easel 0.49+dfsg-1

Package Information

Description	library of C functions for biological sequence analysis (runtime library) Easel is an ANSI C code library for computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies the Pfam protein families database, and by Infernal, the profile stochastic context-free grammar software that underlies the Rfam RNA family database. Easel aims to make similar applications more robust and easier to develop, by providing a set of reusable, documented, and well-tested functions. This package contains the shared Easel library.
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed By	Andreas Tille <tille@debian.org>
Sponsor	tille@debian.org
Distribution	unstable
Architecture	any all
VCS	git: https://salsa.debian.org/med-team/easel.git (browse)
Closes	#860746
Tracker	https://tracker.debian.org/pkg/easel
Uploaded	3 days ago

New Package Report

.changes◂

Source	easel
Version	0.49+dfsg-1
Changed-By	Andreas Tille <tille@debian.org>
Architecture	source amd64 all
Distribution	unstable
Date	Thu, 12 Nov 2026 08:58:12 +0100

Changelog◂

easel (0.49+dfsg-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #860746)

.dsc◂

Priority	optional
Component	main
Package-List	easel-apps deb science optional arch=any easel-doc deb doc optional arch=all libeasel-dev deb libdevel optional arch=any libeasel0 deb libs optional arch=any
Section	science

debian/copyright◂

Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: easel
Source: https://github.com/EddyRivasLab/easel
Files-Excluded: demotic/*

Files: *
Copyright: 1990-2023 Sean R. Eddy
           2015-2023 President and Fellows of Harvard College
           2000-2023 Howard Hughes Medical Institute
           1995-2006 Washington University School of Medicine
           1992-1995 MRC Laboratory of Molecular Biology, UK
License: BSD-3-clause

Files: easel.c
Copyright: 1999-2001 David A. Wheeler
           2004-2007 HHMI Janelia Farm Research Campus # Freely
           2004-2007 HHMI Janelia Farm Research Campus" EASEL_LICENSE "Freely
           1990, 1993 The Regents of the University of California
License: BSD-3-clause

Files: esl_rand64.c
Copyright: 2004, Makoto Matsumoto and Takuji Nishimura
           2016 Kevin Lawler
License: ISC
 Permission to use, copy, modify, and/or distribute this software for
 any purpose with or without fee is hereby granted, provided that the
 above copyright notice and this permission notice appear in all copies.
 .
 THE SOFTWARE IS PROVIDED “AS IS” AND THE AUTHOR DISCLAIMS ALL
 WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES
 OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE
 FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY
 DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER
 IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING
 OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

Files: esl_neon.c
       esl_sse.c
       esl_vmx.c
Copyright: 2007 Julien Pommier
           1992 Stephen Moshier
License: Zlib
 This software is provided 'as-is', without any express or implied
 warranty.  In no event will the authors be held liable for any damages
 arising from the use of this software.
 .
 Permission is granted to anyone to use this software for any purpose,
 including commercial applications, and to alter it and redistribute it
 freely, subject to the following restrictions:
 .
  1. The origin of this software must not be misrepresented; you must not
     claim that you wrote the original software. If you use this software
     in a product, an acknowledgment in the product documentation would be
     appreciated but is not required.
  2. Altered source versions must be plainly marked as such, and must not be
     misrepresented as being the original software.
  3. This notice may not be removed or altered from any source distribution.
       
Files: esl_regexp.c
Copyright: 1986, 1993, 1995 by University of Toronto.
           Written by Henry Spencer
License: Spencer-License
 Permission is granted to anyone to use this software for any
 purpose on any computer system, and to redistribute it in any way,
 subject to the following restrictions:
 .
 1. The author is not responsible for the consequences of use of
    this software, no matter how awful, even if they arise
    from defects in it.
 .
 2. The origin of this software must not be misrepresented, either
    by explicit claim or by omission.
 .
 3. Altered versions must be plainly marked as such, and must not
    be misrepresented (by explicit claim or omission) as being
    the original software.
 .
 4. This notice must not be removed or altered.

Files: esl_stats.*
Copyright: 1993 by Sun Microsystems, Inc. All rights reserved. 
License: SUN
 Developed at SunPro, a Sun Microsystems, Inc. business.
 Permission to use, copy, modify, and distribute this software is
 freely granted, provided that this notice is preserved.
 [as posted by eggcrook at stackexchange.com, 21 Dec 2012]

Files: esl_stopwatch.c
Copyright: 2012, David Robert Nadeau, http:NadeauSoftware.com
License: CC-BY-3.0
 On Debian systems you can find a copy of Creative Commons Attribution 3.0
 license at /usr/share/common-licenses/CC-BY-3.0

Files: m4/ax_check_compile_flag.m4
Copyright: 2008 Guido U. Draheim <guidod@gmx.de>
           2011 Maarten Bosmans <mkbosmans@gmail.com>
License: GPL-3+

Files: m4/ax_check_gnu_make.m4
Copyright: 2008 John Darrington <j.darrington@elvis.murdoch.edu.au>
           2015 Enrico M. Crisostomo <enrico.m.crisostomo@gmail.com>
License: GPL-3+

Files: m4/ax_compiler_vendor.m4
Copyright: 2008 Steven G. Johnson <stevenj@alum.mit.edu>
           2008 Matteo Frigo
License: GPL-3+

Files: m4/ax_gcc_func_attribute.m4
Copyright: 2013 Gabriele Svelto <gabriele.svelto@gmail.com>
License: GPL-3+

Files: m4/ax_prog_cc_mpi.m4
Copyright: 2010,2011 Olaf Lenz <olenz@icp.uni-stuttgart.de>
License: GPL-3+

Files: m4/ax_pthread.m4
Copyright: 2008 Steven G. Johnson <stevenj@alum.mit.edu>
           2011 Daniel Richard G. <skunk@iSKUNK.ORG>
           2019 Marc Stevens <marc.stevens@cwi.nl>
License: GPL-3+

Files: formats/uniprot
Copyright: none
 These files are marked to be copyrighted by the UniProt Consortium, but this
 applies to the UniProt database as a whole, not to the individual records.
License: not-the-CC-BY-ND-3.0
 Despite the following statement:
 .
  Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
  Distributed under the Creative Commons Attribution-NoDerivs License
 .
 The above files, as individual records, are not copyrighted.  The statement is
 for the UniProt as a whole.
Comment: This statement was once discussed and applied in the emboss package
 See https://lists.debian.org/debian-med/2012/03/msg00097.html

Files: debian/*
Copyright: 2017 Michael R. Crusoe <michael.crusoe@gmail.com>
           2026 Andreas Tille <tille@debian.org>
License: BSD-3-clause

License: BSD-3-clause
   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 copyright holder 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 HOLDER 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.

License: GPL-3+
 On Debian systems you can find a full copy of the GNU General Public
 License version 3 at /usr/share/common-licenses/GPL-3

DFSG Assistant LLM REVIEW 1 blocker, 2 important, 7 minor

This is an LLM based review using a Debian Inference based workflow. It was not written by a member of the DFSG team and has not been checked by one. It is not a decision on the package: it may be wrong, and it may have missed things.

Reviewed 2 days ago.

Report◂

DFSG NEW review for easel version 0.49+dfsg-1

Summary

Licensing is DFSG-compliant and debian/copyright is accurate: No
Packaging is of good quality: Yes
Issues: 1 blocker, 2 important, 7 minor
debian/watch: version 5
debian/copyright: machine-readable
Scan before the review: 14 found

Licensing

Every file is under a free licence (BSD-2/3-clause, ISC, Zlib, MIT/X11, Spencer's regexp licence, the Sun permission notice, CC-BY-3.0, GPL-3+ with the Autoconf exception, the all-permissive autoconf-archive notice), so nothing is non-DFSG. The copyright file, however, does not describe the tree accurately: config.guess, config.sub and install-sh are covered only by Files: *, which calls them BSD-3-clause although they are GPL-3+/MIT; the Files: easel.c stanza contains text scraped from a source comment, names a holder easel.c does not claim, and leaves the MIT licence of the Wheeler code out; the later stanzas for esl_stats.*, esl_stopwatch.c, esl_regexp.c, esl_sse/neon/vmx.c and esl_rand64.c override Files: * and so drop the main holders; and Files: * states BSD-3-clause for a LICENSE that grants two conditions.

Packaging

DEP-5 copyright, debhelper compat 14 with a plain dh $@ rules file, d-shlibs for the shared library, autopkgtest, salsa-ci, a sensible four-package split (lib/, -dev, apps, -doc), mpi-default-dev and texlive dependencies that cover what the build runs, and Standards-Version 4.7.4 against Policy 4.7.4.1. Remaining problems are small: man-page generation that nothing installs, a documentation patch that silently drops two chapters, an incomplete Libs.private, and sloppy patch headers.

Issues

blocker licensing 1. config.guess, config.sub and install-sh are called BSD-3-clause in Files: * but are GPL-3+ (with Autoconf exception) and MIT, and their holders are not named ◂

Files: debian/copyright:6-12 (Files: *); config.guess:3,8-25; config.sub:3,8-25; install-sh:10-39
Basis: checked, in the package or with a reference tool
Evidence: config.guess:3 # Copyright 1992-2018 Free Software Foundation, Inc. and config.guess:8 # under the terms of the GNU General Public License ... either version 3 of the License, or (at your option) any later version, with # As a special exception to the GNU General Public License ... you may include it under the same distribution terms (same in config.sub). install-sh:10 # Copyright (C) 1994 X Consortium with # Permission is hereby granted, free of charge, ... and # FSF changes to this file are in the public domain. No stanza for any of the three exists; Files: * says License: BSD-3-clause.
Problem: The only paragraph matching these three files misstates their licence and omits both the Free Software Foundation, Inc. and the X Consortium as copyright holders. A user of the source package is told the wrong terms for files it ships and redistributes.
Fix: Add a stanza for config.guess and config.sub (Copyright: 1992-2018 Free Software Foundation, Inc., License: GPL-3+ with Autoconf exception, with the exception text quoted or summarised) and one for install-sh (Copyright: 1994 X Consortium, License: Expat), plus stand-alone License paragraphs for the two short names.

important licensing 2. Files: easel.c stanza holds text scraped from a code comment, names HHMI Janelia Farm Research Campus as a holder of easel.c, and omits the MIT licence of the Wheeler code ◂

Files: debian/copyright:14-19; easel.c:546-547,566-567,2092-2096
Basis: checked, in the package or with a reference tool
Evidence: debian/copyright:16-17 read 2004-2007 HHMI Janelia Farm Research Campus # Freely and 2004-2007 HHMI Janelia Farm Research Campus" EASEL_LICENSE "Freely, which are lines from the esl_banner() documentation example (easel.c:546 # Copyright (C) 2004-2007 HHMI Janelia Farm Research Campus, easel.c:547 # Freely licensed under the Janelia Software License.). easel.c states of esl_tmpfile(): easel.c:2094 * Licensed under the MIT license; see Appendix C of the HOWTO. with Copyright (C) 1999-2001 David A. Wheeler, and the esl_strsep() copy at easel.c:1487-1499 is the Regents' 3-clause text.
Problem: The stanza is what a reader and automated scanners see for easel.c: two of its four Copyright lines are a mis-grepped documentation snippet (including operator text such as # Freely and ..." EASEL_LICENSE "Freely), an entity that does not hold a copyright in the file is declared, and the whole file is declared BSD-3-clause although the Wheeler-derived part is MIT, whose notice has to be reproduced and is not.
Fix: Reduce the stanza to the real holders (1999-2001 David A. Wheeler, 1990, 1993 The Regents of the University of California) plus the main Easel holders, set License: BSD-3-clause and Expat and add a stand-alone License: Expat paragraph with the MIT text.

important licensing 3. Stanzas for esl_stats.*, esl_stopwatch.c, esl_regexp.c, esl_sse/neon/vmx.c, esl_rand64.c and easel.c override Files: * and drop the main copyright holders of those files ◂

Files: debian/copyright:14-19,37-42,59-65,80-87,88-94 (Files: esl_neon.c/esl_sse.c/esl_vmx.c, esl_regexp.c, esl_stats.*, esl_stopwatch.c)
Basis: checked, in the package or with a reference tool
Evidence: Files: esl_stats.* gives Copyright: 1993 by Sun Microsystems, Inc. All rights reserved. and License: SUN only, yet the Sun code is just esl_stats_erfc() (esl_stats.c:396-400) in a file otherwise written by the lab and covered by LICENSE. Files: esl_stopwatch.c gives David Robert Nadeau and License: CC-BY-3.0 for the whole file, although that code is only the #ifdef eslSTOPWATCH_HIGHRES block (esl_stopwatch.c:264-270). Files: esl_regexp.c gives only University of Toronto, Files: esl_sse.c etc. only Julien Pommier/Stephen Moshier, Files: esl_rand64.c only Matsumoto/Lawler. In copyright-format 1.0 the last matching paragraph applies (copyright-format 6.9), so the Files: * holders Sean R. Eddy, President and Fellows of Harvard College and Howard Hughes Medical Institute are not declared for any of these files.
Problem: Copyright information for six groups of files is wrong on both axes: the main holders disappear, and the borrowed part's licence is presented as the licence of the entire file (most visibly CC-BY-3.0 for esl_stopwatch.c).
Fix: Keep the Files: * holders in each of these stanzas and express the combination, e.g. Copyright: 1990-2023 Sean R. Eddy ... 2012 David Robert Nadeau with License: BSD-3-clause and CC-BY-3.0 (same pattern with Zlib, Spencer-License, SUN), or narrow the patterns to the borrowed part only where it is a separate file.

minor licensing 4. Files: * declares BSD-3-clause, but upstream LICENSE grants a two-clause BSD licence ◂

Files: debian/copyright:6-12,143-166; LICENSE:47-72
Basis: checked, in the package or with a reference tool
Evidence: LICENSE says The Easel library is open source software. It is freely distributed under the terms of the BSD ... license: and then lists only 1. Redistributions of source code must retain ... and 2. Redistributions in binary form must reproduce ..., going straight on to THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS". The stand-alone License: BSD-3-clause paragraph in debian/copyright adds a third condition at line 156 (3. Neither the name of the copyright holder ... may be used to endorse). The tree contains no third-clause text except the FreeBSD esl_strsep() copy in easel.c.
Problem: The licence Debian documents is not the one upstream grants for the bulk of the tree; the copyright file imposes an endorsement restriction that the files do not carry.
Fix: Declare License: BSD-2-clause for Files: * (with a BSD-2-clause stand-alone paragraph) and keep BSD-3-clause only where the text actually is 3-clause (easel.c:1487-1499, the Debian packaging).

minor licensing 5. m4/ax_check_gnu_make.m4 and m4/ax_gcc_func_attribute.m4 are declared GPL-3+, but their own text is the all-permissive autoconf-archive notice ◂

Files: debian/copyright:99-103,109-112; m4/ax_check_gnu_make.m4:56-63; m4/ax_gcc_func_attribute.m4:70-76
Basis: checked, in the package or with a reference tool
Evidence: Both files say Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. None of their text mentions the GNU GPL, unlike ax_check_compile_flag.m4, ax_compiler_vendor.m4, ax_prog_cc_mpi.m4 and ax_pthread.m4, whose License: GPL-3+ stanzas are correct.
Problem: Two permissively licensed files are documented as GPL-3+, so a downstream user is told of obligations the files do not impose (and cannot find the GPL's terms in them).
Fix: Give those two stanzas the all-permissive licence instead (License: permissive, with the quoted Copying and distribution ... without royalty text as the stand-alone paragraph).

minor packaging 6. Man-page handling is dead: mans.patch generates miniapps/*.1 that nothing installs, and the .pp/.PP seds in rules cancel out ◂

Files: debian/patches/mans.patch:12-33; debian/rules:19-26; miniapps/Makefile.in:120-126; miniapps/esl-afetch.man.in:34
Basis: checked, in the package or with a reference tool
Evidence: miniapps/Makefile.in installs $$file.man as $$file.1 (INSTALL -m 0644 $$file.man ${DESTDIR}${man1dir}/$${file}${man1ext}) and never uses a generated .1; the .man files are already substituted by the pre-existing AC_CONFIG_FILES([ miniapps/esl-afetch.man ... ]) list at configure.ac:606-629, so the 22 extra AC_CONFIG_FILES([miniapps/esl-*.1:miniapps/esl-*.man]) lines do nothing. In debian/rules the first sed 's=\.pp=\.PP=g' is undone by the last sed 's=\.PP=\.pp=g', and the templates already use .PP (e.g. esl-afetch.man.in:34), so both are no-ops.
Problem: A quilt patch with no effect on the built package and a rules block that does nothing are maintenance traps: a later change that relies on them (e.g. expecting miniapps/*.1 to be installed) will silently not happen.
Fix: Drop the AC_CONFIG_FILES additions from mans.patch (or narrow the patch to what is actually needed) and delete the two sed passes in override_dh_auto_configure and the miniapps/*.1 line from debian/clean.

minor packaging 7. No man page is installed for easel or its subcommands, and easel-downsample.man.in is shipped but installed by nothing ◂

Files: miniapps/easel-downsample.man.in:1; miniapps/Makefile.in:55-77,120-126; debian/easel-apps.install
Basis: checked, in the package or with a reference tool
Evidence: PROGS and the install loop cover 23 miniapps; the easel multiplexer binary (miniapps/easel.c with cmd_downsample.c, cmd_filter.c, cmd_index.c, cmd_alistat.c) has no easel.1, and easel-downsample.man.in, whose .TH line is .TH "easel downsample" 1 ..., is neither in PROGS nor in configure's substitution list, so make install never installs it.
Problem: easel-apps installs a binary with subcommands that have no manual page, while a ready-made page for one of them sits unused in the source.
Fix: Install easel-downsample.man as easel-downsample.1 from debian/rules, or forward the gap upstream and add an easel.1.

minor packaging 8. docs.patch comments out the vectorops and getopts chapters of the userguide, and the patch description does not say so ◂

Files: debian/patches/docs.patch:57-71; documentation/main.tex:263,466
Basis: checked, in the package or with a reference tool
Evidence: The patch changes - \input{esl_vectorops} to % \input{esl_vectorops} and -\input{esl_getopts} to %\input{esl_getopts}, while its Description: only mentions skipping bibtex, restoring the msaweight/dirichlet examples and adding esl_mixdchlet. The rest of the patch turns the three pdflatex runs into -@pdflatex -interaction=nonstopmode with @test -f main.pdf.
Problem: The PDF shipped in easel-doc silently loses two modules' prose, the patch's own description does not cover it, and the build ignores pdflatex errors, so further content loss would go unnoticed as long as some PDF is produced.
Fix: Document the two omissions in the patch header (or fix the offending LaTeX instead of dropping the sections), and forward the doc fixes upstream.

minor packaging 9. easel.pc's Libs.private omits the MPI libraries, so pkg-config --static cannot link libeasel.a ◂

Files: debian/easel.pc.in:9; debian/rules:36-41; esl_mpi.c:13,54-103
Basis: checked, in the package or with a reference tool
Evidence: debian/easel.pc.in has Libs.private: -lm -lpthread; debian/rules configures with --enable-mpi, and esl_mpi.c contains MPI_Pack_size, MPI_Comm and friends under #if defined(HAVE_MPI) and is part of libeasel.a, which libeasel-dev installs.
Problem: A consumer that links statically with $(pkg-config --static --libs easel) gets unresolved MPI symbols, although the package ships the static library for exactly that use.
Fix: Add the MPI link flags to Libs.private (substituted at build time, or Requires.private: ompi via the MPI pkg-config file).

minor packaging 10. Patch headers are sloppy: export-internal-symbols-for-pyhmmer.patch has two Author fields, spelling.patch has no Forwarded ◂

Files: debian/patches/export-internal-symbols-for-pyhmmer.patch:1-11; debian/patches/spelling.patch:1-3; debian/patches/mans.patch:1-3
Basis: checked, in the package or with a reference tool
Evidence: export-internal-symbols-for-pyhmmer.patch lists Author: Andreas Tille <tille@debian.org> twice (lines 6 and 9), and spelling.patch and mans.patch carry only From:/Description:/Author: with neither Forwarded: nor Last-Update:.
Problem: DEP-3 headers are what the security team and downstream use to triage patches; a duplicated field and a missing forwarding status make that harder, and the spelling fixes are clearly upstreamable.
Fix: Remove the duplicate Author: line, add Forwarded: and Last-Update: to each patch.

Verified ◂

documentation/figures/rna_elements.ai is the Adobe Illustrator original of the rna_elements figure included by documentation/format_wuss.tex; the modifiable source is shipped.
documentation/figures/rna_elements.pdf is the export of documentation/figures/rna_elements.ai, made once upstream; it is included by documentation/format_wuss.tex and is not regenerated by the Debian build.
documentation/figures/rnaseP-bsu-alignment.ai is the Illustrator original of the rnaseP-bsu-alignment figure used by documentation/format_wuss.tex; the source is shipped.
documentation/figures/rnaseP-bsu-alignment.pdf is the export of documentation/figures/rnaseP-bsu-alignment.ai, a documentation figure, not a built file of the build.
documentation/figures/rnaseP-ecoli.ai is the Illustrator original of the rnaseP-ecoli figure used by documentation/format_wuss.tex; the source is shipped.
documentation/figures/rnaseP-ecoli.pdf is the export of documentation/figures/rnaseP-ecoli.ai, a documentation figure, not a build product.
documentation/figures/easel_techtree.ai is the Illustrator original of the module-map diagram; its generator, devkit/techtree.py, is also shipped.
documentation/figures/easel_techtree.pdf is the export of documentation/figures/easel_techtree.ai, referenced by release-notes/RELEASE-0.46.md for the manual; a documentation asset, not a build product.
documentation/figures/evd_basic.pdf is a plot \includegraphics'd by esl_gumbel.tex:96; no authoring source is shipped upstream and the Debian build does not regenerate it, so no build step depends on a missing source.
documentation/figures/evd_location.pdf is a plot included by esl_gumbel.tex:104; same situation as evd_basic.pdf.
documentation/figures/evd_scale.pdf is a plot included by esl_gumbel.tex:107; same situation as evd_basic.pdf.
documentation/figures/gev_density.pdf is a plot included by esl_gev.tex:104; same situation as evd_basic.pdf.
documentation/figures/gev_logdensity.pdf is a plot included by esl_gev.tex:107; same situation as evd_basic.pdf.
Files: formats/uniprot (debian/copyright:121-137): formats/uniprot contains two verbatim UniProtKB records and line 109 carries the database's Distributed under the Creative Commons Attribution-NoDerivs License statement; the stanza reproduces the Debian precedent it cites (emboss, debian-med 2012), and the file is unmodified test data, so the CC-BY-ND wording is not a licence on the file.
The Adobe Systems, Inc. notices in documentation/figures/rna_elements.eps, rnaseP-bsu-alignment.eps and rnaseP-ecoli.eps (%%Copyright: Copyright ... Adobe Systems Incorporated. All Rights Reserved.) are PostScript font-embedding notices for the Type 1 fonts carried inside the EPS, not a claim on the figures; the figure sources are shipped alongside.
David Robert Nadeau is declared in debian/copyright:89; only the URL is malformed (http:NadeauSoftware.com instead of http://NadeauSoftware.com), which is cosmetic. The CC-BY-3.0 pointer to /usr/share/common-licenses/CC-BY-3.0 is a valid file.
Contributors credited in LICENSE need no stanza of their own: the Brown/Lovato gennor() code in esl_random.c:498-500 is described as public domain, and Bob Jenkins' esl_rnd_mix3() lives in a file licensed by Files: *.
esl_alloc.c and the other lab files carry no per-file licence header at all; their terms come from the top-level LICENSE, which I read in full. documentation/copyright.tex repeats the BSD claim for the manual.
debian/lrc.config is an unused duplicate of the list of files that get their own copyright stanzas (m4/*, config.guess, config.sub, install-sh); nothing under debian/ reads it and it is not installed.
Coverage: every file under debian/ was read in full, as were LICENSE, all m4/.m4, install-sh, config.guess, config.sub, both Makefile.in install/build rules, configure.ac's AC_CONFIG_FILES block, and the headers of every source file discussed above. I grepped the whole tree for Copyright, (C), ©, All rights reserved, Creative Commons, non-commercial, NoDeriv, public domain, GNU General/Lesser, Apache, Mozilla, SPDX-License, Licensed under and Permission is hereby granted. Binary files (.ai, *.pdf, *.png, *.eps) were not opened.
uscan found the packaged version as the newest upstream release (upstream 0.49, packaged 0.49+dfsg).
Every pointer of debian/copyright to /usr/share/common-licenses names a file that is there (CC-BY-3.0, GPL-3).

Not confirmed ◂

esl_rand64.c:18-20 states Copyright (C) 2004, Makoto Matsumoto and Takuji Nishimura. All rights reserved. and only links mt19937-64.c, carrying no licence text for it; debian/copyright declares ISC for the whole file, which matches only Kevin Lawler's esl_rand64_Deal(). The referenced upstream file is BSD-3-clause, so the stanza may need BSD-3-clause and ISC; I did not have that file to check.

Proposed changes ◂

None.

Uploader's response to the LLM review

config.* and install-sh should be no-brainer and perhaps the LLM query can be adjusted.

I'll work on the other issues later.

— Andreas Tille (tille), 2 days ago

Other Reviews of this Package

Version	Hash	Allocated	Completed	Reviewer	Status	Details
0.49+dfsg-1	0959f342…	2026-11-12 11:00	2026-11-12 11:00	dfsg-uploader	rejected	VIEW

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