINE(eslDEBUGLEVEL, 0, [no debugging]);;
++ 1) AC_DEFINE(eslDEBUGLEVEL, 1, [debug level 1]);;
++ 2) AC_DEFINE(eslDEBUGLEVEL, 2, [debug level 2]);;
++ 3) AC_DEFINE(eslDEBUGLEVEL, 3, [debug level 3]);;
++ no) AC_DEFINE(eslDEBUGLEVEL, 0, [no debugging]);;
+ *) AC_MSG_ERROR([Unknown argument to --enable-debugging: $enable_debugging]);;
+ esac
+
+@@ -293,7 +293,7 @@ case $enable_threads in
+ esac
+
+ AS_IF([test "x$check_threads" != xno],
+- [ACX_PTHREAD([AC_DEFINE(HMMER_THREADS)
++ [ACX_PTHREAD([AC_DEFINE(HMMER_THREADS, [], [Threads for hmmer])
+ AC_DEFINE(HAVE_PTHREAD)
+ AC_SUBST(PTHREAD_LIBS)
+ AC_SUBST(PTHREAD_CFLAGS)],
+@@ -356,7 +356,7 @@ AC_PROG_CC
+ AC_PROG_INSTALL
+ # MPI : set @CC@ to mpicc, sets @MPILIBS@, defines HAVE_MPI.
+ if test "$enable_mpi" = "yes"; then
+- ACX_MPI([AC_DEFINE(HAVE_MPI)
++ ACX_MPI([AC_DEFINE(HAVE_MPI, [], [MPI enabled])
+ AC_SUBST([MPI_UTESTS], ["mpi_utest"])
+ AC_SUBST([MPI_BENCHMARKS], ["mpi_benchmark"])],
+ AC_MSG_ERROR([MPI library not found for --enable-mpi]))
+@@ -376,7 +376,7 @@ CHECK_GNU_MAKE
+
+ # Select our optimization level in CFLAGS.
+ if test "$enable_debugging" != "no"; then
+- AC_DEFINE(p7_DEBUGGING, 1)
++ AC_DEFINE(p7_DEBUGGING, 1, [p7 debugging level 1])
+ if test "$GCC" = "yes" && test "$sre_cflags_env_set" = "no"; then
+ CFLAGS="-g -Wall"
+ fi
+@@ -454,7 +454,7 @@ if test "$impl_choice" = "sse"; then
+ __m128i b;
+ b = _mm_castps_si128(a);
+ a = _mm_castsi128_ps(b);]])],
+- [AC_DEFINE([HAVE_SSE2_CAST])
++ [AC_DEFINE([HAVE_SSE2_CAST], [], [compiler support for sse2 cast functions])
+ ssecast=yes])
+ AC_MSG_RESULT([$ssecast])
+ CFLAGS="$sre_save_cflags"
+@@ -531,7 +531,7 @@ if test "$impl_choice" = "sse"; then
+ [[_MM_SET_FLUSH_ZERO_MODE (_MM_FLUSH_ZERO_ON);
+ ]])],
+ [ AC_MSG_RESULT([yes])
+- AC_DEFINE([HAVE_FLUSH_ZERO_MODE])],
++ AC_DEFINE([HAVE_FLUSH_ZERO_MODE], [], [_MM_SET_FLUSH_ZERO_MODE is supported])],
+ [ AC_MSG_RESULT([no])]
+ )
+ CFLAGS="$sre_save_cflags"
+@@ -540,16 +540,16 @@ fi
+ # Now, we can enable the appropriate optimized implementation.
+ case "$impl_choice" in
+ sse) AC_MSG_NOTICE([Activating Intel/AMD SSE optimized DP implementation])
+- AC_DEFINE([HAVE_SSE2])
+- AC_DEFINE([p7_IMPL_SSE])
++ AC_DEFINE([HAVE_SSE2], [], [Activating Intel/AMD SSE optimized DP implementation])
++ AC_DEFINE([p7_IMPL_SSE], [], [Activating Intel/AMD SSE optimized DP implementation])
+ AC_SUBST([HMMERIMPLLIB], ["impl_sse/libhmmerimpl.a"])
+ IMPL_CHOICE="sse"
+ INFERNAL_IMPLDIR="impl_sse"
+ ;;
+
+ vmx) AC_MSG_NOTICE([Activating Altivec/VMX optimized DP implementation])
+- AC_DEFINE([HAVE_VMX])
+- AC_DEFINE([p7_IMPL_VMX])
++ AC_DEFINE([HAVE_VMX], [], [Activating Altivec/VMX optimized DP implementation])
++ AC_DEFINE([p7_IMPL_VMX], [], [Activating Altivec/VMX optimized DP implementation])
+ AC_SUBST([HMMERIMPLLIB], ["impl_vmx/libhmmerimpl.a"])
+ IMPL_CHOICE="vmx"
+ INFERNAL_IMPLDIR=""
+@@ -582,7 +582,7 @@ AC_PATH_PROG(HAVE_GZIP, "gzip", "no")
+ if test "${HAVE_GZIP}" = "no"; then
+ AC_MSG_WARN([gzip not found])
+ else
+- AC_DEFINE(HAVE_GZIP)
++ AC_DEFINE(HAVE_GZIP, [], [Use systm gzip library])
+ fi
+
+ # 5. Checks for libraries
+@@ -731,6 +731,29 @@ AC_CONFIG_FILES([easel/testsuite/Makefil
+ AC_CONFIG_FILES([easel/Makefile])
+ AC_CONFIG_FILES([easel/documentation/Makefile])
+
++
++AH_TOP([
++/* RAMLIMIT (in MB) defines how much memory we're
++ * allowed to expend on alignment algorithms without
++ * switching to more efficient memory forms - e.g.
++ * in smallcyk.c
++ */
++#ifndef RAMLIMIT
++#define RAMLIMIT 0
++#endif
++
++/* SRE_CONLEVEL will prob move to squid somewhere.
++ * Set to 1 to activate contract checking, during debugging.
++ */
++#define SRE_CONLEVEL 1
++#if (SRE_CONLEVEL >= 1)
++#include <assert.h>
++#endif
++
++#define CMSEQDBENV "BLASTDB"
++#define CMDBENV "RFAMDB"
++])
++
+ ################################################################
+ # 13. AC_OUTPUT
+ ################################################################
=====================================
debian/patches/format_security.patch
=====================================
@@ -0,0 +1,45 @@
+Author: Andreas Tille
+Last-Update: 2016-06-21 11:19:17 +0200
+Description: Fix format security issues
+
+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);
=====================================
debian/patches/hardening
=====================================
@@ -0,0 +1,118 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: insert CPPFLAGS in easel
+--- infernal.orig/easel/Makefile.in
++++ infernal/easel/Makefile.in
+@@ -549,7 +549,7 @@
+ @${RANLIB} libeasel.a
+
+ ${ALL_OBJS}: %.o : %.c ${HDRS} esl_config.h
+- ${QUIET_CC}${CC} -I. -I${srcdir} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
++ ${QUIET_CC}${CC} -I. -I${srcdir} ${CPPFLAGS} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
+
+
+ # Driver compilation:
+@@ -573,10 +573,10 @@
+ else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+ fi;\
+ if test ${V} ;\
+- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${UTEST_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
++ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+ else echo ' ' GEN $@ ;\
+ fi ;\
+- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
++ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+
+ ${ALL_BENCHMARKS}: libeasel.a
+ @BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\
+@@ -587,10 +587,10 @@
+ else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+ fi;\
+ if test ${V} ;\
+- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
++ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+ else echo ' ' GEN $@ ;\
+ fi ;\
+- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
++ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+
+ ${ALL_EXPERIMENTS}: libeasel.a
+ @BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\
+@@ -601,10 +601,10 @@
+ else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+ fi;\
+ if test ${V} ;\
+- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
++ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+ else echo ' ' GEN $@ ;\
+ fi ;\
+- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
++ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+
+ ${ALL_EXAMPLES}: libeasel.a
+ @BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\
+@@ -614,10 +614,10 @@
+ else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
+ fi ;\
+ if test ${V}; \
+- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
++ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+ else echo ' ' GEN $@ ;\
+ fi ;\
+- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
++ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+
+
+
+--- infernal.orig/easel/miniapps/Makefile.in
++++ infernal/easel/miniapps/Makefile.in
+@@ -94,13 +94,13 @@
+ check: ${PROGS} easel
+
+ easel: % : %.c ../libeasel.a ${SUBCMDOBJS}
+- ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}
++ ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} ${CPPFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}
+
+ ${PROGS}: % : %.c ../libeasel.a
+- ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}
++ ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} ${CPPFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}
+
+ ${SUBCMDOBJS}: %.o : %.c ../libeasel.a
+- ${QUIET_CC}${CC} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
++ ${QUIET_CC}${CC} ${CPPFLAGS} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
+
+ install: ${PROGS}
+ ${INSTALL} -m 0755 easel ${DESTDIR}${bindir}/
+--- infernal.orig/hmmer/profmark/Makefile.in
++++ infernal/hmmer/profmark/Makefile.in
+@@ -43,12 +43,12 @@
+ dev: ${PROGS}
+
+ ${PROGS}: % : %.o ../${ESLDIR}/libeasel.a ../src/libhmmer.a
+- ${QUIET_GEN}${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}
++ ${QUIET_GEN}${CC} ${CPPFLAGS} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}
+
+ ${PROGOBJS}: ../src/hmmer.h ../src/p7_config.h
+
+ .c.o:
+- ${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $<
++ ${QUIET_CC}${CC} ${CPPFLAGS} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $<
+
+ clean:
+ -rm -f *.o *~ ${PROGS}
+--- infernal.orig/rmark/Makefile.in
++++ infernal/rmark/Makefile.in
+@@ -43,12 +43,12 @@
+ dev: ${PROGS}
+
+ ${PROGS}: % : %.o ../${HMMERDIR}/src/libhmmer.a ../${ESLDIR}/libeasel.a
+- ${QUIET_GEN}${CC} ${CFLAGS} ${DEFS} ${LDFLAGS} -L../${HMMERDIR}/src -L../${ESLDIR} -L${SRCDIR} -o $@ $@.o ${LIBS}
++ ${QUIET_GEN}${CC} ${CPPFLAGS} ${CFLAGS} ${DEFS} ${LDFLAGS} -L../${HMMERDIR}/src -L../${ESLDIR} -L${SRCDIR} -o $@ $@.o ${LIBS}
+
+ ${PROGOBJS}: ../${HMMERDIR}/src/hmmer.h ../${HMMERDIR}/src/p7_config.h ../src/infernal.h ../src/config.h
+
+ .c.o:
+- ${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${DEFS} -o $@ -c $<
++ ${QUIET_CC}${CC} ${CPPFLAGS} ${ESLINC} ${SRCINC} ${CFLAGS} ${DEFS} -o $@ -c $<
+
+ distclean: clean
+ -rm -f Makefile
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,4 @@
+#format_security.patch
+#autoreconf.patch
+spelling.patch
+hardening
=====================================
debian/patches/spelling.patch
=====================================
@@ -0,0 +1,91 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 16 Jul 2018 07:59:38 +0200
+Description: Fix spelling
+
+Index: infernal/src/cm_modelmaker.c
+===================================================================
+--- infernal.orig/src/cm_modelmaker.c
++++ infernal/src/cm_modelmaker.c
+@@ -1361,7 +1361,7 @@ ConsensusModelmaker(const ESL_ALPHABET *
+ */
+ esl_wuss_nopseudo(ss_cons, ss_cons); /* remove pknots in place */
+ ESL_ALLOC(ct, (clen+1) * sizeof(int));
+- if ((status = esl_wuss2ct(ss_cons, clen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus string is inconsisent in ConsensusModelMaker().");
++ if ((status = esl_wuss2ct(ss_cons, clen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus string is inconsistent in ConsensusModelMaker().");
+
+ /* 2. Construct a guide tree.
+ * This codes is borrowed from HandModelmaker(), where it
+Index: infernal/documentation/manpages/cmalign.man
+===================================================================
+--- infernal.orig/documentation/manpages/cmalign.man
++++ infernal/documentation/manpages/cmalign.man
+@@ -309,7 +309,7 @@ only cells within the bands need be allo
+
+ Importantly, HMM banding sacrifices the guarantee of determining the
+ optimally accurarte or optimal alignment, which will be missed if it
+-lies outside the bands. The tau paramater is the amount of probability
++lies outside the bands. The tau parameter is the amount of probability
+ mass considered negligible during HMM band calculation; lower values
+ of tau yield greater speedups but also a greater chance of missing the
+ optimal alignment. The default tau is 1E-7, determined empirically as
+@@ -500,7 +500,7 @@ in previous versions of
+ .B --mapstr
+ Must be used in combination with
+ .BI --mapali " <f>".
+-Propogate structural information for any pseudoknots that exist in
++Propagate structural information for any pseudoknots that exist in
+ .I <f>
+ to the output alignment. A similar option to this one was called
+ .B --withstr
+Index: infernal/documentation/manpages/cmcalibrate.man
+===================================================================
+--- infernal.orig/documentation/manpages/cmcalibrate.man
++++ infernal/documentation/manpages/cmcalibrate.man
+@@ -51,7 +51,7 @@ Interface) can be also be used for paral
+ .B --mpi
+ option if Infernal was built with MPI enabled, but using more than 161
+ processors is not recommended because increasing past 161 won't
+-accelerate the calibration. See the Installation seciton of the user
++accelerate the calibration. See the Installation section of the user
+ guide for more information.
+
+ .PP
+Index: infernal/hmmer/src/p7_builder.c
+===================================================================
+--- infernal.orig/hmmer/src/p7_builder.c
++++ infernal/hmmer/src/p7_builder.c
+@@ -481,7 +481,7 @@ p7_Builder(P7_BUILDER *bld, ESL_MSA *msa
+ *
+ * Args: bld - build configuration
+ * sq - query sequence
+- * bg - null model (needed to paramaterize insert emission probs)
++ * bg - null model (needed to parameterize insert emission probs)
+ * opt_hmm - optRETURN: new HMM
+ * opt_gm - optRETURN: profile corresponding to <hmm>
+ * opt_om - optRETURN: optimized profile corresponding to <gm>
+Index: infernal/documentation/manpages/cmscan.man
+===================================================================
+--- infernal.orig/documentation/manpages/cmscan.man
++++ infernal/documentation/manpages/cmscan.man
+@@ -746,7 +746,7 @@ option.
+
+ .TP
+ .B --oskip
+-Omit any hit h from the tabular output file that satisifies the
++Omit any hit h from the tabular output file that satisfies the
+ following: another hit h2 overlaps with h and the E-value of h2 is
+ lower than that of h. Hit h will not appear in the tabular output
+ file, although it will still exist in the standard output.
+Index: infernal/documentation/manpages/cmstat.man
+===================================================================
+--- infernal.orig/documentation/manpages/cmstat.man
++++ infernal/documentation/manpages/cmstat.man
+@@ -115,7 +115,7 @@ include Rfam GA, TC, and/or NC bit score
+ and/or
+ .B --cut_nc
+ options can be used to display E-values that correspond to the bit
+-score thresholds. Seperate bit scores or E-values will be displayed
++score thresholds. Separate bit scores or E-values will be displayed
+ for each of the four possible CM search algorithm and model
+ configuration pairs: local Inside, local CYK, glocal Inside and glocal
+ CYK.
=====================================
debian/rules
=====================================
@@ -0,0 +1,51 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+include /usr/share/dpkg/default.mk
+pkgdata:=infernal
+sampledir:=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples
+sampledir_lib:=$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_TARGET_MULTIARCH)/$(DEB_SOURCE)/examples
+
+%:
+ dh $@
+
+override_dh_auto_clean:
+ if [ -r Makefile ]; then $(MAKE) distclean; fi
+ -cd documentation/userguide && if [ -r Makefile ]; then make distclean; fi
+ -cd easel/documentation && if [ -r Makefile ]; then make distclean; fi
+ dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1
+ rm -f testsuite/i49.tbl
+
+override_dh_compress :
+ dh_compress -X.pdf
+
+override_dh_auto_build:
+ dh_auto_build -- V=1
+
+override_dh_auto_install:
+ $(MAKE) install -j$(shell nproc) AM_UPDATE_INFO_DIR=no V=1 prefix=$(CURDIR)/debian/tmp
+
+override_dh_install:
+ dh_install
+ for bin in `ls $(CURDIR)/debian/infernal/usr/lib/infernal` ; do \
+ if [ $$bin != cmalign ] ; then \
+ ln -s cmalign $(CURDIR)/debian/infernal/usr/bin/$$bin ; \
+ fi ; \
+ done
+
+override_dh_installexamples:
+ dh_installexamples
+ mkdir -p $(sampledir)
+ mkdir -p $(sampledir_lib)/src/
+ mkdir -p $(sampledir_lib)/easel/miniapps/
+ find ./src -name "*test" -exec cp \{\} $(sampledir_lib)/src/ \;
+ cp ./src/itest_brute $(sampledir_lib)/src/
+ cp ./easel/miniapps/esl-reformat $(sampledir_lib)/easel/miniapps/
+ cp ./easel/miniapps/esl-shuffle $(sampledir_lib)/easel/miniapps/
+ cp ./easel/miniapps/esl-sfetch $(sampledir_lib)/easel/miniapps/
+ cd $(sampledir) && ln -s ../../../../lib/$(DEB_TARGET_MULTIARCH)/$(DEB_SOURCE)/examples/easel ./easel \
+ && ln -s ../../../../lib/$(DEB_TARGET_MULTIARCH)/$(DEB_SOURCE)/examples/src ./src
+ cp -aR testsuite $(sampledir)/
+ cp ./easel/devkit/sqc $(sampledir)/
=====================================
debian/source/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, python3
+Restrictions:
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+pkg="infernal"
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+
+cp -Lr /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+
+find . -name "*.gz" -exec gunzip \{\} \;
+
+chmod -R +x .
+
+echo infernal testsuite
+find /usr/bin -name "cm*" -exec ln -s \{\} src/ \;
+./sqc 2 ./testsuite/testsuite.sqc . ./testsuite/..
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,22 @@
+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
+ PMID: 19307242
+ year: 2009
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/10/1335
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/10/1335.pdf
+Registry:
+- Name: OMICtools
+ Entry: OMICS_00977
+- Name: SciCrunch
+ Entry: SCR_011809
+- Name: conda:bioconda
+ Entry: infernal
+- Name: bio.tools
+ Entry: NA # infernal_cmscan does not fit
+Bug-Submit: eric.nawrocki at nih.gov
=====================================
debian/watch
=====================================
@@ -0,0 +1,3 @@
+version=4
+opts="uversionmangle=s/(rc\d+)/~$1/" \
+http://eddylab.org/infernal/ infernal-([^-]*)\.tar\.gz
View it on GitLab: https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2
--
View it on GitLab: https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2
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