Review: 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
| Date | Thu, 12 Nov 2026 08:58:12 +0100 |
|---|---|
| Source | easel |
| Version | 0.49+dfsg-1 |
| Changed-By | Andreas Tille <tille@debian.org> |
| Architecture | source amd64 all |
| Distribution | unstable |
Changelog
easel (0.49+dfsg-1) unstable; urgency=medium . * Initial release. (Closes: #860746)
.dsc
| 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 |
| Priority | optional |
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: © 2004-2016 Sean R. Eddy
© 2004-2016 Howard Hughes Medical Institute
© 2015-2016 President and Fellows of Harvard College
© 2004-2006 Washington University School of Medicine
License: BSD-3-clause
Files: debian/*
Copyright: © 2017 Michael R. Crusoe <michael.crusoe@gmail.com>
License: BSD-3-clause
License: BSD-3-clause
Redistribution and use in source and binary forms, with or without
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Files: esl_stopwatch.c
Copyright: 2012, David Robert Nadeau, http:NadeauSoftware.com
License: CC-BY-3.0
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DFSG Assistant LLM REVIEW 2 blocker, 0 important, 4 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 3 days ago.
Report
DFSG NEW review for easel version 0.49+dfsg-1
Summary
- Licensing is DFSG-compliant and
debian/copyrightis accurate: No - Packaging is of good quality: No
- Issues: 2 blocker, 0 important, 4 minor
- debian/watch: version 5
- debian/copyright: machine-readable
- Scan before the review: 13 found
Licensing
Most of the tree is BSD-licensed and DFSG-free, but formats/uniprot is a UniProt record that states it is distributed under the Creative Commons Attribution-NoDerivs licence, which is non-free. debian/copyright is also far from complete: its Files: * stanza declares BSD-3-clause and four holders for the whole tree, while about twenty files carry other licences and holders (GPL-3+ macros in m4/, config.guess/config.sub, X11 install-sh, Henry Spencer's regexp, Sun's erfc, MT19937-64 and ISC code in esl_rand64.c, zlib-licensed SIMD kernels, Wheeler's MIT code and the FreeBSD strsep in easel.c, and the MRC Laboratory of Molecular Biology in LICENSE), whose notices are not reproduced.
Packaging
The structure is sound and current: compat 14, --buildsystem defaults with d-shlibs for the shared library, Multi-Arch: same on libeasel0, hardening +all, a working -doc package with doc-base, and Standards-Version: 4.7.4 against Policy 4.7.4.1. But Build-Depends lists help2man and libgsl-dev, neither of which the build uses; override_dh_auto_test runs make tests, which only compiles the unit-test binaries, so no test is ever executed at build time and the autopkgtest only builds the example; and /usr/bin/easel is installed without a manual page. All findings are minor, but each should be fixed before upload.
Issues
blocker licensing 1. debian/copyright claims BSD-3-clause for the whole tree, but m4/, config.guess, config.sub, install-sh, esl_regexp.c, esl_stats.*, esl_rand64.c, esl_sse/neon/vmx.c and easel.c carry other licences and holders ◂
- Files: debian/copyright:6-11 (
Files: *),m4/ax_pthread.m4:60-75,m4/ax_check_compile_flag.m4:29-46,m4/ax_compiler_vendor.m4,m4/ax_prog_cc_mpi.m4,m4/ax_check_gnu_make.m4:53-60,m4/ax_gcc_func_attribute.m4:67-74,config.guess:1-25,config.sub:1-25,install-sh:8-33,esl_regexp.c:444-462,esl_stats.c:395-401,esl_stats.h:33-39,esl_rand64.c:18-26,esl_sse.c:678-707,esl_neon.c:716-745,esl_vmx.c:519-548,easel.c:1485-1500,easel.c:2090-2097,LICENSE:1-10 - Basis: checked, in the package or with a reference tool
- Evidence:
m4/ax_pthread.m4:65: "This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License ... either version 3 of the License, or (at your option) any later version.";config.guess:3: "Copyright 1992-2018 Free Software Foundation, Inc." (GPL-3+ with the Autoconf exception at :20);install-sh:10: "Copyright (C) 1994 X Consortium" (MIT/X11 text);esl_regexp.c:446: "Copyright (c) 1986, 1993, 1995 by University of Toronto.";esl_stats.c:396: "Copyright (C) 1993 by Sun Microsystems, Inc. All rights reserved." / "Permission to use, copy, modify, and distribute this software is freely granted";esl_rand64.c:20: "Copyright (C) 2004, Makoto Matsumoto and Takuji Nishimura. All rights reserved." and:25: "Copyright (2016) Kevin Lawler. Released under ISC License.";esl_sse.c:680: "Copyright (C) 1992 Stephen Moshier" and "The zlib license";easel.c:1487: "The Regents of the University of California";easel.c:2093: "Licensed under the MIT license";LICENSE:6: "Copyright (C) 1992-1995 MRC Laboratory of Molecular Biology, UK";debian/copyright:6-11saysFiles: */License: BSD-3-clausewith only Eddy, HHMI, Harvard and Washington University. - Problem: The licence short name is wrong for about twenty files and the holders named in the files' own notices are absent (FSF; Steven G. Johnson, Daniel Richard G., Marc Stevens, Guido U. Draheim, Maarten Bosmans, John Darrington, Enrico M. Crisostomo, Gabriele Svelto; X Consortium; Henry Spencer/University of Toronto; Sun Microsystems; Matsumoto/Nishimura and Kevin Lawler; Julien Pommier and Stephen Moshier; the Regents of the University of California; David A. Wheeler; MRC Laboratory of Molecular Biology). The notices that zlib, ISC, MIT, X11, Sun and Spencer's licences require to be reproduced are not in
debian/copyright, and the Autoconf exception of the GPL-3+ files is not quoted either.debian/copyrighttherefore does not describe the copyright and licensing of every file (Policy 12.5). The GPL-3+ files are build-time-only (autoconf macros, config.guess/sub), so they create no licence conflict with the BSD library. - Fix: Add
Files:stanzas for each group with the correct holders and short names (GPL-3+ with Autoconf exception for the four ax_*.m4 and for config.guess/config.sub, with the exception text quoted and GPL-3 referred to /usr/share/common-licenses/GPL-3; the unlimitedCopying and distribution ... without royaltytext for ax_check_gnu_make.m4 and ax_gcc_func_attribute.m4; X11 for install-sh; the Spencer/University of Toronto notice for esl_regexp.[ch]; Sun's notice for esl_stats.[ch]; BSD-3-clause for MT19937-64 plus ISC for esl_rand64.c; zlib for the SIMD files; MIT for the esl_tmpfile() part of easel.c and BSD-3-clause for its strsep() part), and add MRC Laboratory of Molecular Biology to the holder list.
blocker licensing 2. formats/uniprot carries an explicit Creative Commons Attribution-NoDerivs notice, a non-free licence ◂
- Files:
formats/uniprot:108-109 - Basis: checked, in the package or with a reference tool
- Evidence:
CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/termsandCC Distributed under the Creative Commons Attribution-NoDerivs License. - Problem: A NoDerivs licence forbids distributing modified versions, so the file does not meet DFSG 3 and cannot be in main. It is in the +dfsg tarball (
Files-Excludednames onlydemotic/*) and nodebian/copyrightstanza covers it (theFiles: *stanza claims it as BSD-3-clause). The record is not referenced by any test or by the source; it is unused test data. - Fix: Repack without it (add
formats/uniprottoFiles-Excluded/the repack filter) and delete it, or replace it with a record of the same format under a free licence;formats/emblis a similar record with no such notice.
minor
licensing
3. Files: * declares BSD-3-clause but upstream's LICENSE grants the 2-clause BSD licence
◂
- Files:
debian/copyright:6-11,debian/copyright:17-45,LICENSE - Basis: checked, in the package or with a reference tool
- Evidence: The licence in
LICENSElists only conditions "1. Redistributions of source code must retain the above copyright notice..." and "2. Redistributions in binary form must reproduce the above copyright notice..." followed by the disclaimer; the stand-aloneLicense: BSD-3-clausetext indebian/copyrightadds "3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products...". - Problem: The licence Debian records for the bulk of the tree is not the one the holder granted: the extra endorsement clause is an additional restriction that
LICENSEdoes not impose. (Three-clause text does appear in easel.c's FreeBSDstrsep()and indocumentation/copyright.tex, so the two cases need separating rather than one blanket claim.) - Fix: Use
BSD-2-clauseforFiles: *with the 2-clause text fromLICENSE, and keep the 3-clause text in a separate stanza covering the files that really carry it (e.g.easel.c).
minor packaging 4. Build-Depends lists help2man and libgsl-dev, neither of which the build uses ◂
- Files:
debian/control:11-12,debian/rules:28,configure.ac:183 - Basis: checked, in the package or with a reference tool
- Evidence:
help2man,andlibgsl-dev,inBuild-Depends;help2manappears nowhere else in the tree (the man pages are generated fromminiapps/*.man.inby sed and configure);debian/rules:28endsCC=mpicc # --with-gsl, so GSL is not enabled, andconfigure.ac:183defaultswith_gsl=no. - Problem: Two build dependencies are installed in every build without being used;
interface_gsl.cis compiled only underHAVE_LIBGSL, which the commented-out--with-gslnever defines. - Fix: Drop
help2manandlibgsl-devfromBuild-Depends, or enable--with-gsland keep the latter.
minor
packaging
5. override_dh_auto_test runs make tests, which only compiles the unit-test binaries; the test suite is never run
◂
- Files:
debian/rules:46-47,Makefile.in:538-545,debian/tests/run-unit-test - Basis: checked, in the package or with a reference tool
- Evidence:
override_dh_auto_test:/$(MAKE) tests;Makefile.in:538tests: ${ALL_UTESTS}builds andMakefile.in:541check:builds and then runsminiapps/checkandtestsuite/check; the autopkgtest only copiesdebian/exampleand builds/runsreadseq. - Problem: About ninety unit-test binaries are built during the build and discarded without being executed, and autopkgtest does not run them either, so the upstream test suite runs nowhere.
- Fix: Use
$(MAKE) checkinoverride_dh_auto_test(addingpython3toBuild-Dependswith<!nocheck>), or add adebian/tests/entry that runs the upstream unit tests, and fix or dropmake testsaccordingly.
minor packaging 6. /usr/bin/easel, the multi-call program with subcommands, is installed without a manual page ◂
- Files:
miniapps/Makefile.in:46-112,miniapps/easel.c,debian/easel-apps.install - Basis: checked, in the package or with a reference tool
- Evidence:
all: ${PROGS} easelbuildseasel, andinstall:installs$$file.manfor${PROGS}only;easelis not inPROGSand there is nominiapps/easel.man.in(onlyesl-*.man.inand the unusedeasel-downsample.man.in). - Problem: Policy 12.1: "Each program, utility, and function should have an associated manual page" and "If no manual page is available, this is considered as a bug".
debian/easel-apps.installships all ofusr/bin/*, soeasel(with its alistat/downsample/filter/index subcommands) is the one binary without a page. - Fix: Add
miniapps/easel.man.indocumentingeaseland its subcommands, generate it with the other pages, and install it.
Verified ◂
- Inventory and coverage: 447 files; all of
debian/read in full; every file that carries a copyright or licence notice read (LICENSE, all m4/.m4, config.guess, config.sub, install-sh, the SIMD modules, esl_rand64.c, esl_stats., esl_regexp.*, esl_random.c, easel.c, esl_stopwatch.c); a tree-wide grep for Copyright/(C)/SPDX-License-Identifier/Licensed under/Permission is hereby granted/All rights reserved, excluding.pc/(there is nodebian/cargo-checksum.json). - The thirteen scanned documents are documentation inputs, not build products of this package:
documentation/figures/easel_techtree.ai,documentation/figures/easel_techtree.pdf,documentation/figures/rna_elements.ai,documentation/figures/rna_elements.pdf,documentation/figures/rnaseP-bsu-alignment.ai,documentation/figures/rnaseP-bsu-alignment.pdf,documentation/figures/rnaseP-ecoli.ai,documentation/figures/rnaseP-ecoli.pdfare Adobe Illustrator documents (PDF-compatible) shipped with their editable sources and with.eps/.pngrenditions, anddocumentation/figures/evd_basic.pdf,evd_location.pdf,evd_scale.pdf,gev_density.pdf,gev_logdensity.pdfare plots included with\includegraphicsbyesl_gumbel.tex:96-107andesl_gev.tex:104-107, whose LaTeX sources are present but whose plotting scripts are not shipped; the Userguide PDF itself is built at build time fromdocumentation/main.texusingdevkit/autodocanddevkit/cexcerpt, both present in the tree. - The Adobe Systems copyright lines in
documentation/figures/rna_elements.eps,rnaseP-bsu-alignment.epsandrnaseP-ecoli.epsare Illustrator DSC%%Copyright:headers and an embedded Adobe font/Notice, not a licence claim over the figures' content. - Of the holders the scan flagged, the third-party code authors are covered by the first issue; the "HHMI Janelia Farm Research Campus # Freely ..." strings at
easel.c:546,566andesl_getopts.c:167are the generatedEASEL_COPYRIGHT/EASEL_LICENSEconfigure text (a sample header written by the program), not a licence of those files; David Robert Nadeau is named in theesl_stopwatch.cstanza (the URL is misspelthttp:NadeauSoftware.com); the MRC Laboratory of Molecular Biology is inLICENSE:6only. esl_stopwatch.cis CC-BY-3.0 with its full text indebian/copyright; CC-BY-3.0 is DFSG-free and its notice in the file matches the stanza.- The SIMD files' borrowed routines are the zlib-licensed
ssemathderivatives of Julien Pommier (esl_sse.c:678-707,esl_neon.c:716-745,esl_vmx.c:519-548); the Cephes/Moshier attribution in the same comment is a credit line for those derivatives ("may be used freely"), not a separate restriction. Files-Excluded: demotic/*matches the tree:demotic/is absent.- Test data
formats/(fasta, genbank, embl, BLOSUM62, wag.dat, ...) andesl_msa_testfiles/carry no licence notices; BLOSUM62 and WAG are numeric matrices from the cited papers. - No font files (.ttf/.otf/.pfb/.afm) are in the tree.
- Packaging basics checked:
3.0 (quilt), compat 14, hardening+all, dpkg buildflags,Multi-Arch: sameonlibeasel0, headers andeasel.pcin the multiarch devel path, doc-base plus a generated PDF ineasel-doc, no maintainer scripts needed, Vcs-* and Homepage present, changelogunstablewith an ITP closure and a coherent version, no remaining lintian-class problems in the files read. Standards-Version: 4.7.4is current against Policy 4.7.4.1 (first two components 4.7).- There is no generated
configurein the tarball, but autoconf arrives through debhelper's dependency on dh-autoreconf, andconfigure.acpulls the m4 macros in withm4_include, so this is not a missing Build-Depends. - uscan found the packaged version as the newest upstream release (upstream
0.49, packaged0.49+dfsg).
Not confirmed ◂
- d-shlibs is not installed on the reviewing system, so
d-shlibmove's${devlibs:Depends}output and itss/(libmpi40|libopen_mpi40|libmpich12)-dev/mpi-default-dev/override could not be checked; whetherlibeasel-devends up depending onmpi-default-dev(needed, because the installedesl_mpi.hincludes<mpi.h>whenHAVE_MPIis defined) is therefore unknown. debian/rules:29runssed 's=\.PP=\.pp=g'over theminiapps/*.manfiles thatminiapps/Makefile.in:112installs as/usr/share/man/man1/esl-*.1, after configure has generated them from the.man.intemplates; a build would show whether the shipped pages really keep the undefined.ppmacro instead of.PP(the.1files added bydebian/patches/mans.patchare generated but never installed).
Proposed changes ◂
None.
Uploader's response to the LLM review
The uploader rejected this upload in response to the review.
Review Information
rejected — allocated to dfsg-uploader 3 days ago, started 3 days ago, completed 3 days ago.
Final Comment
The uploader rejected this upload in response to the automated (LLM) review of it, so that they can fix the problems it found and upload again.
The uploader said:
Please reject