Debian Med Packaging Team

At the time of the last Lintian run, the following possible problems were found in packages maintained by Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>, listed by source package. See also the report showing only errors and warnings. Also see their QA overview.

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/abacas.git
  • vcs-git https://anonscm.debian.org/git/debian-med/abacas.git

abacas

• W manpage-has-errors-from-man
  • usr/share/man/man1/abacas.1.gz 20: warning [p 1, 3.0i, div `an-div', 0.0i]: cannot adjust line

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 24)
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

abyss

• X binary-file-built-without-LFS-support
  • usr/lib/abyss/KAligner
  • usr/lib/abyss/PathConsensus
  • usr/lib/abyss/abyss-align
• W binary-without-manpage
  • usr/bin/DistanceEst
  • usr/bin/DistanceEst
  • usr/bin/abyss-fixmate
  • usr/bin/abyss-fixmate
• I possible-documentation-but-no-doc-base-registration
• I spelling-error-in-binary
  • usr/lib/abyss/Consensus ommited omitted
  • usr/lib/abyss/Consensus ommited omitted
  • usr/lib/abyss/PathConsensus wether whether
  • usr/lib/abyss/PathConsensus wether whether
  • usr/lib/abyss/SimpleGraph paramter parameter
  • usr/lib/abyss/SimpleGraph paramter parameter
  • usr/lib/abyss/abyss-align wether whether
  • usr/lib/abyss/abyss-align wether whether
  • usr/lib/abyss/abyss-sealer superceded superseded
  • usr/lib/abyss/abyss-sealer superceded superseded
  • usr/lib/abyss/abyss-tofastq ouput output
  • usr/lib/abyss/abyss-tofastq ouput output
• I spelling-error-in-manpage
  • usr/share/man/man1/abyss-pe.1.gz varible variable
  • usr/share/man/man1/abyss-pe.1.gz varible variable
• E wrong-path-for-interpreter
  • usr/lib/abyss/abyss-fatoagp (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/abyss/abyss-fatoagp (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/abyss/abyss-samtoafg (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/abyss/abyss-samtoafg (#!/usr/bin/env != /usr/bin/perl)

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • ftp://ftp.sanger.ac.uk/pub/project/acedb/SUPPORTED/ACEDB-source\.([0-9.]+)\.tar\.gz
• P file-contains-trailing-whitespace
  • debian/changelog (line 147)
• I override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
  • (line 37)
• P package-uses-old-debhelper-compat-version
  • 10
• P source-contains-empty-directory
  • waction/
  • wdemo/database/
  • wdoc/Interfaces/
  • wemap/
  • whelp/syntax/
  • wsyn/
  • wt1/
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/acedb.git
  • vcs-git https://anonscm.debian.org/git/debian-med/acedb.git

acedb-other

• X binary-file-built-without-LFS-support
  • usr/bin/efetch
• I hardening-no-fortify-functions
  • usr/bin/efetch
  • usr/bin/efetch

• P debian-watch-does-not-check-gpg-signature
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/adapterremoval.git
  • vcs-git https://anonscm.debian.org/git/debian-med/adapterremoval.git

adapterremoval

• X binary-file-built-without-LFS-support
  • usr/bin/AdapterRemoval
• I hardening-no-fortify-functions
  • usr/bin/AdapterRemoval
  • usr/bin/AdapterRemoval
• W manpage-has-errors-from-man
  • usr/share/man/man1/AdapterRemoval.1.gz 232: warning [p 4, 4.3i]: can't break line
  • usr/share/man/man1/AdapterRemoval.1.gz 232: warning [p 4, 4.3i]: can't break line
• W privacy-breach-generic
  • usr/share/doc/adapterremoval/README.html [<img alt="coveralls" src="https://img.shields.io/coveralls/mikkelschubert/adapterremoval.svg" />] (https://img.shields.io/coveralls/mikkelschubert/adapterremoval.svg)
  • usr/share/doc/adapterremoval/README.html [<img alt="coveralls" src="https://img.shields.io/coveralls/mikkelschubert/adapterremoval.svg" />] (https://img.shields.io/coveralls/mikkelschubert/adapterremoval.svg)
  • usr/share/doc/adapterremoval/README.html [<img alt="travis" src="https://img.shields.io/travis/mikkelschubert/adapterremoval/master.svg" />] (https://img.shields.io/travis/mikkelschubert/adapterremoval/master.svg)
  • usr/share/doc/adapterremoval/README.html [<img alt="travis" src="https://img.shields.io/travis/mikkelschubert/adapterremoval/master.svg" />] (https://img.shields.io/travis/mikkelschubert/adapterremoval/master.svg)
• I spelling-error-in-binary
  • usr/bin/AdapterRemoval pres press
• I spelling-error-in-manpage
  • usr/share/man/man1/AdapterRemoval.1.gz lenght length
  • usr/share/man/man1/AdapterRemoval.1.gz lenght length
  • usr/share/man/man1/AdapterRemoval.1.gz multipled multiplied
  • usr/share/man/man1/AdapterRemoval.1.gz multipled multiplied

• I debian-rules-contains-unnecessary-get-orig-source-target
• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/adun.app.git
  • vcs-git https://anonscm.debian.org/git/debian-med/adun.app.git

adun-core (0.81-11+b1; main)

• X binary-file-built-without-LFS-support
  • usr/bin/AdunServer
  • usr/lib/GNUstep/Frameworks/AdunKernel.framework/Versions/0/libAdunKernel.so.0.13
  • usr/lib/GNUstep/Frameworks/MolTalk.framework/Versions/3/libMolTalk.so.3.0.1
  • usr/lib/GNUstep/Frameworks/ULFramework.framework/Versions/0/libULFramework.so.0.6
• X shlib-calls-exit
  • usr/lib/GNUstep/Frameworks/AdunKernel.framework/Versions/0/libAdunKernel.so.0.13
  • usr/lib/GNUstep/Frameworks/AdunKernel.framework/Versions/0/libAdunKernel.so.0.13
  • usr/lib/adun.app/libXMLLib.so.0.1
  • usr/lib/adun.app/libXMLLib.so.0.1
  • usr/lib/adun.app/libadun_base.so.0.0.1
  • usr/lib/adun.app/libadun_base.so.0.0.1
• I spelling-error-in-binary
  • usr/lib/GNUstep/Frameworks/AdunKernel.framework/Versions/0/libAdunKernel.so.0.13 onthe on the
  • usr/lib/GNUstep/Frameworks/AdunKernel.framework/Versions/0/libAdunKernel.so.0.13 onthe on the
  • usr/lib/GNUstep/Frameworks/MolTalk.framework/Versions/3/libMolTalk.so.3.0.1 CONECT CONNECT
  • usr/lib/GNUstep/Frameworks/MolTalk.framework/Versions/3/libMolTalk.so.3.0.1 CONECT CONNECT

adun.app (0.81-11+b1; main)

• X binary-file-built-without-LFS-support
  • usr/lib/GNUstep/Applications/UL.app/UL
• I wrong-section-according-to-package-name
  • adun.app => gnustep
  • adun.app => gnustep

• I debian-rules-parses-dpkg-parsechangelog
  • (line 5)
• O debian-watch-does-not-check-gpg-signature
• I out-of-date-standards-version
  • 4.1.4 (released 2018-04-05) (current is 4.2.0)
• P package-uses-deprecated-source-override-location
• P source-contains-empty-directory
  • data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/
  • data/share/vendor/

aegean

• X binary-file-built-without-LFS-support
  • usr/bin/canon-gff3
  • usr/bin/gaeval
  • usr/bin/locuspocus
  • usr/bin/parseval
  • usr/bin/pmrna
  • usr/bin/tidygff3
  • usr/bin/xtractore

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 168)
  • debian/changelog (line 29)
  • debian/changelog (line 35)
  • debian/changelog (line 4)
  • debian/changelog (line 48)
  • debian/changelog (line 49)
  • debian/changelog (line 5)
  • debian/changelog (line 53)
  • debian/changelog (line 55)
  • debian/changelog (line 56)
  • debian/changelog (line 66)
  • debian/changelog (line 68)
  • debian/rules (line 18)
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• I unused-file-paragraph-in-dep5-copyright
  • paragraph at line 41
• I wildcard-matches-nothing-in-dep5-copyright
  • debian/bundle-glademm.patch (paragraph at line 41)

aeskulap

• I desktop-entry-lacks-keywords-entry
  • usr/share/applications/aeskulap.desktop
  • usr/share/applications/aeskulap.desktop

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://www.aevol.fr/download/
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-does-not-install-examples
  • examples/
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/aevol.git
  • vcs-git https://anonscm.debian.org/git/debian-med/aevol.git

aevol

• X binary-file-built-without-LFS-support
  • usr/bin/aevol_create
  • usr/bin/aevol_misc_ancestor_robustness
  • usr/bin/aevol_misc_ancestor_stats
  • usr/bin/aevol_misc_create_eps
  • usr/bin/aevol_misc_extract
  • usr/bin/aevol_misc_lineage
  • usr/bin/aevol_misc_mutagenesis
  • usr/bin/aevol_misc_robustness
  • usr/bin/aevol_misc_view
  • usr/bin/aevol_modify
  • usr/bin/aevol_propagate
  • usr/bin/aevol_run
• W binary-without-manpage
  • usr/bin/aevol_misc_ancestor_robustness
  • usr/bin/aevol_misc_ancestor_robustness
  • usr/bin/aevol_misc_mutagenesis
  • usr/bin/aevol_misc_mutagenesis
• W manpage-has-errors-from-man
  • usr/share/man/man1/aevol_misc_ancestor_stats.1.gz 1: warning: macro `/"test' not defined
  • usr/share/man/man1/aevol_misc_ancestor_stats.1.gz 1: warning: macro `/"test' not defined
  • usr/share/man/man1/aevol_misc_view.1.gz 1: warning: macro `/"test' not defined
  • usr/share/man/man1/aevol_misc_view.1.gz 1: warning: macro `/"test' not defined
• I spelling-error-in-binary
  • usr/bin/aevol_create alignement alignment
  • usr/bin/aevol_create alignement alignment
  • usr/bin/aevol_create occured occurred
  • usr/bin/aevol_create occured occurred
  • usr/bin/aevol_create paramater parameter
  • usr/bin/aevol_create paramater parameter
  • usr/bin/aevol_create recepient recipient
  • usr/bin/aevol_create recepient recipient
  • usr/bin/aevol_misc_ancestor_robustness alignement alignment
  • usr/bin/aevol_misc_ancestor_robustness alignement alignment
  • usr/bin/aevol_misc_ancestor_robustness occured occurred
  • usr/bin/aevol_misc_ancestor_robustness occured occurred
  • usr/bin/aevol_misc_ancestor_robustness paramater parameter
  • usr/bin/aevol_misc_ancestor_robustness paramater parameter
  • usr/bin/aevol_misc_ancestor_robustness recepient recipient
  • usr/bin/aevol_misc_ancestor_robustness recepient recipient
  • usr/bin/aevol_misc_ancestor_stats alignement alignment
  • usr/bin/aevol_misc_ancestor_stats alignement alignment
  • usr/bin/aevol_misc_ancestor_stats occured occurred
  • usr/bin/aevol_misc_ancestor_stats occured occurred
  • usr/bin/aevol_misc_ancestor_stats paramater parameter
  • usr/bin/aevol_misc_ancestor_stats paramater parameter
  • usr/bin/aevol_misc_ancestor_stats recepient recipient
  • usr/bin/aevol_misc_ancestor_stats recepient recipient
  • usr/bin/aevol_misc_create_eps alignement alignment
  • usr/bin/aevol_misc_create_eps alignement alignment
  • usr/bin/aevol_misc_create_eps occured occurred
  • usr/bin/aevol_misc_create_eps occured occurred
  • usr/bin/aevol_misc_create_eps paramater parameter
  • usr/bin/aevol_misc_create_eps paramater parameter
  • usr/bin/aevol_misc_create_eps recepient recipient
  • usr/bin/aevol_misc_create_eps recepient recipient
  • usr/bin/aevol_misc_extract alignement alignment
  • usr/bin/aevol_misc_extract alignement alignment
  • usr/bin/aevol_misc_extract occured occurred
  • usr/bin/aevol_misc_extract occured occurred
  • usr/bin/aevol_misc_extract paramater parameter
  • usr/bin/aevol_misc_extract paramater parameter
  • usr/bin/aevol_misc_extract recepient recipient
  • usr/bin/aevol_misc_extract recepient recipient
  • usr/bin/aevol_misc_lineage alignement alignment
  • usr/bin/aevol_misc_lineage alignement alignment
  • usr/bin/aevol_misc_lineage occured occurred
  • usr/bin/aevol_misc_lineage occured occurred
  • usr/bin/aevol_misc_lineage paramater parameter
  • usr/bin/aevol_misc_lineage paramater parameter
  • usr/bin/aevol_misc_lineage recepient recipient
  • usr/bin/aevol_misc_lineage recepient recipient
  • usr/bin/aevol_misc_mutagenesis alignement alignment
  • usr/bin/aevol_misc_mutagenesis alignement alignment
  • usr/bin/aevol_misc_mutagenesis occured occurred
  • usr/bin/aevol_misc_mutagenesis occured occurred
  • usr/bin/aevol_misc_mutagenesis paramater parameter
  • usr/bin/aevol_misc_mutagenesis paramater parameter
  • usr/bin/aevol_misc_mutagenesis recepient recipient
  • usr/bin/aevol_misc_mutagenesis recepient recipient
  • usr/bin/aevol_misc_robustness alignement alignment
  • usr/bin/aevol_misc_robustness alignement alignment
  • usr/bin/aevol_misc_robustness occured occurred
  • usr/bin/aevol_misc_robustness occured occurred
  • usr/bin/aevol_misc_robustness paramater parameter
  • usr/bin/aevol_misc_robustness paramater parameter
  • usr/bin/aevol_misc_robustness recepient recipient
  • usr/bin/aevol_misc_robustness recepient recipient
  • usr/bin/aevol_misc_view alignement alignment
  • usr/bin/aevol_misc_view alignement alignment
  • usr/bin/aevol_misc_view occured occurred
  • usr/bin/aevol_misc_view occured occurred
  • usr/bin/aevol_misc_view paramater parameter
  • usr/bin/aevol_misc_view paramater parameter
  • usr/bin/aevol_misc_view recepient recipient
  • usr/bin/aevol_misc_view recepient recipient
  • usr/bin/aevol_modify alignement alignment
  • usr/bin/aevol_modify alignement alignment
  • usr/bin/aevol_modify modifed modified
  • usr/bin/aevol_modify modifed modified
  • usr/bin/aevol_modify occured occurred
  • usr/bin/aevol_modify occured occurred
  • usr/bin/aevol_modify paramater parameter
  • usr/bin/aevol_modify paramater parameter
  • usr/bin/aevol_modify recepient recipient
  • usr/bin/aevol_modify recepient recipient
  • usr/bin/aevol_propagate alignement alignment
  • usr/bin/aevol_propagate alignement alignment
  • usr/bin/aevol_propagate occured occurred
  • usr/bin/aevol_propagate occured occurred
  • usr/bin/aevol_propagate paramater parameter
  • usr/bin/aevol_propagate paramater parameter
  • usr/bin/aevol_propagate recepient recipient
  • usr/bin/aevol_propagate recepient recipient
  • usr/bin/aevol_run alignement alignment
  • usr/bin/aevol_run alignement alignment
  • usr/bin/aevol_run occured occurred
  • usr/bin/aevol_run occured occurred
  • usr/bin/aevol_run paramater parameter
  • usr/bin/aevol_run paramater parameter
  • usr/bin/aevol_run recepient recipient
  • usr/bin/aevol_run recepient recipient

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://johnhommer.com/academic/code/aghermann/source/aghermann-([\d\.]+).tar.xz
• P package-uses-old-debhelper-compat-version
  • 9
• P source-contains-empty-directory
  • m4/
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/aghermann.git
  • vcs-git https://anonscm.debian.org/git/debian-med/aghermann.git

aghermann (1.1.2-1+b1; main)

• X binary-file-built-without-LFS-support
  • usr/bin/agh-profile-gen
  • usr/bin/aghermann
  • usr/bin/edfcat
  • usr/bin/edfhed
  • usr/bin/edfhed-gtk
  • usr/lib/i386-linux-gnu/aghermann/libmetrics.so
  • usr/lib/i386-linux-gnu/aghermann/libsigfile.so
• I hardening-no-bindnow
  • usr/bin/agh-profile-gen
  • usr/bin/agh-profile-gen
  • usr/bin/aghermann
  • usr/bin/aghermann
  • usr/bin/edfcat
  • usr/bin/edfcat
  • usr/bin/edfhed
  • usr/bin/edfhed
  • usr/bin/edfhed-gtk
  • usr/bin/edfhed-gtk
  • usr/lib/i386-linux-gnu/aghermann/libmetrics.so
  • usr/lib/i386-linux-gnu/aghermann/libsigfile.so
  • usr/lib/i386-linux-gnu/aghermann/libsigproc.so
  • usr/lib/x86_64-linux-gnu/aghermann/libmetrics.so
  • usr/lib/x86_64-linux-gnu/aghermann/libsigfile.so
  • usr/lib/x86_64-linux-gnu/aghermann/libsigproc.so
• I spelling-error-in-binary
  • usr/bin/aghermann unintialized uninitialized
  • usr/bin/aghermann unintialized uninitialized
  • usr/lib/i386-linux-gnu/aghermann/libsigproc.so Unitialized Uninitialized

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/alien-hunter.git
  • vcs-git https://anonscm.debian.org/git/debian-med/alien-hunter.git

alien-hunter

• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
• W package-installs-java-bytecode
  • usr/share/alien_hunter/ChangepointLeft$1.class
  • usr/share/alien_hunter/ChangepointLeft.class
  • usr/share/alien_hunter/ChangepointRight$1.class
  • usr/share/alien_hunter/ChangepointRight.class

• P debian-watch-does-not-check-gpg-signature
• I out-of-date-standards-version
  • 4.1.4 (released 2018-04-05) (current is 4.2.0)
• I testsuite-autopkgtest-missing

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 132)
  • debian/changelog (line 134)
  • debian/changelog (line 244)
  • debian/changelog (line 58)
• I testsuite-autopkgtest-missing

altree

• I hardening-no-bindnow
  • usr/lib/i386-linux-gnu/perl5/5.26/auto/ALTree/CUtils/CUtils.so
  • usr/lib/x86_64-linux-gnu/perl5/5.26/auto/ALTree/CUtils/CUtils.so
• I spelling-error-in-manpage
  • usr/share/man/man1/altree.1p.gz allows to allows one to
  • usr/share/man/man1/altree.1p.gz allows to allows one to

altree-examples

• X duplicate-files
  • usr/share/doc/altree-examples/create_file/phy-paml_file/NUM usr/share/doc/altree-examples/create_file/phy-paml_file/nb_cas_control.txt usr/share/doc/altree-examples/paml/unrooted_absent/association/nb_cas_control.txt usr/share/doc/altree-examples/phylip/ancestor_absent/association/nb_cas_controls.txt usr/share/doc/altree-examples/phylip/outgroup_absent/association/nb_cas_controls.txt
  • usr/share/doc/altree-examples/create_file/phy-paml_file/trio.phy usr/share/doc/altree-examples/create_file/phy-paml_file/trio.prephy
  • usr/share/doc/altree-examples/paml/tree_building_using_phyML/trio2.phy usr/share/doc/altree-examples/paml/unrooted_absent/association/trio2.phy usr/share/doc/altree-examples/paml/unrooted_present/association/trio2.phy usr/share/doc/altree-examples/paml/unrooted_present/localisation/trio2.phy
  • usr/share/doc/altree-examples/paml/tree_building_using_phyML/trio2.phy_phyml_tree.txt usr/share/doc/altree-examples/paml/unrooted_absent/association/trio2.phy_phyml_tree.txt usr/share/doc/altree-examples/paml/unrooted_present/association/trio2.phy_phyml_tree.txt usr/share/doc/altree-examples/paml/unrooted_present/localisation/trio2.phy_phyml_tree.txt
  • usr/share/doc/altree-examples/paml/unrooted_absent/association/baseml.ctl usr/share/doc/altree-examples/paml/unrooted_present/association/baseml.ctl
  • usr/share/doc/altree-examples/paml/unrooted_absent/association/rst1 usr/share/doc/altree-examples/paml/unrooted_present/association/rst1 usr/share/doc/altree-examples/paml/unrooted_present/localisation/rst1
  • usr/share/doc/altree-examples/paml/unrooted_present/association/nb_cas_control.txt usr/share/doc/altree-examples/paml/unrooted_present/localisation/nb_cas_controls.txt
  • usr/share/doc/altree-examples/paup/ancestor_absent/association/nb_cas_control.txt usr/share/doc/altree-examples/paup/ancestor_absent/localisation/nb_cas_control.txt usr/share/doc/altree-examples/paup/outgr_absent/association/nb_cas_control.txt usr/share/doc/altree-examples/paup/outgr_absent/localisation/nb_cas_control.txt usr/share/doc/altree-examples/paup/unrooted_absent/association/nb_cas_control.txt usr/share/doc/altree-examples/paup/unrooted_absent/localisation/nb_cas_control.txt
  • usr/share/doc/altree-examples/paup/ancestor_present/association/caco.paup usr/share/doc/altree-examples/paup/ancestor_present/localisation/caco.paup
  • usr/share/doc/altree-examples/paup/ancestor_present/localisation/nb_cas_control.txt usr/share/doc/altree-examples/paup/outgr_present/association/nb_cas_control.txt usr/share/doc/altree-examples/paup/outgr_present/localisation/nb_cas_control.txt
  • usr/share/doc/altree-examples/paup/outgr_absent/association/caco.paup usr/share/doc/altree-examples/paup/outgr_absent/localisation/caco.paup usr/share/doc/altree-examples/paup/outgr_present/association/caco.paup usr/share/doc/altree-examples/paup/outgr_present/localisation/caco.paup
  • usr/share/doc/altree-examples/paup/outgr_absent/localisation/caco.loc usr/share/doc/altree-examples/paup/outgr_present/localisation/caco.loc
  • usr/share/doc/altree-examples/paup/unrooted_present/association/nb_cas_control.txt usr/share/doc/altree-examples/paup/unrooted_present/localisation/nb_cas_control.txt
  • usr/share/doc/altree-examples/phylip/outgroup_absent/association/outfile.gz usr/share/doc/altree-examples/phylip/outgroup_present/association/outfile.gz
  • usr/share/doc/altree-examples/phylip/outgroup_absent/association/outtree.gz usr/share/doc/altree-examples/phylip/outgroup_present/association/outtree.gz
  • usr/share/doc/altree-examples/phylip/outgroup_absent/association/trio.phy usr/share/doc/altree-examples/phylip/outgroup_present/association/trio.phy

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 149)
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

amap-align

• X binary-file-built-without-LFS-support
  • usr/bin/amap
• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
  • usr/share/common-licenses/GPL
• I hardening-no-fortify-functions
  • usr/bin/amap
  • usr/bin/amap

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 140)
  • debian/changelog (line 21)
  • debian/changelog (line 285)
  • debian/changelog (line 30)
  • debian/changelog (line 32)
  • debian/changelog (line 33)
  • debian/changelog (line 34)
  • debian/changelog (line 42)
  • debian/changelog (line 67)
  • debian/changelog (line 76)
  • debian/changelog (line 77)
  • debian/control (line 4)
• P source-contains-empty-directory
  • doc/reference/tmpl/
• I testsuite-autopkgtest-missing
• P wiki-copyright-format-uri
  • http://wiki.debian.org/Proposals/CopyrightFormat

amide (1.0.5-11+b1; main)

• X binary-file-built-without-LFS-support
  • usr/bin/amide
• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GFDL
  • usr/share/common-licenses/GFDL
• I desktop-entry-lacks-keywords-entry
  • usr/share/applications/amide.desktop
  • usr/share/applications/amide.desktop
• I spelling-error-in-binary
  • usr/bin/amide caculate calculate
  • usr/bin/amide caculate calculate
  • usr/bin/amide discontinous discontinuous
  • usr/bin/amide discontinous discontinuous
  • usr/bin/amide reseting resetting
  • usr/bin/amide reseting resetting

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 102)
  • debian/changelog (line 177)
  • debian/changelog (line 182)
  • debian/rules (line 40)
• W obsolete-url-in-packaging
  • debian/control http://code.google.com/p/ampliconnoise/
• P package-uses-old-debhelper-compat-version
  • 10
• P source-contains-empty-directory
  • bin/
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/ampliconnoise.git
  • vcs-git https://anonscm.debian.org/git/debian-med/ampliconnoise.git

ampliconnoise (1.29-7+b1; main)

• X binary-file-built-without-LFS-support
  • usr/bin/FCluster
  • usr/bin/FastaUnique
  • usr/bin/NDist
  • usr/bin/Perseus
  • usr/bin/PerseusD
  • usr/bin/PyroDist
  • usr/bin/PyroNoise
  • usr/bin/PyroNoiseA
  • usr/bin/PyroNoiseM
  • usr/bin/SeqDist
  • usr/bin/SeqNoise
  • usr/bin/SplitClusterClust
  • usr/bin/SplitClusterEven
• I hardening-no-fortify-functions
  • usr/bin/FCluster
  • usr/bin/FCluster
  • usr/bin/FastaUnique
  • usr/bin/FastaUnique
  • usr/bin/NDist
  • usr/bin/NDist
  • usr/bin/Perseus
  • usr/bin/Perseus
  • usr/bin/PerseusD
  • usr/bin/PerseusD
  • usr/bin/PyroDist
  • usr/bin/PyroDist
  • usr/bin/PyroNoise
  • usr/bin/PyroNoise
  • usr/bin/PyroNoiseA
  • usr/bin/PyroNoiseA
  • usr/bin/PyroNoiseM
  • usr/bin/PyroNoiseM
  • usr/bin/SeqDist
  • usr/bin/SeqDist
  • usr/bin/SeqNoise
  • usr/bin/SeqNoise
  • usr/bin/SplitClusterClust
  • usr/bin/SplitClusterClust
  • usr/bin/SplitClusterEven
  • usr/bin/SplitClusterEven

ampliconnoise-dbgsym (1.29-7+b1; main)

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/5b/baf470ff4021df694fe31848569e906309c527.debug
  • usr/lib/debug/.build-id/df/88df37a9849ebcf2acbd80bbc788aa94d7209f.debug

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 82)
  • debian/control (line 22)
  • debian/control (line 23)
  • debian/control (line 24)
  • debian/control (line 25)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/andi.git
  • vcs-git https://anonscm.debian.org/git/debian-med/andi.git

andi

• X binary-file-built-without-LFS-support
  • usr/bin/andi
• I spelling-error-in-binary
  • usr/bin/andi exlusive exclusive
  • usr/bin/andi exlusive exclusive

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://bioinf.eva.mpg.de/anfo/
• P file-contains-trailing-whitespace
  • debian/changelog (line 65)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/anfo.git
  • vcs-git https://anonscm.debian.org/git/debian-med/anfo.git

anfo

• I spelling-error-in-manpage
  • usr/share/man/man1/anfo-tool.1.gz choosen chosen
  • usr/share/man/man1/anfo-tool.1.gz choosen chosen
  • usr/share/man/man1/anfo-tool.1.gz occuring occurring
  • usr/share/man/man1/anfo-tool.1.gz occuring occurring
  • usr/share/man/man1/anfo-tool.1.gz representaion representation
  • usr/share/man/man1/anfo-tool.1.gz representaion representation
  • usr/share/man/man1/anfo.1.gz optinally optionally
  • usr/share/man/man1/anfo.1.gz optinally optionally

libanfo0

• I hardening-no-fortify-functions
  • usr/lib/i386-linux-gnu/libanfo.so.0.0.0
  • usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0
• I no-symbols-control-file
  • usr/lib/i386-linux-gnu/libanfo.so.0.0.0
  • usr/lib/x86_64-linux-gnu/libanfo.so.0.0.0

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn(.*).tgz
• P file-contains-trailing-whitespace
  • debian/changelog (line 68)
• I out-of-date-standards-version
  • 4.1.4 (released 2018-04-05) (current is 4.2.0)

aragorn

• X binary-file-built-without-LFS-support
  • usr/bin/aragorn

• I debian-rules-parses-dpkg-parsechangelog
  • (line 9)
• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://download.arb-home.de/release/
• P file-contains-trailing-whitespace
  • debian/changelog (line 123)
  • debian/changelog (line 129)
  • debian/changelog (line 174)
  • debian/changelog (line 282)
  • debian/changelog (line 53)
  • debian/changelog (line 725)
  • debian/changelog (line 88)
  • debian/changelog (line 91)
  • debian/rules (line 117)
  • debian/rules (line 4)
  • debian/rules (line 97)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• X maybe-not-arch-all-binnmuable
  • arb -> arb-common
• I missing-explanation-for-contrib-or-non-free-package
• I testsuite-autopkgtest-missing

arb

• I hardening-no-bindnow
  • usr/lib/arb/bin/CAP2
  • usr/lib/arb/bin/CAP2
  • usr/lib/arb/bin/Restriction
  • usr/lib/arb/bin/Restriction
  • usr/lib/arb/bin/Zuk_to_gen
  • usr/lib/arb/bin/Zuk_to_gen
  • usr/lib/arb/bin/arb_2_ascii
  • usr/lib/arb/bin/arb_2_ascii
  • usr/lib/arb/bin/arb_2_bin
  • usr/lib/arb/bin/arb_2_bin
  • usr/lib/arb/bin/arb_a2ps
  • usr/lib/arb/bin/arb_a2ps
  • usr/lib/arb/bin/arb_consensus_tree
  • usr/lib/arb/bin/arb_consensus_tree
  • usr/lib/arb/bin/arb_convert_aln
  • usr/lib/arb/bin/arb_convert_aln
  • usr/lib/arb/bin/arb_db_server
  • usr/lib/arb/bin/arb_db_server
  • usr/lib/arb/bin/arb_dist
  • usr/lib/arb/bin/arb_dist
  • usr/lib/arb/bin/arb_dnarates
  • usr/lib/arb/bin/arb_dnarates
  • usr/lib/arb/bin/arb_edit4
  • usr/lib/arb/bin/arb_edit4
  • usr/lib/arb/bin/arb_export_rates
  • usr/lib/arb/bin/arb_export_rates
  • usr/lib/arb/bin/arb_export_tree
  • usr/lib/arb/bin/arb_export_tree
  • usr/lib/arb/bin/arb_flush_mem
  • usr/lib/arb/bin/arb_flush_mem
  • usr/lib/arb/bin/arb_gene_probe
  • usr/lib/arb/bin/arb_gene_probe
  • usr/lib/arb/bin/arb_help2xml
  • usr/lib/arb/bin/arb_help2xml
  • usr/lib/arb/bin/arb_message
  • usr/lib/arb/bin/arb_message
  • usr/lib/arb/bin/arb_naligner
  • usr/lib/arb/bin/arb_naligner
  • usr/lib/arb/bin/arb_name_server
  • usr/lib/arb/bin/arb_name_server
  • usr/lib/arb/bin/arb_notify
  • usr/lib/arb/bin/arb_notify
  • usr/lib/arb/bin/arb_ntree
  • usr/lib/arb/bin/arb_ntree
  • usr/lib/arb/bin/arb_pars
  • usr/lib/arb/bin/arb_pars
  • usr/lib/arb/bin/arb_phylo
  • usr/lib/arb/bin/arb_phylo
  • usr/lib/arb/bin/arb_primer
  • usr/lib/arb/bin/arb_primer
  • usr/lib/arb/bin/arb_probe
  • usr/lib/arb/bin/arb_probe
  • usr/lib/arb/bin/arb_proto_2_xsub
  • usr/lib/arb/bin/arb_proto_2_xsub
  • usr/lib/arb/bin/arb_pt_server
  • usr/lib/arb/bin/arb_pt_server
  • usr/lib/arb/bin/arb_read_tree
  • usr/lib/arb/bin/arb_read_tree
  • usr/lib/arb/bin/arb_replace
  • usr/lib/arb/bin/arb_replace
  • usr/lib/arb/bin/arb_rnacma
  • usr/lib/arb/bin/arb_rnacma
  • usr/lib/arb/bin/arb_treegen
  • usr/lib/arb/bin/arb_treegen
  • usr/lib/arb/bin/arb_wetc
  • usr/lib/arb/bin/arb_wetc
  • usr/lib/arb/bin/axml
  • usr/lib/arb/bin/axml
  • usr/lib/arb/bin/clustalv
  • usr/lib/arb/bin/clustalv
  • usr/lib/arb/bin/count
  • usr/lib/arb/bin/count
  • usr/lib/arb/bin/findall
  • usr/lib/arb/bin/findall
  • usr/lib/arb/bin/lsadt
  • usr/lib/arb/bin/lsadt
  • usr/lib/arb/bin/sho_helix
  • usr/lib/arb/bin/sho_helix
  • usr/lib/arb/bin/varpos
  • usr/lib/arb/bin/varpos
• I hardening-no-fortify-functions
  • usr/lib/arb/bin/CAP2
  • usr/lib/arb/bin/CAP2
  • usr/lib/arb/bin/Restriction
  • usr/lib/arb/bin/Restriction
  • usr/lib/arb/bin/Zuk_to_gen
  • usr/lib/arb/bin/Zuk_to_gen
  • usr/lib/arb/bin/arb_a2ps
  • usr/lib/arb/bin/arb_a2ps
  • usr/lib/arb/bin/arb_treegen
  • usr/lib/arb/bin/arb_treegen
  • usr/lib/arb/bin/axml
  • usr/lib/arb/bin/axml
  • usr/lib/arb/bin/clustalv
  • usr/lib/arb/bin/clustalv
  • usr/lib/arb/bin/count
  • usr/lib/arb/bin/count
  • usr/lib/arb/bin/findall
  • usr/lib/arb/bin/findall
  • usr/lib/arb/bin/lsadt
  • usr/lib/arb/bin/lsadt
  • usr/lib/arb/bin/sho_helix
  • usr/lib/arb/bin/sho_helix
  • usr/lib/arb/bin/varpos
  • usr/lib/arb/bin/varpos
• I spelling-error-in-binary
  • usr/lib/arb/bin/arb_consensus_tree lengH length
  • usr/lib/arb/bin/arb_db_server doesnt doesn't
  • usr/lib/arb/bin/arb_db_server doesnt doesn't
  • usr/lib/arb/bin/arb_dist doesnt doesn't
  • usr/lib/arb/bin/arb_dist doesnt doesn't
  • usr/lib/arb/bin/arb_edit4 Wont Won't
  • usr/lib/arb/bin/arb_edit4 Wont Won't
  • usr/lib/arb/bin/arb_edit4 doesnt doesn't
  • usr/lib/arb/bin/arb_edit4 doesnt doesn't
  • usr/lib/arb/bin/arb_export_tree lengH length
  • usr/lib/arb/bin/arb_naligner aligne align
  • usr/lib/arb/bin/arb_naligner aligne align
  • usr/lib/arb/bin/arb_naligner doesnt doesn't
  • usr/lib/arb/bin/arb_naligner doesnt doesn't
  • usr/lib/arb/bin/arb_naligner enought enough
  • usr/lib/arb/bin/arb_naligner enought enough
  • usr/lib/arb/bin/arb_name_server doesnt doesn't
  • usr/lib/arb/bin/arb_name_server doesnt doesn't
  • usr/lib/arb/bin/arb_ntree Likelyhood Likelihood
  • usr/lib/arb/bin/arb_ntree Likelyhood Likelihood
  • usr/lib/arb/bin/arb_ntree Mor More
  • usr/lib/arb/bin/arb_ntree Mor More
  • usr/lib/arb/bin/arb_ntree doesnt doesn't
  • usr/lib/arb/bin/arb_ntree doesnt doesn't
  • usr/lib/arb/bin/arb_ntree lengH length
  • usr/lib/arb/bin/arb_ntree pres press
  • usr/lib/arb/bin/arb_pars doesnt doesn't
  • usr/lib/arb/bin/arb_pars doesnt doesn't
  • usr/lib/arb/bin/arb_probe doesnt doesn't
  • usr/lib/arb/bin/arb_probe doesnt doesn't
  • usr/lib/arb/bin/arb_pt_server doesnt doesn't
  • usr/lib/arb/bin/arb_pt_server doesnt doesn't
• I spelling-error-in-copyright
  • explicite explicit
  • explicite explicit
  • wont won't
  • wont won't

arb-common

• W duplicate-changelog-files
  • usr/share/doc/arb-common/arb_CHANGES.txt.gz usr/share/doc/arb-common/changelog.gz usr/share/doc/arb/arb_CHANGES.txt.gz
• X duplicate-files
  • usr/share/doc/arb-common/arb_LICENSE.txt.gz usr/share/doc/arb/arb_LICENSE.txt.gz
  • usr/share/doc/arb-common/arb_README.txt.gz usr/share/doc/arb/arb_README.txt.gz
  • usr/share/doc/arb-common/examples/demo.arb.gz usr/share/doc/arb/examples/demo.arb.gz
• I package-contains-documentation-outside-usr-share-doc
  • usr/lib/arb/PERL_SCRIPTS/BIOPERL/README
  • usr/lib/arb/SH/README
  • usr/share/arb/motifHack/README
• I spelling-error-in-copyright
  • explicite explicit
  • wont won't
• I unused-override
  • package-contains-timestamped-gzip usr/lib/arb/lib/help/*.gz

arb-doc

• I spelling-error-in-copyright
  • explicite explicit
  • wont won't

libarb

• I hardening-no-bindnow
  • usr/lib/arb/lib/ARB.so
  • usr/lib/arb/lib/ARB.so
  • usr/lib/arb/lib/libARBDB.so
  • usr/lib/arb/lib/libARBDB.so
  • usr/lib/arb/lib/libAWT.so
  • usr/lib/arb/lib/libAWT.so
  • usr/lib/arb/lib/libCORE.so
  • usr/lib/arb/lib/libCORE.so
  • usr/lib/arb/lib/libWINDOW.so
  • usr/lib/arb/lib/libWINDOW.so
• I spelling-error-in-binary
  • usr/lib/arb/lib/libARBDB.so colums columns
  • usr/lib/arb/lib/libARBDB.so colums columns
• I spelling-error-in-copyright
  • explicite explicit
  • explicite explicit
  • wont won't
  • wont won't

libarb-dev

• I spelling-error-in-binary
  • usr/lib/arb/SL/TREE_WRITE/TREE_WRITE.a lengH length
• I spelling-error-in-copyright
  • explicite explicit
  • explicite explicit
  • wont won't
  • wont won't

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I testsuite-autopkgtest-missing

arden

• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)
• X duplicate-files
  • usr/share/doc/arden/html/frames.html usr/share/doc/arden/html/index.html

• P debian-watch-does-not-check-gpg-signature
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

art-nextgen-simulation-tools

• I spelling-error-in-binary
  • usr/bin/art_454 unreconized unrecognized
  • usr/bin/art_454 unreconized unrecognized
  • usr/bin/art_SOLiD lenght length
  • usr/bin/art_SOLiD lenght length
  • usr/bin/art_SOLiD unreconized unrecognized
  • usr/bin/art_SOLiD unreconized unrecognized

art-nextgen-simulation-tools-profiles

• I package-contains-documentation-outside-usr-share-doc
  • usr/share/art-nextgen-simulation-tools/ART_profiler_454/README
  • usr/share/art-nextgen-simulation-tools/ART_profiler_illumina/README

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/control (line 43)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
  • (line 46)
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/artemis.git
  • vcs-git https://anonscm.debian.org/git/debian-med/artemis.git

artemis

• W bad-jar-name
  • usr/share/java/BamView.jar
  • usr/share/java/DNAPlotter.jar

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

• I debian-watch-file-is-missing
• I testsuite-autopkgtest-missing
• I vcs-field-not-canonical
  • https://salsa.debian.org/med-team/assemblytics.git https://salsa.debian.org/med-team/assemblytics

assemblytics

• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://bioinf.uni-greifswald.de/augustus/binaries/augustus-(.*)\.tar\.gz
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-does-not-install-examples
  • auxprogs/homGeneMapping/examples/
  • examples/
• P source-contains-empty-directory
  • auxprogs/homGeneMapping/bin/

augustus

• X binary-file-built-without-LFS-support
  • usr/bin/aln2wig
  • usr/bin/augustus
  • usr/bin/bam2hints
  • usr/bin/compileSpliceCands
  • usr/bin/etraining
  • usr/bin/fastBlockSearch
  • usr/bin/homGeneMapping
• I hardening-no-bindnow
  • usr/bin/utrrnaseq
  • usr/bin/utrrnaseq
• I hardening-no-fortify-functions
  • usr/bin/fastBlockSearch
  • usr/bin/fastBlockSearch
  • usr/bin/homGeneMapping
  • usr/bin/homGeneMapping
  • usr/bin/joingenes
  • usr/bin/joingenes
• I package-contains-documentation-outside-usr-share-doc
  • usr/share/augustus/scripts/README.autoAug
  • usr/share/augustus/scripts/README.autoAug
• I spelling-error-in-binary
  • usr/bin/bam2wig Allows to Allows one to
  • usr/bin/bam2wig Allows to Allows one to
  • usr/bin/compileSpliceCands Dont Don't
  • usr/bin/compileSpliceCands Dont Don't
  • usr/bin/compileSpliceCands arround around
  • usr/bin/compileSpliceCands arround around
  • usr/bin/joingenes noone no one
  • usr/bin/joingenes noone no one
  • usr/bin/utrrnaseq occured occurred
  • usr/bin/utrrnaseq occured occurred
• I spelling-error-in-manpage
  • usr/share/man/man1/bam2hints.1.gz separeted separated
  • usr/share/man/man1/bam2hints.1.gz separeted separated
  • usr/share/man/man1/bam2wig.1.gz Allows to Allows one to
  • usr/share/man/man1/bam2wig.1.gz Allows to Allows one to
  • usr/share/man/man1/homGeneMapping.1.gz direcory directory
  • usr/share/man/man1/homGeneMapping.1.gz direcory directory

augustus-data

• I package-contains-documentation-outside-usr-share-doc
  • usr/share/augustus/config/species/ancylostoma_ceylanicum/README.TXT
  • usr/share/augustus/config/species/camponotus_floridanus/README.TXT
  • usr/share/augustus/config/species/chicken/README.TXT
  • usr/share/augustus/config/species/ciona/README.TXT
  • usr/share/augustus/config/species/human/README.TXT
  • usr/share/augustus/config/species/mnemiopsis_leidyi/README.TXT
  • usr/share/augustus/config/species/nematostella_vectensis/README.TXT
  • usr/share/augustus/config/species/pneumocystis/README.TXT
  • usr/share/augustus/config/species/rice/README.TXT
  • usr/share/augustus/config/species/s_aureus/README.TXT
  • usr/share/augustus/config/species/schistosoma2/README.TXT
  • usr/share/augustus/config/species/strongylocentrotus_purpuratus/README.TXT
  • usr/share/augustus/config/species/wheat/README.txt
  • usr/share/augustus/config/species/zebrafish/README.TXT

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://vina.scripps.edu/download.html
• P unversioned-copyright-format-uri
  • http://dep.debian.net/deps/dep5/

autodock-vina

• P debian-changelog-line-too-short
  • DEP5 (line 15)
  • DEP5 (line 15)
• I hardening-no-fortify-functions
  • usr/bin/vina
  • usr/bin/vina
• I spelling-error-in-binary
  • usr/bin/vina inconsisent inconsistent
  • usr/bin/vina inconsisent inconsistent

• I debian-rules-contains-unnecessary-get-orig-source-target
• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
• P file-contains-trailing-whitespace
  • debian/changelog (line 167)
  • debian/changelog (line 200)
  • debian/changelog (line 249)
  • debian/control (line 83)
  • debian/rules (line 69)
  • debian/rules (line 70)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• P source-contains-empty-directory
  • autodock/Tests/AutoDockTools/
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/autodocksuite.git
  • vcs-git https://anonscm.debian.org/git/debian-med/autodocksuite.git

autodock

• X binary-file-built-without-LFS-support
  • usr/bin/autodock4
• I hardening-no-bindnow
  • usr/bin/autodock4
  • usr/bin/autodock4
• X non-consecutive-debian-revision
  • 4.2.6-5 -> 4.2.6-3
  • 4.2.6-5 -> 4.2.6-3
• I spelling-error-in-binary
  • usr/bin/autodock4 conect connect
  • usr/bin/autodock4 conect connect
• I spelling-error-in-manpage
  • usr/share/man/man1/autodock4.1.gz perfoms performs
  • usr/share/man/man1/autodock4.1.gz perfoms performs
• I unused-override
  • spelling-error-in-binary usr/bin/autodock4 Ang And
  • spelling-error-in-binary usr/bin/autodock4 Ang And

autodock-getdata

• X non-consecutive-debian-revision
  • 4.2.6-5 -> 4.2.6-3

autodock-test

• X non-consecutive-debian-revision
  • 4.2.6-5 -> 4.2.6-3

autogrid

• X binary-file-built-without-LFS-support
  • usr/bin/autogrid4
• I hardening-no-bindnow
  • usr/bin/autogrid4
  • usr/bin/autogrid4
• X non-consecutive-debian-revision
  • 4.2.6-5 -> 4.2.6-3
  • 4.2.6-5 -> 4.2.6-3

autogrid-test

• X non-consecutive-debian-revision
  • 4.2.6-5 -> 4.2.6-3

• W ancient-python-version-field
  • x-python-version 2.5
• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz
• P file-contains-trailing-whitespace
  • debian/rules (line 12)
• P no-dep5-copyright
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/autodocktools.git
  • vcs-git https://anonscm.debian.org/git/debian-med/autodocktools.git

autodocktools

• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

axe-demultiplexer

• X binary-file-built-without-LFS-support
  • usr/bin/axe-demux
• I spelling-error-in-binary
  • usr/bin/axe-demux confict conflict
  • usr/bin/axe-demux confict conflict
• I spelling-error-in-manpage
  • usr/share/man/man1/axe-demux.1.gz confict conflict
  • usr/share/man/man1/axe-demux.1.gz confict conflict

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/control (line 38)
  • debian/rules (line 19)
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/baitfisher.git
  • vcs-git https://anonscm.debian.org/debian-med/baitfisher.git

baitfisher

• I example-wrong-path-for-interpreter
  • usr/share/doc/baitfisher/examples/Example-without-alignment-cutting/BaitFilter-analysis/run-BaitFilter (#!/usr/bin/bash != /bin/bash)
  • usr/share/doc/baitfisher/examples/Example-without-alignment-cutting/run-command (#!/usr/bin/bash != /bin/bash)
• I hardening-no-bindnow
  • usr/bin/BaitFilter
  • usr/bin/BaitFisher
• I hardening-no-fortify-functions
  • usr/bin/BaitFilter
  • usr/bin/BaitFisher
• W manpage-has-useless-whatis-entry
  • usr/share/man/man1/BaitFilter.1.gz
  • usr/share/man/man1/BaitFisher.1.gz
• I spelling-error-in-binary
  • usr/bin/BaitFilter FEATUE FEATURE
  • usr/bin/BaitFilter Unkown Unknown
  • usr/bin/BaitFilter consequtively consecutively
  • usr/bin/BaitFilter formated formatted
  • usr/bin/BaitFilter formating formatting
  • usr/bin/BaitFilter paramters parameters
  • usr/bin/BaitFilter preceeded preceded
  • usr/bin/BaitFilter specifiy specify
  • usr/bin/BaitFisher Unkown Unknown
  • usr/bin/BaitFisher alignemnt alignment
  • usr/bin/BaitFisher occured occurred
  • usr/bin/BaitFisher refernce reference
• I spelling-error-in-manpage
  • usr/share/man/man1/BaitFilter.1.gz specifiy specify
  • usr/share/man/man1/BaitFilter.1.gz specifiy specify
  • usr/share/man/man1/BaitFilter.1.gz specifiy specify

baitfisher-dbgsym

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/4d/5db4841ac6ec9ee5d9752bf024ead977a749c8.debug
  • usr/lib/debug/.build-id/e9/9d12bd30ea3fcd85809c4d224ac36a5c1335bc.debug

• P debian-watch-does-not-check-gpg-signature
• I out-of-date-standards-version
  • 4.1.5 (released 2018-07-04) (current is 4.2.0)
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

bali-phy

• X duplicate-files
  • usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987/sod-prank.1.fasta usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987/sod-prank.2.fasta
  • usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987/sod-prank.1.fasta usr/share/doc/bali-phy/examples/sequences/Feng-Doolittle-1987/sod-prank.2.fasta
• W manpage-has-bad-whatis-entry
  • usr/share/man/man1/alignment-cat.1.gz
  • usr/share/man/man1/alignment-cat.1.gz
  • usr/share/man/man1/alignment-chop-internal.1.gz
  • usr/share/man/man1/alignment-chop-internal.1.gz
  • usr/share/man/man1/alignment-consensus.1.gz
  • usr/share/man/man1/alignment-consensus.1.gz
  • usr/share/man/man1/alignment-draw.1.gz
  • usr/share/man/man1/alignment-draw.1.gz
  • usr/share/man/man1/alignment-find.1.gz
  • usr/share/man/man1/alignment-find.1.gz
  • usr/share/man/man1/alignment-gild.1.gz
  • usr/share/man/man1/alignment-gild.1.gz
  • usr/share/man/man1/alignment-indices.1.gz
  • usr/share/man/man1/alignment-indices.1.gz
  • usr/share/man/man1/alignment-info.1.gz
  • usr/share/man/man1/alignment-info.1.gz
  • usr/share/man/man1/alignment-max.1.gz
  • usr/share/man/man1/alignment-max.1.gz
  • usr/share/man/man1/alignment-thin.1.gz
  • usr/share/man/man1/alignment-thin.1.gz
  • usr/share/man/man1/alignment-translate.1.gz
  • usr/share/man/man1/alignment-translate.1.gz
  • usr/share/man/man1/alignments-diff.1.gz
  • usr/share/man/man1/alignments-diff.1.gz
  • usr/share/man/man1/bali-phy.1.gz
  • usr/share/man/man1/bali-phy.1.gz
  • usr/share/man/man1/bp-analyze.1.gz
  • usr/share/man/man1/bp-analyze.1.gz
  • usr/share/man/man1/cut-range.1.gz
  • usr/share/man/man1/cut-range.1.gz
  • usr/share/man/man1/draw-tree.1.gz
  • usr/share/man/man1/draw-tree.1.gz
  • usr/share/man/man1/mctree-mean-lengths.1.gz
  • usr/share/man/man1/mctree-mean-lengths.1.gz
  • usr/share/man/man1/model_P.1.gz
  • usr/share/man/man1/model_P.1.gz
  • usr/share/man/man1/pickout.1.gz
  • usr/share/man/man1/pickout.1.gz
  • usr/share/man/man1/statreport.1.gz
  • usr/share/man/man1/statreport.1.gz
  • usr/share/man/man1/stats-select.1.gz
  • usr/share/man/man1/stats-select.1.gz
  • usr/share/man/man1/subsample.1.gz
  • usr/share/man/man1/subsample.1.gz
  • usr/share/man/man1/tree-mean-lengths.1.gz
  • usr/share/man/man1/tree-mean-lengths.1.gz
  • usr/share/man/man1/tree-tool.1.gz
  • usr/share/man/man1/tree-tool.1.gz
  • usr/share/man/man1/trees-bootstrap.1.gz
  • usr/share/man/man1/trees-bootstrap.1.gz
  • usr/share/man/man1/trees-consensus.1.gz
  • usr/share/man/man1/trees-consensus.1.gz
  • usr/share/man/man1/trees-distances.1.gz
  • usr/share/man/man1/trees-distances.1.gz
  • usr/share/man/man1/trees-to-SRQ.1.gz
  • usr/share/man/man1/trees-to-SRQ.1.gz
• I possible-documentation-but-no-doc-base-registration
• I spelling-error-in-binary
  • usr/bin/bali-phy buil build
  • usr/bin/bali-phy ment meant

bali-phy-dbgsym

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/00/0ee899ad79376e2e9ca7f6ca98b6ecdbc40073.debug
  • usr/lib/debug/.build-id/02/89c4da7c07c456168ad96dbe9ce1b332d66868.debug
  • usr/lib/debug/.build-id/06/85ad789ac9b6403833a0bd3b5b99163b3dad98.debug
  • usr/lib/debug/.build-id/0b/a5167f462a600f864e39deef1f1e02b8092d00.debug
  • usr/lib/debug/.build-id/15/7aa613c088ca6cd40bb645e2eb47586cfeeeeb.debug
  • usr/lib/debug/.build-id/2f/5bf3731543594e0a46b4fa999ae71cf5d37943.debug
  • usr/lib/debug/.build-id/41/f82cc941f91b53c55eeee85bf640cf8e5619a4.debug
  • usr/lib/debug/.build-id/42/5e09e7cdf56270bdb320adf0fea8b102ad615d.debug
  • usr/lib/debug/.build-id/42/dd0a2276d9917e1801e6a0c6ac8436344b7b77.debug
  • usr/lib/debug/.build-id/46/7da3495c3b36834f702d79d159af03b874733a.debug
  • usr/lib/debug/.build-id/4c/b72d0e6c53a8c662b909eb7d67b359fc63b56a.debug
  • usr/lib/debug/.build-id/52/5de1fe760a12097454feafe40edc65bc48f763.debug
  • usr/lib/debug/.build-id/5a/c23e601a3ad27fc75c91b156db32be580351a2.debug
  • usr/lib/debug/.build-id/60/bad84d68134ffe91ec35a423e07c2712f1f652.debug
  • usr/lib/debug/.build-id/64/a1895e3047d2127785d2e6d5d36a67c7c78bbc.debug
  • usr/lib/debug/.build-id/67/c3dab6a05f1217ea3fedc1d029cab36b6e5853.debug
  • usr/lib/debug/.build-id/69/66aa95ae2b1f3ddfafa82523406d9da20d09d3.debug
  • usr/lib/debug/.build-id/7b/6f4de616345691b8272fa4ead562688c14d0e7.debug
  • usr/lib/debug/.build-id/7c/128e1e25eb8695b115d8453d67ea10ace07f68.debug
  • usr/lib/debug/.build-id/7d/8f73565c0c2f90d3ccb871dcbf66f4439b8cbd.debug
  • usr/lib/debug/.build-id/7f/55bd7d8d77766752e379c12296c7d037015053.debug
  • usr/lib/debug/.build-id/80/3ec5449191e85434f94e1156f53049c00b4456.debug
  • usr/lib/debug/.build-id/80/85e850d9dccd92d42b5d49c7024503cc6f58ee.debug
  • usr/lib/debug/.build-id/8b/46816acce0e23ceacd2ae890d72022d1291fb7.debug
  • usr/lib/debug/.build-id/91/eec0d7c065f32253d75ad17bce54816101d288.debug
  • usr/lib/debug/.build-id/a3/08ded1e67e5661ce855f9c142604c937665b40.debug
  • usr/lib/debug/.build-id/b3/32724cfa1b907c1a6ad0f507c322018dee4f8b.debug
  • usr/lib/debug/.build-id/b4/db6b3cc9e8c2b3f0d062b063ef78ecd8be534f.debug
  • usr/lib/debug/.build-id/ba/c8a77822df97fb508da8ec9d4053c3fbd1ed35.debug
  • usr/lib/debug/.build-id/bf/a79317e02881f0741cc91085eeb0147d050084.debug
  • usr/lib/debug/.build-id/c5/8b7f41d1670d3b4200684c276fd490660b0c1f.debug
  • usr/lib/debug/.build-id/c9/6d7c1f1c9da89c0bc38f3f49489fffafa95502.debug
  • usr/lib/debug/.build-id/ca/76a14db5b6e431e350616aeb73691054b5ba75.debug
  • usr/lib/debug/.build-id/d0/d028a2ae41b61429b9260b58d9b3cc58e5664a.debug
  • usr/lib/debug/.build-id/d5/72445fcb4806e43314b57d608803374cac26bc.debug
  • usr/lib/debug/.build-id/e0/9406dc7ba14b7ffd92a6c1bdfea26e2e91127d.debug
  • usr/lib/debug/.build-id/e1/29f882d9a217247827a2ccb0916560d0f1e43d.debug
  • usr/lib/debug/.build-id/e6/85bb0c95d1251d71f267288b2815e71b461f3c.debug
  • usr/lib/debug/.build-id/f2/7ecfae9b4f1207fc770f654b66231cf6db997f.debug
  • usr/lib/debug/.build-id/f6/08fce3429024af52abd492da24694bb4ddad78.debug
  • usr/lib/debug/.build-id/fa/2516dc9b6aef467361f8858727e1275ba2a20c.debug
  • usr/lib/debug/.build-id/fa/58dc5ae19c88c7a0e4d7ac35a36da01c89df57.debug

• W changelog-should-mention-nmu
• W debian-rules-should-not-set-CFLAGS-from-noopt
• P debian-watch-does-not-check-gpg-signature
• P duplicate-in-relation-field
  • in source build-depends: dh-python, dh-python
• P file-contains-trailing-whitespace
  • debian/changelog (line 131)
  • debian/changelog (line 247)
  • debian/changelog (line 269)
  • debian/control (line 100)
  • debian/control (line 101)
  • debian/control (line 104)
  • debian/control (line 105)
  • debian/control (line 117)
  • debian/control (line 118)
  • debian/control (line 119)
  • debian/control (line 120)
  • debian/control (line 121)
  • debian/control (line 124)
  • debian/control (line 125)
  • debian/control (line 139)
  • debian/control (line 140)
  • debian/control (line 141)
  • debian/control (line 142)
  • debian/control (line 154)
  • debian/control (line 155)
  • debian/control (line 156)
  • debian/control (line 157)
  • debian/control (line 171)
  • debian/control (line 172)
  • debian/control (line 173)
  • debian/control (line 174)
  • debian/control (line 186)
  • debian/control (line 187)
  • debian/control (line 188)
  • debian/control (line 211)
  • debian/control (line 212)
  • debian/control (line 213)
  • debian/control (line 53)
  • debian/control (line 54)
  • debian/control (line 55)
  • debian/control (line 56)
  • debian/control (line 57)
  • debian/control (line 60)
  • debian/control (line 61)
  • debian/control (line 74)
  • debian/control (line 75)
  • debian/control (line 76)
  • debian/control (line 77)
  • debian/control (line 78)
  • debian/control (line 81)
  • debian/control (line 82)
  • debian/control (line 97)
  • debian/control (line 98)
  • debian/control (line 99)
  • debian/rules (line 1)
  • debian/rules (line 145)
  • debian/rules (line 158)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 9
• W python-foo-but-no-python3-foo
  • python-ball
  • python-ballview
• W source-nmu-has-incorrect-version-number
  • 1.4.3~beta1-3
• W spelling-error-in-patch-description
  • debian/patches/fix-PoseClustering_Test-replace-file-compare-with-deserialize.patch comparision comparison
  • debian/patches/link_against_x11.patch explicitely explicitly
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/ball.git
  • vcs-git https://anonscm.debian.org/git/debian-med/ball.git

ballview (1.4.3~beta1-3+b1; main)

• I desktop-entry-lacks-keywords-entry
  • usr/share/applications/ballview.desktop
• W desktop-mime-but-no-exec-code
  • usr/share/applications/ballview.desktop
• I hardening-no-fortify-functions
  • usr/bin/BALLView
• I spelling-error-in-binary
  • usr/bin/BALLView dont don't
  • usr/bin/BALLView informations information
  • usr/bin/BALLView occured occurred

libball1.4 (1.4.3~beta1-3+b1; main)

• X binary-file-built-without-LFS-support
  • usr/lib/libBALL.so.1.4
• W dev-pkg-without-shlib-symlink
  • usr/lib/libBALL.so.1.4 usr/lib/libBALL.so
• I hardening-no-fortify-functions
  • usr/lib/libBALL.so.1.4
• I no-symbols-control-file
  • usr/lib/libBALL.so.1.4
• X shlib-calls-exit
  • usr/lib/libBALL.so.1.4
• I spelling-error-in-binary
  • usr/lib/libBALL.so.1.4 CONECT CONNECT
  • usr/lib/libBALL.so.1.4 childs children
  • usr/lib/libBALL.so.1.4 enought enough
  • usr/lib/libBALL.so.1.4 errorneous erroneous
  • usr/lib/libBALL.so.1.4 featues features
  • usr/lib/libBALL.so.1.4 implmented implemented
  • usr/lib/libBALL.so.1.4 intialization initialization
  • usr/lib/libBALL.so.1.4 occured occurred
  • usr/lib/libBALL.so.1.4 paramters parameters
  • usr/lib/libBALL.so.1.4 registerd registered
  • usr/lib/libBALL.so.1.4 seperator separator
  • usr/lib/libBALL.so.1.4 standart standard
  • usr/lib/libBALL.so.1.4 unkown unknown
  • usr/lib/libBALL.so.1.4 woNT won't

libball1.4-doc

• X duplicate-files
  • usr/share/doc/libball1.4/html/BALL/d0/d00/VIEW_2KERNEL_2kernel_8doc.html usr/share/doc/libball1.4/html/BALL/db/d6a/KERNEL_2kernel_8doc.html
  • usr/share/doc/libball1.4/html/BALL/d0/d85/COMMON_2common_8doc.html usr/share/doc/libball1.4/html/BALL/d0/ded/MOLMEC_2COMMON_2common_8doc.html
  • usr/share/doc/libball1.4/html/BALL/d2/dad/DATATYPE_2datatype_8doc.html usr/share/doc/libball1.4/html/BALL/d4/d2e/VIEW_2DATATYPE_2datatype_8doc.html
  • usr/share/doc/libball1.4/html/BALL/search/all_0.js usr/share/doc/libball1.4/html/BALL/search/groups_0.js
  • usr/share/doc/libball1.4/html/BALL/search/all_1.js usr/share/doc/libball1.4/html/BALL/search/defines_0.js
  • usr/share/doc/libball1.4/html/BALL/search/all_1c.js usr/share/doc/libball1.4/html/BALL/search/functions_1a.js

libballview1.4 (1.4.3~beta1-3+b1; main)

• W dev-pkg-without-shlib-symlink
  • usr/lib/libVIEW.so.1.4 usr/lib/libVIEW.so
• I hardening-no-fortify-functions
  • usr/lib/libVIEW.so.1.4
• I no-symbols-control-file
  • usr/lib/libVIEW.so.1.4
• O package-name-doesnt-match-sonames
  • libVIEW1.4
• I spelling-error-in-binary
  • usr/lib/libVIEW.so.1.4 Dont Don't
  • usr/lib/libVIEW.so.1.4 Informations Information
  • usr/lib/libVIEW.so.1.4 Uknown Unknown
  • usr/lib/libVIEW.so.1.4 an other another
  • usr/lib/libVIEW.so.1.4 beeing being
  • usr/lib/libVIEW.so.1.4 calulate calculate
  • usr/lib/libVIEW.so.1.4 choosen chosen
  • usr/lib/libVIEW.so.1.4 correspoding corresponding
  • usr/lib/libVIEW.so.1.4 doesnt doesn't
  • usr/lib/libVIEW.so.1.4 executeable executable
  • usr/lib/libVIEW.so.1.4 mininum minimum
  • usr/lib/libVIEW.so.1.4 occured occurred
  • usr/lib/libVIEW.so.1.4 orgin origin
  • usr/lib/libVIEW.so.1.4 reseting resetting
  • usr/lib/libVIEW.so.1.4 succesfully successfully
  • usr/lib/libVIEW.so.1.4 sucessfully successfully
  • usr/lib/libVIEW.so.1.4 unkown unknown

libballview1.4-dev (1.4.3~beta1-3+b1; main)

• I package-contains-documentation-outside-usr-share-doc
  • usr/include/BALL/VIEW/UIC/README
• O package-contains-empty-directory
  • usr/lib/

python-ball (1.4.3~beta1-3+b1; main)

• X binary-file-built-without-LFS-support
  • usr/lib/python2.7/dist-packages/BALLCore.i386-linux-gnu.so

• W debian-rules-should-not-set-CFLAGS-from-noopt
• P debian-watch-does-not-check-gpg-signature
• P duplicate-in-relation-field
  • in source build-depends: dh-python, dh-python
• P file-contains-trailing-whitespace
  • debian/changelog (line 146)
  • debian/changelog (line 262)
  • debian/changelog (line 284)
  • debian/control (line 100)
  • debian/control (line 101)
  • debian/control (line 104)
  • debian/control (line 105)
  • debian/control (line 117)
  • debian/control (line 118)
  • debian/control (line 119)
  • debian/control (line 120)
  • debian/control (line 121)
  • debian/control (line 124)
  • debian/control (line 125)
  • debian/control (line 139)
  • debian/control (line 140)
  • debian/control (line 141)
  • debian/control (line 142)
  • debian/control (line 154)
  • debian/control (line 155)
  • debian/control (line 156)
  • debian/control (line 157)
  • debian/control (line 171)
  • debian/control (line 172)
  • debian/control (line 173)
  • debian/control (line 174)
  • debian/control (line 186)
  • debian/control (line 187)
  • debian/control (line 188)
  • debian/control (line 211)
  • debian/control (line 212)
  • debian/control (line 213)
  • debian/control (line 53)
  • debian/control (line 54)
  • debian/control (line 55)
  • debian/control (line 56)
  • debian/control (line 57)
  • debian/control (line 60)
  • debian/control (line 61)
  • debian/control (line 74)
  • debian/control (line 75)
  • debian/control (line 76)
  • debian/control (line 77)
  • debian/control (line 78)
  • debian/control (line 81)
  • debian/control (line 82)
  • debian/control (line 97)
  • debian/control (line 98)
  • debian/control (line 99)
  • debian/rules (line 1)
  • debian/rules (line 145)
  • debian/rules (line 158)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• W python-foo-but-no-python3-foo
  • python-ball
  • python-ballview
• W spelling-error-in-patch-description
  • debian/patches/fix-PoseClustering_Test-replace-file-compare-with-deserialize.patch comparision comparison
  • debian/patches/link_against_x11.patch explicitely explicitly
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/ball.git
  • vcs-git https://anonscm.debian.org/git/debian-med/ball.git

ballview

• I desktop-entry-lacks-keywords-entry
  • usr/share/applications/ballview.desktop
• W desktop-mime-but-no-exec-code
  • usr/share/applications/ballview.desktop
• I hardening-no-fortify-functions
  • usr/bin/BALLView
• I spelling-error-in-binary
  • usr/bin/BALLView dont don't
  • usr/bin/BALLView informations information
  • usr/bin/BALLView occured occurred
• W spelling-error-in-changelog
  • upsteam upstream

libball1.4

• W dev-pkg-without-shlib-symlink
  • usr/lib/libBALL.so.1.4 usr/lib/libBALL.so
• I hardening-no-fortify-functions
  • usr/lib/libBALL.so.1.4
• I no-symbols-control-file
  • usr/lib/libBALL.so.1.4
• X shlib-calls-exit
  • usr/lib/libBALL.so.1.4
• I spelling-error-in-binary
  • usr/lib/libBALL.so.1.4 CONECT CONNECT
  • usr/lib/libBALL.so.1.4 childs children
  • usr/lib/libBALL.so.1.4 enought enough
  • usr/lib/libBALL.so.1.4 errorneous erroneous
  • usr/lib/libBALL.so.1.4 featues features
  • usr/lib/libBALL.so.1.4 implmented implemented
  • usr/lib/libBALL.so.1.4 intialization initialization
  • usr/lib/libBALL.so.1.4 occured occurred
  • usr/lib/libBALL.so.1.4 paramters parameters
  • usr/lib/libBALL.so.1.4 registerd registered
  • usr/lib/libBALL.so.1.4 seperator separator
  • usr/lib/libBALL.so.1.4 standart standard
  • usr/lib/libBALL.so.1.4 unkown unknown
  • usr/lib/libBALL.so.1.4 woNT won't
• W spelling-error-in-changelog
  • upsteam upstream

libball1.4-data

• W spelling-error-in-changelog
  • upsteam upstream

libball1.4-dev

• W spelling-error-in-changelog
  • upsteam upstream

libball1.4-doc

• X duplicate-files
  • usr/share/doc/libball1.4/html/BALL/d0/d00/VIEW_2KERNEL_2kernel_8doc.html usr/share/doc/libball1.4/html/BALL/db/d6a/KERNEL_2kernel_8doc.html
  • usr/share/doc/libball1.4/html/BALL/d0/d85/COMMON_2common_8doc.html usr/share/doc/libball1.4/html/BALL/d0/ded/MOLMEC_2COMMON_2common_8doc.html
  • usr/share/doc/libball1.4/html/BALL/d2/dad/DATATYPE_2datatype_8doc.html usr/share/doc/libball1.4/html/BALL/d4/d2e/VIEW_2DATATYPE_2datatype_8doc.html
  • usr/share/doc/libball1.4/html/BALL/search/all_0.js usr/share/doc/libball1.4/html/BALL/search/groups_0.js
  • usr/share/doc/libball1.4/html/BALL/search/all_1.js usr/share/doc/libball1.4/html/BALL/search/defines_0.js
  • usr/share/doc/libball1.4/html/BALL/search/all_1c.js usr/share/doc/libball1.4/html/BALL/search/functions_1a.js
• W spelling-error-in-changelog
  • upsteam upstream

libballview1.4

• W dev-pkg-without-shlib-symlink
  • usr/lib/libVIEW.so.1.4 usr/lib/libVIEW.so
• I hardening-no-fortify-functions
  • usr/lib/libVIEW.so.1.4
• I no-symbols-control-file
  • usr/lib/libVIEW.so.1.4
• O package-name-doesnt-match-sonames
  • libVIEW1.4
• I spelling-error-in-binary
  • usr/lib/libVIEW.so.1.4 Dont Don't
  • usr/lib/libVIEW.so.1.4 Informations Information
  • usr/lib/libVIEW.so.1.4 Uknown Unknown
  • usr/lib/libVIEW.so.1.4 an other another
  • usr/lib/libVIEW.so.1.4 beeing being
  • usr/lib/libVIEW.so.1.4 calulate calculate
  • usr/lib/libVIEW.so.1.4 choosen chosen
  • usr/lib/libVIEW.so.1.4 correspoding corresponding
  • usr/lib/libVIEW.so.1.4 doesnt doesn't
  • usr/lib/libVIEW.so.1.4 executeable executable
  • usr/lib/libVIEW.so.1.4 mininum minimum
  • usr/lib/libVIEW.so.1.4 occured occurred
  • usr/lib/libVIEW.so.1.4 orgin origin
  • usr/lib/libVIEW.so.1.4 reseting resetting
  • usr/lib/libVIEW.so.1.4 succesfully successfully
  • usr/lib/libVIEW.so.1.4 sucessfully successfully
  • usr/lib/libVIEW.so.1.4 unkown unknown
• W spelling-error-in-changelog
  • upsteam upstream

libballview1.4-dev

• I package-contains-documentation-outside-usr-share-doc
  • usr/include/BALL/VIEW/UIC/README
• O package-contains-empty-directory
  • usr/lib/
• W spelling-error-in-changelog
  • upsteam upstream

python-ball

• W spelling-error-in-changelog
  • upsteam upstream

python-ballview

• W spelling-error-in-changelog
  • upsteam upstream

• P debian-watch-does-not-check-gpg-signature
• X deprecated-configure-filename
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing

libbambamc0

• X binary-file-built-without-LFS-support
  • usr/lib/i386-linux-gnu/libbambamc.so.0.0.50
• I hardening-no-bindnow
  • usr/lib/i386-linux-gnu/libbambamc.so.0.0.50
  • usr/lib/x86_64-linux-gnu/libbambamc.so.0.0.50
• I no-symbols-control-file
  • usr/lib/i386-linux-gnu/libbambamc.so.0.0.50
  • usr/lib/x86_64-linux-gnu/libbambamc.so.0.0.50

• I debian-rules-contains-unnecessary-get-orig-source-target
• I debian-rules-parses-dpkg-parsechangelog
  • (line 4)
  • (line 41)
  • (line 42)
• W debian-rules-uses-unnecessary-dh-argument
  • dh ... --parallel (line 10)
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 4)
  • debian/changelog (line 6)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/bamtools.git
  • vcs-git https://anonscm.debian.org/git/debian-med/bamtools.git

• I debian-rules-contains-unnecessary-get-orig-source-target
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 39)
  • debian/changelog (line 41)
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

libbamtools-doc

• X duplicate-files
  • usr/share/doc/libbamtools-dev/html/search/all_10.js usr/share/doc/libbamtools-dev/html/search/variables_d.js
  • usr/share/doc/libbamtools-dev/html/search/all_15.js usr/share/doc/libbamtools-dev/html/search/variables_12.js
  • usr/share/doc/libbamtools-dev/html/search/all_17.js usr/share/doc/libbamtools-dev/html/search/variables_13.js
  • usr/share/doc/libbamtools-dev/html/search/all_18.js usr/share/doc/libbamtools-dev/html/search/functions_12.js
  • usr/share/doc/libbamtools-dev/html/search/all_4.js usr/share/doc/libbamtools-dev/html/search/functions_3.js
  • usr/share/doc/libbamtools-dev/html/search/all_7.js usr/share/doc/libbamtools-dev/html/search/functions_6.js
  • usr/share/doc/libbamtools-dev/html/search/all_9.js usr/share/doc/libbamtools-dev/html/search/functions_8.js
  • usr/share/doc/libbamtools-dev/html/search/all_a.js usr/share/doc/libbamtools-dev/html/search/variables_7.js

libbamtools2.5.1

• I no-symbols-control-file
  • usr/lib/i386-linux-gnu/libbamtools.so.2.5.1
  • usr/lib/x86_64-linux-gnu/libbamtools.so.2.5.1
• X shlib-calls-exit
  • usr/lib/i386-linux-gnu/libbamtools.so.2.5.1
  • usr/lib/x86_64-linux-gnu/libbamtools.so.2.5.1

• I debian-rules-contains-unnecessary-get-orig-source-target
• I debian-rules-parses-dpkg-parsechangelog
  • (line 5)
• O debian-watch-does-not-check-gpg-signature
• I out-of-date-standards-version
  • 3.9.8 (released 2016-04-06) (current is 4.2.0)
• P package-does-not-install-examples
  • examples/
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

barrnap

• E wrong-path-for-interpreter
  • usr/bin/barrnap (#!/usr/bin/env != /usr/bin/perl)

• P debian-watch-does-not-check-gpg-signature
• I override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
  • (line 15)
• X upstream-metadata-file-is-missing

bart

• X binary-file-built-without-LFS-support
  • usr/bin/bart

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• I vcs-field-not-canonical
  • https://salsa.debian.org/med-team/bart-view.git https://salsa.debian.org/med-team/bart-view

bart-view

• X binary-file-built-without-LFS-support
  • usr/lib/bart/commands/view
• I hardening-no-bindnow
  • usr/lib/bart/commands/view
  • usr/lib/bart/commands/view

• P debian-watch-does-not-check-gpg-signature
• O testsuite-dependency-has-unparsable-elements
  • "\n?@" (in paragraph starting at line 1)
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

bcftools

• W binary-without-manpage
  • usr/bin/guess-ploidy.py
  • usr/bin/plot-roh.py
  • usr/bin/run-roh.pl
• X dependency-on-python-version-marked-for-end-of-life
  • (Suggests: python)
• I hardening-no-bindnow
  • usr/bin/bcftools
  • usr/lib/x86_64-linux-gnu/bcftools/GTisec.so
  • usr/lib/x86_64-linux-gnu/bcftools/GTsubset.so
  • usr/lib/x86_64-linux-gnu/bcftools/ad-bias.so
  • usr/lib/x86_64-linux-gnu/bcftools/af-dist.so
  • usr/lib/x86_64-linux-gnu/bcftools/check-ploidy.so
  • usr/lib/x86_64-linux-gnu/bcftools/check-sparsity.so
  • usr/lib/x86_64-linux-gnu/bcftools/color-chrs.so
  • usr/lib/x86_64-linux-gnu/bcftools/contrast.so
  • usr/lib/x86_64-linux-gnu/bcftools/counts.so
  • usr/lib/x86_64-linux-gnu/bcftools/dosage.so
  • usr/lib/x86_64-linux-gnu/bcftools/fill-AN-AC.so
  • usr/lib/x86_64-linux-gnu/bcftools/fill-from-fasta.so
  • usr/lib/x86_64-linux-gnu/bcftools/fill-tags.so
  • usr/lib/x86_64-linux-gnu/bcftools/fixploidy.so
  • usr/lib/x86_64-linux-gnu/bcftools/fixref.so
  • usr/lib/x86_64-linux-gnu/bcftools/frameshifts.so
  • usr/lib/x86_64-linux-gnu/bcftools/guess-ploidy.so
  • usr/lib/x86_64-linux-gnu/bcftools/impute-info.so
  • usr/lib/x86_64-linux-gnu/bcftools/isecGT.so
  • usr/lib/x86_64-linux-gnu/bcftools/mendelian.so
  • usr/lib/x86_64-linux-gnu/bcftools/missing2ref.so
  • usr/lib/x86_64-linux-gnu/bcftools/prune.so
  • usr/lib/x86_64-linux-gnu/bcftools/setGT.so
  • usr/lib/x86_64-linux-gnu/bcftools/split.so
  • usr/lib/x86_64-linux-gnu/bcftools/tag2tag.so
  • usr/lib/x86_64-linux-gnu/bcftools/trio-switch-rate.so
• W script-with-language-extension
  • usr/bin/color-chrs.pl
  • usr/bin/guess-ploidy.py
  • usr/bin/plot-roh.py
  • usr/bin/run-roh.pl
  • usr/bin/vcfutils.pl
• I spelling-error-in-manpage
  • usr/share/man/man1/bcftools.1.gz contruction construction
  • usr/share/man/man1/bcftools.1.gz wich which
• E wrong-path-for-interpreter
  • usr/bin/color-chrs.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/plot-vcfstats (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/run-roh.pl (#!/usr/bin/env != /usr/bin/perl)

• P debian-watch-does-not-check-gpg-signature
• P source-contains-empty-directory
  • src/cimg/
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/beads.git
  • vcs-git https://anonscm.debian.org/git/debian-med/beads.git

beads

• X binary-file-built-without-LFS-support
  • usr/bin/beads
  • usr/bin/qtbeads
• W binary-without-manpage
  • usr/bin/qtbeads
  • usr/bin/qtbeads
• I desktop-entry-lacks-keywords-entry
  • usr/share/applications/beads.desktop
  • usr/share/applications/beads.desktop
• I spelling-error-in-binary
  • usr/bin/beads assignement assignment
  • usr/bin/beads assignement assignment
  • usr/bin/qtbeads assignement assignment
  • usr/bin/qtbeads assignement assignment
  • usr/bin/qtbeads developped developed
  • usr/bin/qtbeads developped developed
  • usr/bin/qtbeads occured occurred
  • usr/bin/qtbeads occured occurred

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/rules (line 17)
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/beagle.git
  • vcs-git https://anonscm.debian.org/git/debian-med/beagle.git

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/control (line 103)
  • debian/control (line 104)
  • debian/control (line 106)
  • debian/control (line 107)
  • debian/control (line 108)
  • debian/control (line 109)
  • debian/control (line 110)
  • debian/control (line 45)
  • debian/control (line 46)
  • debian/control (line 48)
  • debian/control (line 49)
  • debian/control (line 50)
  • debian/control (line 51)
  • debian/control (line 52)
  • debian/control (line 64)
  • debian/control (line 65)
  • debian/control (line 67)
  • debian/control (line 68)
  • debian/control (line 69)
  • debian/control (line 70)
  • debian/control (line 71)
  • debian/control (line 84)
  • debian/control (line 85)
  • debian/control (line 87)
  • debian/control (line 88)
  • debian/control (line 89)
  • debian/control (line 90)
  • debian/control (line 91)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P source-contains-empty-directory
  • lib/
  • release/Linux/lib/
  • release_phylogeography/common/lib/
• I testsuite-autopkgtest-missing

beast-mcmc

• W binary-without-manpage
  • usr/bin/beast-tracer
  • usr/bin/loganalyser
  • usr/bin/logcombiner
  • usr/bin/treeannotator
  • usr/bin/treestat

beast-mcmc-doc

• I possible-documentation-but-no-doc-base-registration

beast-mcmc-examples

• X duplicate-files
  • usr/share/doc/beast-mcmc/examples/EmpiricalCodonModels/codon-data/ecmdata/freqs_zs.csv usr/share/doc/beast-mcmc/examples/EmpiricalCodonModels/codon-data/pcadata/freqs.csv
  • usr/share/doc/beast-mcmc/examples/EmpiricalCodonModels/codon-data/ecmdata/inirates.csv.gz usr/share/doc/beast-mcmc/examples/EmpiricalCodonModels/codon-data/ecmdata/rates_zs.csv.gz

libnucleotidelikelihoodcore0

• I hardening-no-bindnow
  • usr/lib/libNucleotideLikelihoodCore.so.0
  • usr/lib/libNucleotideLikelihoodCore.so.0
• I no-symbols-control-file
  • usr/lib/libNucleotideLikelihoodCore.so.0
  • usr/lib/libNucleotideLikelihoodCore.so.0

libnucleotidelikelihoodcore0-dbgsym

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/80/b24c2b87bfd56a5b0dc5540627bbf59ceb1beb.debug
  • usr/lib/debug/.build-id/a5/6d36e425b496b7bf79ab85f9d6c96cb21e0c90.debug

• I debian-rules-parses-dpkg-parsechangelog
  • (line 9)
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/control (line 34)
  • debian/control (line 35)
  • debian/control (line 37)
  • debian/control (line 38)
  • debian/control (line 39)
  • debian/control (line 40)
  • debian/control (line 41)
  • debian/control (line 54)
  • debian/control (line 55)
  • debian/control (line 57)
  • debian/control (line 58)
  • debian/control (line 59)
  • debian/control (line 60)
  • debian/control (line 61)
  • debian/control (line 73)
  • debian/control (line 74)
  • debian/control (line 76)
  • debian/control (line 77)
  • debian/control (line 78)
  • debian/control (line 79)
  • debian/control (line 80)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• P source-contains-empty-directory
  • lib/bundler/
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/beast2-mcmc.git
  • vcs-git https://anonscm.debian.org/git/debian-med/beast2-mcmc.git

beast2-mcmc-doc

• I possible-documentation-but-no-doc-base-registration

beast2-mcmc-examples

• X duplicate-files
  • usr/share/doc/beast-mcmc/examples/nexus/26.nex.gz usr/share/doc/beast-mcmc/examples/nexus/gopher.nex.gz

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 27)
  • debian/changelog (line 32)
  • debian/changelog (line 49)
  • debian/changelog (line 56)
  • debian/rules (line 47)
  • debian/rules (line 48)
  • debian/rules (line 49)
• I testsuite-autopkgtest-missing

bedops

• X binary-file-built-without-LFS-support
  • usr/bin/bedextract
  • usr/bin/bedmap
  • usr/bin/bedops
  • usr/bin/closest-features
  • usr/bin/sort-bed
• W binary-without-manpage
  • usr/bin/bam2bed_gnuParallel
  • usr/bin/bam2bed_gnuParallel
  • usr/bin/bam2bed_sge
  • usr/bin/bam2bed_sge
  • usr/bin/bam2bed_slurm
  • usr/bin/bam2bed_slurm
  • usr/bin/bam2starch_gnuParallel
  • usr/bin/bam2starch_gnuParallel
  • usr/bin/bam2starch_sge
  • usr/bin/bam2starch_sge
  • usr/bin/bam2starch_slurm
  • usr/bin/bam2starch_slurm
  • usr/bin/starchcluster_gnuParallel
  • usr/bin/starchcluster_gnuParallel
  • usr/bin/starchcluster_sge
  • usr/bin/starchcluster_sge
  • usr/bin/starchcluster_slurm
  • usr/bin/starchcluster_slurm
• W csh-considered-harmful
  • usr/bin/bam2bed_gnuParallel
  • usr/bin/bam2bed_gnuParallel
  • usr/bin/bam2bed_sge
  • usr/bin/bam2bed_sge
  • usr/bin/bam2bed_slurm
  • usr/bin/bam2bed_slurm
  • usr/bin/bam2starch_gnuParallel
  • usr/bin/bam2starch_gnuParallel
  • usr/bin/bam2starch_sge
  • usr/bin/bam2starch_sge
  • usr/bin/bam2starch_slurm
  • usr/bin/bam2starch_slurm
  • usr/bin/starchcluster_gnuParallel
  • usr/bin/starchcluster_gnuParallel
  • usr/bin/starchcluster_sge
  • usr/bin/starchcluster_sge
  • usr/bin/starchcluster_slurm
  • usr/bin/starchcluster_slurm
• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)
  • (Depends: python)
• I hardening-no-bindnow
  • usr/bin/convert2bed
  • usr/bin/convert2bed
• I hardening-no-fortify-functions
  • usr/bin/bedextract
  • usr/bin/bedextract
  • usr/bin/bedmap
  • usr/bin/bedmap
  • usr/bin/bedops
  • usr/bin/bedops
  • usr/bin/bedops-starch
  • usr/bin/bedops-starch
  • usr/bin/closest-features
  • usr/bin/closest-features
  • usr/bin/convert2bed
  • usr/bin/convert2bed
  • usr/bin/sort-bed
  • usr/bin/sort-bed
  • usr/bin/starchcat
  • usr/bin/starchcat
  • usr/bin/starchstrip
  • usr/bin/starchstrip
  • usr/bin/unstarch
  • usr/bin/unstarch
• W manpage-has-errors-from-man
  • usr/share/man/man1/bedops-starch.1.gz 30: warning [p 1, 5.3i]: can't break line
  • usr/share/man/man1/bedops-starch.1.gz 30: warning [p 1, 5.3i]: can't break line
  • usr/share/man/man1/starchcat.1.gz 38: warning [p 1, 7.3i]: can't break line
  • usr/share/man/man1/starchcat.1.gz 38: warning [p 1, 7.3i]: can't break line
  • usr/share/man/man1/starchstrip.1.gz 52: warning [p 1, 10.5i]: can't break line
  • usr/share/man/man1/starchstrip.1.gz 52: warning [p 1, 10.5i]: can't break line
  • usr/share/man/man1/unstarch.1.gz 27: warning [p 1, 4.3i]: cannot adjust line
  • usr/share/man/man1/unstarch.1.gz 27: warning [p 1, 4.3i]: cannot adjust line
• W manpage-has-useless-whatis-entry
  • usr/share/man/man1/bam2bed.1.gz
  • usr/share/man/man1/bam2bed.1.gz
  • usr/share/man/man1/bam2starch.1.gz
  • usr/share/man/man1/bam2starch.1.gz
  • usr/share/man/man1/bedextract.1.gz
  • usr/share/man/man1/bedextract.1.gz
  • usr/share/man/man1/bedmap.1.gz
  • usr/share/man/man1/bedmap.1.gz
  • usr/share/man/man1/bedops-starch.1.gz
  • usr/share/man/man1/bedops-starch.1.gz
  • usr/share/man/man1/bedops.1.gz
  • usr/share/man/man1/bedops.1.gz
  • usr/share/man/man1/closest-features.1.gz
  • usr/share/man/man1/closest-features.1.gz
  • usr/share/man/man1/convert2bed.1.gz
  • usr/share/man/man1/convert2bed.1.gz
  • usr/share/man/man1/gff2bed.1.gz
  • usr/share/man/man1/gff2bed.1.gz
  • usr/share/man/man1/gff2starch.1.gz
  • usr/share/man/man1/gff2starch.1.gz
  • usr/share/man/man1/gtf2bed.1.gz
  • usr/share/man/man1/gtf2bed.1.gz
  • usr/share/man/man1/gtf2starch.1.gz
  • usr/share/man/man1/gtf2starch.1.gz
  • usr/share/man/man1/gvf2bed.1.gz
  • usr/share/man/man1/gvf2bed.1.gz
  • usr/share/man/man1/gvf2starch.1.gz
  • usr/share/man/man1/gvf2starch.1.gz
  • usr/share/man/man1/psl2bed.1.gz
  • usr/share/man/man1/psl2bed.1.gz
  • usr/share/man/man1/psl2starch.1.gz
  • usr/share/man/man1/psl2starch.1.gz
  • usr/share/man/man1/rmsk2bed.1.gz
  • usr/share/man/man1/rmsk2bed.1.gz
  • usr/share/man/man1/rmsk2starch.1.gz
  • usr/share/man/man1/rmsk2starch.1.gz
  • usr/share/man/man1/sam2bed.1.gz
  • usr/share/man/man1/sam2bed.1.gz
  • usr/share/man/man1/sam2starch.1.gz
  • usr/share/man/man1/sam2starch.1.gz
  • usr/share/man/man1/sort-bed.1.gz
  • usr/share/man/man1/sort-bed.1.gz
  • usr/share/man/man1/starch-diff.1.gz
  • usr/share/man/man1/starch-diff.1.gz
  • usr/share/man/man1/starchcat.1.gz
  • usr/share/man/man1/starchcat.1.gz
  • usr/share/man/man1/starchstrip.1.gz
  • usr/share/man/man1/starchstrip.1.gz
  • usr/share/man/man1/unstarch.1.gz
  • usr/share/man/man1/unstarch.1.gz
  • usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz
  • usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz
  • usr/share/man/man1/update-sort-bed-slurm.1.gz
  • usr/share/man/man1/update-sort-bed-slurm.1.gz
  • usr/share/man/man1/update-sort-bed-starch-slurm.1.gz
  • usr/share/man/man1/update-sort-bed-starch-slurm.1.gz
  • usr/share/man/man1/vcf2bed.1.gz
  • usr/share/man/man1/vcf2bed.1.gz
  • usr/share/man/man1/vcf2starch.1.gz
  • usr/share/man/man1/vcf2starch.1.gz
  • usr/share/man/man1/wig2bed.1.gz
  • usr/share/man/man1/wig2bed.1.gz
  • usr/share/man/man1/wig2starch.1.gz
  • usr/share/man/man1/wig2starch.1.gz

bedops-dbgsym

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/37/04cd41caac58f0a9e98e4fe25e131c9da357f0.debug
  • usr/lib/debug/.build-id/df/68589f8dcf01355d227a9dc6affe683ba7ab92.debug

bedops-doc

• X duplicate-files
  • usr/share/doc/bedops/html/_images/reference_bedextract_mechanism.png usr/share/doc/bedops/html/_images/reference_bedextract_mechanism1.png

• I debian-rules-contains-unnecessary-get-orig-source-target
• I debian-rules-parses-dpkg-parsechangelog
  • (line 7)
  • (line 8)
• P debian-watch-does-not-check-gpg-signature
• W dep5-copyright-license-name-not-unique
  • (paragraph at line 100)
  • mit (paragraph at line 28)
• W dep5-file-paragraph-references-header-paragraph
  • gpl-2 (paragraph at line 22)
• P file-contains-trailing-whitespace
  • debian/changelog (line 23)
  • debian/rules (line 43)
• I out-of-date-standards-version
  • 3.9.8 (released 2016-04-06) (current is 4.2.0)
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• I unused-license-paragraph-in-dep5-copyright
  • gpl-3+ (paragraph at line 100)
  • mit (paragraph at line 100)
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/bedtools.git
  • vcs-git https://anonscm.debian.org/git/debian-med/bedtools.git

bedtools

• W binary-without-manpage
  • usr/bin/annotateBed
  • usr/bin/bamToBed
  • usr/bin/bamToFastq
  • usr/bin/bed12ToBed6
  • usr/bin/bedToBam
  • usr/bin/bedToIgv
  • usr/bin/bedpeToBam
  • usr/bin/bedtools
  • usr/bin/closestBed
  • usr/bin/clusterBed
  • usr/bin/complementBed
  • usr/bin/coverageBed
  • usr/bin/expandCols
  • usr/bin/fastaFromBed
  • usr/bin/flankBed
  • usr/bin/genomeCoverageBed
  • usr/bin/getOverlap
  • usr/bin/groupBy
  • usr/bin/intersectBed
  • usr/bin/linksBed
  • usr/bin/mapBed
  • usr/bin/maskFastaFromBed
  • usr/bin/mergeBed
  • usr/bin/multiBamCov
  • usr/bin/multiIntersectBed
  • usr/bin/nucBed
  • usr/bin/pairToBed
  • usr/bin/pairToPair
  • usr/bin/randomBed
  • usr/bin/shiftBed
  • usr/bin/shuffleBed
  • usr/bin/slopBed
  • usr/bin/sortBed
  • usr/bin/subtractBed
  • usr/bin/tagBam
  • usr/bin/unionBedGraphs
  • usr/bin/windowBed
  • usr/bin/windowMaker
• I spelling-error-in-binary
  • usr/bin/bedtools postive positive

bedtools-dbgsym

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/16/d99793d5cd655de9bbcb393f482abb96d0a419.debug

bedtools-test

• W executable-not-elf-or-script
  • usr/share/bedtools/data/knownGene.hg18.chr21.bed
• I package-contains-documentation-outside-usr-share-doc
  • usr/share/bedtools/test/fisher/README.md
• W script-not-executable
  • usr/share/bedtools/test/bamtobed/test-bamtobed.sh
  • usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
  • usr/share/bedtools/test/closest/kclosest/test-kclosest.sh
  • usr/share/bedtools/test/closest/sortAndNaming/test-sort-and-naming.sh
  • usr/share/bedtools/test/closest/test-closest.sh
  • usr/share/bedtools/test/cluster/test-cluster.sh
  • usr/share/bedtools/test/complement/test-complement.sh
  • usr/share/bedtools/test/coverage/test-coverage.sh
  • usr/share/bedtools/test/expand/test-expand.sh
  • usr/share/bedtools/test/fisher/cmp.sh
  • usr/share/bedtools/test/fisher/get.sh
  • usr/share/bedtools/test/fisher/shuf.sh
  • usr/share/bedtools/test/fisher/test-fisher.sh
  • usr/share/bedtools/test/flank/test-flank.sh
  • usr/share/bedtools/test/general/test-general.sh
  • usr/share/bedtools/test/getfasta/test-getfasta.sh
  • usr/share/bedtools/test/groupBy/test-groupby.sh
  • usr/share/bedtools/test/intersect/multi_intersect/test-multi_intersect.sh
  • usr/share/bedtools/test/intersect/sortAndNaming/test-sort-and-naming.sh
  • usr/share/bedtools/test/intersect/test-intersect.sh
  • usr/share/bedtools/test/jaccard/test-jaccard.sh
  • usr/share/bedtools/test/makewindows/test-makewindows.sh
  • usr/share/bedtools/test/map/test-map.sh
  • usr/share/bedtools/test/merge/test-merge.sh
  • usr/share/bedtools/test/multicov/test-multicov.sh
  • usr/share/bedtools/test/reldist/test-reldist.sh
  • usr/share/bedtools/test/sample/test-sample.sh
  • usr/share/bedtools/test/shift/test-shift.sh
  • usr/share/bedtools/test/shuffle/test-shuffle.sh
  • usr/share/bedtools/test/slop/test-slop.sh
  • usr/share/bedtools/test/sort/test-sort.sh
  • usr/share/bedtools/test/spacing/test-spacing.sh
  • usr/share/bedtools/test/split/test-split.sh
  • usr/share/bedtools/test/subtract/test-subtract.sh
  • usr/share/bedtools/test/test.sh

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 49)
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

bedtools

• W binary-without-manpage
  • usr/bin/annotateBed
  • usr/bin/bamToBed
  • usr/bin/bamToFastq
  • usr/bin/bed12ToBed6
  • usr/bin/bedToBam
  • usr/bin/bedToIgv
  • usr/bin/bedpeToBam
  • usr/bin/bedtools
  • usr/bin/closestBed
  • usr/bin/clusterBed
  • usr/bin/complementBed
  • usr/bin/coverageBed
  • usr/bin/expandCols
  • usr/bin/fastaFromBed
  • usr/bin/flankBed
  • usr/bin/genomeCoverageBed
  • usr/bin/getOverlap
  • usr/bin/groupBy
  • usr/bin/intersectBed
  • usr/bin/linksBed
  • usr/bin/mapBed
  • usr/bin/maskFastaFromBed
  • usr/bin/mergeBed
  • usr/bin/multiBamCov
  • usr/bin/multiIntersectBed
  • usr/bin/nucBed
  • usr/bin/pairToBed
  • usr/bin/pairToPair
  • usr/bin/randomBed
  • usr/bin/shiftBed
  • usr/bin/shuffleBed
  • usr/bin/slopBed
  • usr/bin/sortBed
  • usr/bin/subtractBed
  • usr/bin/tagBam
  • usr/bin/unionBedGraphs
  • usr/bin/windowBed
  • usr/bin/windowMaker
• I spelling-error-in-binary
  • usr/bin/bedtools postive positive

bedtools-dbgsym

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/80/ff25dec4eb06f32356c685e18a4efc19d49099.debug

bedtools-test

• W executable-not-elf-or-script
  • usr/share/bedtools/data/knownGene.hg18.chr21.bed
  • usr/share/bedtools/test/sort/b.bed
• I package-contains-documentation-outside-usr-share-doc
  • usr/share/bedtools/test/fisher/README.md
• W script-not-executable
  • usr/share/bedtools/test/bamtobed/test-bamtobed.sh
  • usr/share/bedtools/test/bed12tobed6/test-bed12tobed6.sh
  • usr/share/bedtools/test/closest/kclosest/test-kclosest.sh
  • usr/share/bedtools/test/closest/sortAndNaming/test-sort-and-naming.sh
  • usr/share/bedtools/test/closest/test-closest.sh
  • usr/share/bedtools/test/cluster/test-cluster.sh
  • usr/share/bedtools/test/complement/test-complement.sh
  • usr/share/bedtools/test/expand/test-expand.sh
  • usr/share/bedtools/test/fisher/cmp.sh
  • usr/share/bedtools/test/fisher/get.sh
  • usr/share/bedtools/test/fisher/shuf.sh
  • usr/share/bedtools/test/fisher/test-fisher.sh
  • usr/share/bedtools/test/flank/test-flank.sh
  • usr/share/bedtools/test/general/test-general.sh
  • usr/share/bedtools/test/getfasta/test-getfasta.sh
  • usr/share/bedtools/test/groupby/test-groupby.sh
  • usr/share/bedtools/test/intersect/multi_intersect/test-multi_intersect.sh
  • usr/share/bedtools/test/intersect/sortAndNaming/test-sort-and-naming.sh
  • usr/share/bedtools/test/intersect/test-intersect.sh
  • usr/share/bedtools/test/jaccard/test-jaccard.sh
  • usr/share/bedtools/test/makewindows/test-makewindows.sh
  • usr/share/bedtools/test/map/test-map.sh
  • usr/share/bedtools/test/merge/test-merge.sh
  • usr/share/bedtools/test/multicov/test-multicov.sh
  • usr/share/bedtools/test/negativecontrol/test-negativecontrol.sh
  • usr/share/bedtools/test/reldist/test-reldist.sh
  • usr/share/bedtools/test/sample/test-sample.sh
  • usr/share/bedtools/test/shift/test-shift.sh
  • usr/share/bedtools/test/shuffle/test-shuffle.sh
  • usr/share/bedtools/test/slop/test-slop.sh
  • usr/share/bedtools/test/sort/test-sort.sh
  • usr/share/bedtools/test/spacing/test-spacing.sh
  • usr/share/bedtools/test/split/test-split.sh
  • usr/share/bedtools/test/subtract/test-subtract.sh

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 36)
  • debian/changelog (line 39)
  • debian/changelog (line 41)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I out-of-date-standards-version
  • 4.1.3 (released 2017-12-27) (current is 4.2.0)
• I testsuite-autopkgtest-missing

berkeley-express

• X binary-file-built-without-LFS-support
  • usr/lib/debian-med/bin/express

• P debian-watch-does-not-check-gpg-signature
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/eagle.git
  • vcs-git https://anonscm.debian.org/git/debian-med/eagle.git

bio-eagle

• X binary-file-built-without-LFS-support
  • usr/lib/debian-med/bin/eagle

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/rules (line 13)
• I out-of-date-standards-version
  • 4.1.4 (released 2018-04-05) (current is 4.2.0)
• I tar-errors-from-source
  • Ignoring unknown extended header keyword 'LIBARCHIVE.creationtime'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.dev'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.ino'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
  • Ignoring unknown extended header keyword 'SCHILY.nlink'
• I testsuite-autopkgtest-missing

bio-rainbow

• P debian-changelog-line-too-short
  • DEP3 (line 17)
  • DEP3 (line 17)
  • DEP5 (line 18)
  • DEP5 (line 18)
• W manpage-has-errors-from-man
  • usr/share/man/man1/bio-rainbow.1.gz 35: warning [p 1, 6.2i]: cannot adjust line
  • usr/share/man/man1/bio-rainbow.1.gz 35: warning [p 1, 6.2i]: cannot adjust line
• O script-with-language-extension
  • usr/bin/select_all_rbcontig.pl
  • usr/bin/select_all_rbcontig.pl
  • usr/bin/select_best_rbcontig.pl
  • usr/bin/select_best_rbcontig.pl
  • usr/bin/select_best_rbcontig_plus_read1.pl
  • usr/bin/select_best_rbcontig_plus_read1.pl
  • usr/bin/select_sec_rbcontig.pl
  • usr/bin/select_sec_rbcontig.pl

• P debian-watch-does-not-check-gpg-signature
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/bio-tradis.git
  • vcs-git https://anonscm.debian.org/git/debian-med/bio-tradis.git

bio-tradis

• X application-in-library-section
  • perl usr/bin/add_tradis_tags usr/bin/bacteria_tradis usr/bin/check_tradis_tags usr/bin/combine_tradis_plots usr/bin/filter_tradis_tags usr/bin/remove_tradis_tags usr/bin/tradis_comparison usr/bin/tradis_essentiality usr/bin/tradis_gene_insert_sites usr/bin/tradis_merge_plots usr/bin/tradis_plot
• E wrong-path-for-interpreter
  • usr/bin/add_tradis_tags (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/bacteria_tradis (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/check_tradis_tags (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/combine_tradis_plots (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/filter_tradis_tags (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/remove_tradis_tags (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/tradis_gene_insert_sites (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/tradis_merge_plots (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/tradis_plot (#!/usr/bin/env != /usr/bin/perl)

• I debian-rules-contains-unnecessary-get-orig-source-target
• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://www.bioinformatics.org/biococoa/downloads/
• P file-contains-trailing-whitespace
  • debian/changelog (line 75)
• P no-dep5-copyright
• P package-does-not-use-debhelper-or-cdbs
• P source-contains-empty-directory
  • BCAppKit/2.0-cleanup/
  • BCFoundation/2.0-cleanup/
  • BCFoundation/Tests/TestFiles/
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biococoa.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biococoa.git

libbiococoa-dev (2.2.2-3+b1; main)

• I possible-documentation-but-no-doc-base-registration

libbiococoa2 (2.2.2-3+b1; main)

• X binary-file-built-without-LFS-support
  • usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2
• I hardening-no-bindnow
  • usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2
  • usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2
• X shlib-calls-exit
  • usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2
  • usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2

libbiococoa2-dbgsym (2.2.2-3+b1; main)

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/af/68f7db54523d0fb047772bdbb1255d77559e43.debug
  • usr/lib/debug/.build-id/d6/625b4946e0905e34b4bfa82e9780db7c7b2409.debug

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 26)
  • debian/changelog (line 45)
  • debian/rules (line 20)
  • debian/rules (line 36)
• P source-contains-empty-directory
  • reports/
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biojava-live.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biojava-live.git

libbiojava-java

• I javalib-but-no-public-jars
• I possible-documentation-but-no-doc-base-registration

libbiojava-java-demos

• X duplicate-files
  • usr/share/doc/libbiojava-java-demos/examples/dp/fake.fasta.gz usr/share/doc/libbiojava-java-demos/examples/files/fake.fasta.gz
  • usr/share/doc/libbiojava-java-demos/examples/dp/fakepromoter.xml.gz usr/share/doc/libbiojava-java-demos/examples/files/fakepromoter.xml.gz
  • usr/share/doc/libbiojava-java-demos/examples/files/AL121903.embl.gz usr/share/doc/libbiojava-java-demos/examples/gff/AL121903.embl.gz usr/share/doc/libbiojava-java-demos/examples/seq/AL121903.embl.gz
  • usr/share/doc/libbiojava-java-demos/examples/files/AL121903.genbank.gz usr/share/doc/libbiojava-java-demos/examples/seq/AL121903.genbank.gz
  • usr/share/doc/libbiojava-java-demos/examples/files/varC4-2.gff.gz usr/share/doc/libbiojava-java-demos/examples/gff/varC4-2.gff.gz

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 10)
  • debian/changelog (line 17)
  • debian/changelog (line 3)
  • debian/changelog (line 33)
  • debian/changelog (line 59)
  • debian/changelog (line 65)
  • debian/rules (line 97)
• W global-files-wildcard-not-first-paragraph-in-dep5-copyright
  • (paragraph at line 36)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I missing-explanation-for-repacked-upstream-tarball
• I override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
  • (line 58)
• P package-uses-old-debhelper-compat-version
  • 10
• W patch-file-present-but-not-mentioned-in-series
  • fix_code_to_support_latest_jmol
  • fix_uselog4j1
  • java8_compatibility.patch
• W spelling-error-in-patch-description
  • debian/patches/fix_itext_class_updates an other another
• I testsuite-autopkgtest-missing
• I unused-file-paragraph-in-dep5-copyright
  • paragraph at line 14
  • paragraph at line 5
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biojava4-live.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biojava4-live.git
• I wildcard-matches-nothing-in-dep5-copyright
  • biojava-forester (paragraph at line 14)
  • biojava-jcolorbrewer (paragraph at line 5)

libbiojava4-java

• O empty-binary-package
• I javalib-but-no-public-jars

• W debian-rules-sets-DEB_BUILD_OPTIONS
  • line 5
• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/

python3-biomaj3

• X application-in-library-section
  • python usr/bin/biomaj_migrate_database.py
• W binary-without-manpage
  • usr/bin/biomaj_migrate_database.py
• X library-package-name-for-application
  • usr/bin/biomaj_migrate_database.py
• W script-with-language-extension
  • usr/bin/biomaj_migrate_database.py
• I unknown-field-in-control
  • python-egg-name

• W debian-rules-sets-DEB_BUILD_OPTIONS
  • line 3
• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 9
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biomaj3-cli.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biomaj3-cli.git

python3-biomaj3-cli

• X application-in-library-section
  • python usr/bin/biomaj-cli usr/bin/biomaj-cli.py
• W binary-without-manpage
  • usr/bin/biomaj-cli
  • usr/bin/biomaj-cli.py
• X library-package-name-for-application
  • usr/bin/biomaj-cli usr/bin/biomaj-cli.py
• W script-with-language-extension
  • usr/bin/biomaj-cli.py
• I unknown-field-in-control
  • python-egg-name

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 10)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 9
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biomaj3-core.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biomaj3-core.git

python3-biomaj3-core

• I unknown-field-in-control
  • python-egg-name

• W debian-rules-sets-DEB_BUILD_OPTIONS
  • line 3
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 3)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 9
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biomaj3-daemon.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biomaj3-daemon.git

python3-biomaj3-daemon

• X application-in-library-section
  • python usr/bin/biomaj-daemon-consumer usr/bin/biomaj-daemon-web usr/bin/biomaj_daemon_consumer.py
• W binary-without-manpage
  • usr/bin/biomaj-daemon-consumer
  • usr/bin/biomaj-daemon-web
  • usr/bin/biomaj_daemon_consumer.py
• X library-package-name-for-application
  • usr/bin/biomaj-daemon-consumer usr/bin/biomaj-daemon-web usr/bin/biomaj_daemon_consumer.py
• W script-with-language-extension
  • usr/bin/biomaj_daemon_consumer.py
• I unknown-field-in-control
  • python-egg-name

• W debian-rules-sets-DEB_BUILD_OPTIONS
  • line 3
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 4)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 9
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biomaj3-download.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biomaj3-download.git

python3-biomaj3-download

• X application-in-library-section
  • python usr/bin/biomaj-download-consumer usr/bin/biomaj-download-web usr/bin/biomaj_download_consumer.py
• W binary-without-manpage
  • usr/bin/biomaj-download-consumer
  • usr/bin/biomaj-download-web
  • usr/bin/biomaj_download_consumer.py
• X library-package-name-for-application
  • usr/bin/biomaj-download-consumer usr/bin/biomaj-download-web usr/bin/biomaj_download_consumer.py
• W script-with-language-extension
  • usr/bin/biomaj_download_consumer.py
• I unknown-field-in-control
  • python-egg-name

• W debian-rules-sets-DEB_BUILD_OPTIONS
  • line 3
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 4)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 9
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biomaj3-process.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biomaj3-process.git

python3-biomaj3-process

• X application-in-library-section
  • python usr/bin/biomaj-process-consumer usr/bin/biomaj-process-web usr/bin/biomaj_process_consumer.py
• W binary-without-manpage
  • usr/bin/biomaj-process-consumer
  • usr/bin/biomaj-process-web
  • usr/bin/biomaj_process_consumer.py
• X library-package-name-for-application
  • usr/bin/biomaj-process-consumer usr/bin/biomaj-process-web usr/bin/biomaj_process_consumer.py
• W script-with-language-extension
  • usr/bin/biomaj_process_consumer.py
• I unknown-field-in-control
  • python-egg-name

• W debian-rules-sets-DEB_BUILD_OPTIONS
  • line 3
• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I out-of-date-standards-version
  • 4.0.0 (released 2017-05-28) (current is 4.2.0)
• P package-uses-old-debhelper-compat-version
  • 9
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biomaj3-user.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biomaj3-user.git

python3-biomaj3-user

• X application-in-library-section
  • python usr/bin/biomaj-users usr/bin/biomaj-users-web usr/bin/biomaj-users.py
• W binary-without-manpage
  • usr/bin/biomaj-users
  • usr/bin/biomaj-users-web
  • usr/bin/biomaj-users.py
• X library-package-name-for-application
  • usr/bin/biomaj-users usr/bin/biomaj-users-web usr/bin/biomaj-users.py
• W script-with-language-extension
  • usr/bin/biomaj-users.py
• I unknown-field-in-control
  • python-egg-name

• P co-maintained-package-with-no-vcs-fields
• W debian-rules-sets-DEB_BUILD_OPTIONS
  • line 3
• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I out-of-date-standards-version
  • 4.0.0 (released 2017-05-28) (current is 4.2.0)
• P package-uses-old-debhelper-compat-version
  • 9
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing

python3-biomaj3-zipkin

• I extended-description-is-probably-too-short
• I unknown-field-in-control
  • python-egg-name

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 115)
  • debian/changelog (line 124)
  • debian/changelog (line 142)
  • debian/changelog (line 268)
  • debian/changelog (line 406)
  • debian/changelog (line 90)
  • debian/rules (line 25)
• W obsolete-url-in-packaging
  • debian/copyright http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz
• P package-uses-old-debhelper-compat-version
  • 10
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/git/debian-med/bioperl.git
  • vcs-git https://anonscm.debian.org/git/debian-med/bioperl.git

bioperl

• W binary-without-manpage
  • usr/bin/bp_das_server
  • usr/bin/bp_seqfeature_delete
  • usr/bin/bp_seqfeature_gff3
• E wrong-path-for-interpreter
  • usr/bin/bp_find-blast-matches (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/bp_seqcut (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/bp_seqfeature_gff3 (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/bp_seqpart (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/doc/bioperl/examples/root/exceptions3.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/doc/bioperl/examples/root/exceptions4.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/doc/bioperl/examples/searchio/custom_writer.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/doc/bioperl/examples/searchio/hspwriter.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/doc/bioperl/examples/searchio/rawwriter.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/doc/bioperl/examples/tools/seq_pattern.pl (#!/usr/bin/env != /usr/bin/perl)

libbio-perl-perl

• W manpage-has-bad-whatis-entry
  • usr/share/man/man3/Bio::Root::Build.3pm.gz
  • usr/share/man/man3/Bio::Root::Exception.3pm.gz
  • usr/share/man/man3/Bio::Root::IO.3pm.gz
  • usr/share/man/man3/Bio::Root::Root.3pm.gz
  • usr/share/man/man3/Bio::Root::RootI.3pm.gz
  • usr/share/man/man3/Bio::Root::Storable.3pm.gz
  • usr/share/man/man3/Bio::Root::Test.3pm.gz
  • usr/share/man/man3/Bio::Root::Utilities.3pm.gz
  • usr/share/man/man3/Bio::Root::Version.3pm.gz
  • usr/share/man/man3/Bio::SearchIO::hmmer3.3pm.gz
  • usr/share/man/man3/Bio::Tools::SeqPattern::Backtranslate.3pm.gz
  • usr/share/man/man3/Bio::TreeIO::NewickParser.3pm.gz
  • usr/share/man/man3/Bio::TreeIO::newick.3pm.gz
• W manpage-has-errors-from-man
  • usr/share/man/man3/Bio::SeqIO::bsml.3pm.gz 357: warning [p 4, 0.2i]: can't break line
• X perl-module-name-not-mentioned-in-description
  • Bio::Perl
• I spelling-error-in-manpage
  • usr/share/man/man3/Bio::LiveSeq::AARange.3pm.gz everytime every time
  • usr/share/man/man3/Bio::PhyloNetwork::muVector.3pm.gz substract subtract
  • usr/share/man/man3/Bio::PopGen::HtSNP.3pm.gz happend happened
  • usr/share/man/man3/Bio::Seq::LargeSeqI.3pm.gz resetable resettable
  • usr/share/man/man3/Bio::Structure::Entry.3pm.gz Conect Connect
  • usr/share/man/man3/Bio::Structure::Entry.3pm.gz conect connect
  • usr/share/man/man3/Bio::Structure::Entry.3pm.gz conect connect
  • usr/share/man/man3/Bio::Structure::Entry.3pm.gz conect connect
  • usr/share/man/man3/Bio::Structure::Entry.3pm.gz conect connect
  • usr/share/man/man3/Bio::Tools::Analysis::Protein::ELM.3pm.gz concensus consensus

• W changelog-should-mention-nmu
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 140)
  • debian/changelog (line 92)
• X libmodule-build-perl-needs-to-be-in-build-depends
• W obsolete-url-in-packaging
  • debian/control http://search.cpan.org/dist/BioPerl-Run/
• I override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
  • (line 31)
• P package-uses-old-debhelper-compat-version
  • 10
• W patch-file-present-but-not-mentioned-in-series
  • adjust_bowtie_tests.patch
  • skip_tests_for_samtools.patch
• W source-nmu-has-incorrect-version-number
  • 1.7.2-3
• W spelling-error-in-patch-description
  • debian/patches/skip_tests_for_phyml.patch completed completed (duplicate word) completed
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/git/debian-med/bioperl-run.git
  • vcs-git https://anonscm.debian.org/git/debian-med/bioperl-run.git

bioperl-run

• W script-with-language-extension
  • usr/bin/bp_bioperl_application_installer.pl
  • usr/bin/bp_multi_hmmsearch.pl
  • usr/bin/bp_panalysis.pl
  • usr/bin/bp_papplmaker.pl
  • usr/bin/bp_run_neighbor.pl
  • usr/bin/bp_run_protdist.pl

libbio-perl-run-perl

• I extended-description-is-probably-too-short
• W manpage-has-bad-whatis-entry
  • usr/share/man/man3/Bio::Tools::Run::Alignment::Blat.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::Phylo::FastTree.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::Phylo::Raxml.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::Primate.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::Prints.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::Profile.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::Signalp.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm.gz
  • usr/share/man/man3/Bio::Tools::Run::Vista.3pm.gz
• W manpage-has-errors-from-pod2man
  • usr/share/man/man3/Bio::DB::SoapEUtilities::Result.3pm.gz:415
  • usr/share/man/man3/Bio::Tools::Run::ERPIN.3pm.gz:317
• I spelling-error-in-manpage
  • usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm.gz arugment argument
  • usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm.gz allows to allows one to
  • usr/share/man/man3/Bio::Tools::Run::BWA.3pm.gz contruction construction
  • usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm.gz argment argument
  • usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm.gz retrive retrieve
  • usr/share/man/man3/Bio::Tools::Run::Hmmer.3pm.gz specifiy specify
  • usr/share/man/man3/Bio::Tools::Run::Maq.3pm.gz contruction construction
  • usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm.gz flexability flexibility
  • usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm.gz documetation documentation
  • usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm.gz bootstap bootstrap
  • usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm.gz orginal original
  • usr/share/man/man3/Bio::Tools::Run::Phylo::PhyloBase.3pm.gz desribe describe
  • usr/share/man/man3/Bio::Tools::Run::Phylo::PhyloBase.3pm.gz desribe describe
  • usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm.gz explicitely explicitly
  • usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm.gz exeception exception
  • usr/share/man/man3/Bio::Tools::Run::WrapperBase::CommandExts.3pm.gz contruction construction

• I debian-rules-parses-dpkg-parsechangelog
  • (line 9)
• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://eddylab.org/software/squid/
• P file-contains-trailing-whitespace
  • debian/changelog (line 114)
  • debian/changelog (line 23)
  • debian/changelog (line 25)
  • debian/changelog (line 26)
  • debian/changelog (line 28)
  • debian/changelog (line 29)
  • debian/changelog (line 31)
  • debian/changelog (line 32)
  • debian/changelog (line 33)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I out-of-date-standards-version
  • 3.9.8 (released 2016-04-06) (current is 4.2.0)
• P package-uses-old-debhelper-compat-version
  • 10
• P source-contains-empty-directory
  • Scripts/
  • Shiva/
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• X upstream-metadata-file-is-missing
• W useless-autoreconf-build-depends
  • autotools-dev
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/biosquid.git
  • vcs-git https://anonscm.debian.org/git/debian-med/biosquid.git

biosquid

• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
  • usr/share/common-licenses/GPL
• I hardening-no-fortify-functions
  • usr/bin/revcomp
  • usr/bin/revcomp

libsquid-dev

• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
  • usr/share/common-licenses/GPL

libsquid1

• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
  • usr/share/common-licenses/GPL
• I no-symbols-control-file
  • usr/lib/i386-linux-gnu/libsquid.so.1.0.0
  • usr/lib/x86_64-linux-gnu/libsquid.so.1.0.0
• X shlib-calls-exit
  • usr/lib/i386-linux-gnu/libsquid.so.1.0.0
  • usr/lib/x86_64-linux-gnu/libsquid.so.1.0.0

• P debian-watch-does-not-check-gpg-signature
• I testsuite-autopkgtest-missing

biosyntax-example

• I duplicated-compressed-file
  • usr/share/doc/biosyntax/examples/nt-seq/test2.fq.gz

• I debian-rules-contains-unnecessary-get-orig-source-target
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/rules (line 83)
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/bitseq.git
  • vcs-git https://anonscm.debian.org/git/debian-med/bitseq.git

bitseq

• W binary-without-manpage
  • usr/bin/biocUpdate
  • usr/bin/biocUpdate
  • usr/bin/checkTR
  • usr/bin/checkTR
• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/LGPL
  • usr/share/common-licenses/LGPL
• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)
  • (Depends: python)

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P source-contains-empty-directory
  • libcpp/
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/blasr.git
  • vcs-git https://anonscm.debian.org/git/debian-med/blasr.git

blasr

• W binary-without-manpage
  • usr/bin/bam2bax
  • usr/bin/bam2plx
  • usr/bin/bax2bam
• I hardening-no-bindnow
  • usr/bin/bam2bax
  • usr/bin/bam2plx
  • usr/bin/bax2bam
  • usr/bin/blasr
  • usr/bin/loadPulses
  • usr/bin/pls2fasta
  • usr/bin/samFilter
  • usr/bin/samtoh5
  • usr/bin/samtom4
  • usr/bin/sawriter
  • usr/bin/sdpMatcher
  • usr/bin/toAfg
• I hardening-no-fortify-functions
  • usr/bin/bam2bax
  • usr/bin/bam2plx
  • usr/bin/blasr
• I spelling-error-in-binary
  • usr/bin/bam2bax ouptut output
  • usr/bin/bam2plx ouptut output
  • usr/bin/loadPulses defualt default
  • usr/bin/loadPulses opiton option
• I spelling-error-in-manpage
  • usr/share/man/man1/loadPulses.1.gz Defualt Default

• I debian-rules-contains-unnecessary-get-orig-source-target
• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/blimps-([0-9.]+)\.tar\.gz
• I out-of-date-standards-version
  • 4.1.1 (released 2017-09-27) (current is 4.2.0)
• P package-uses-old-debhelper-compat-version
  • 10
• P source-contains-prebuilt-binary
  • bin/Linux/LAMA
  • bin/Linux/LAMA_search
  • bin/Linux/addseqs
  • bin/Linux/biassed_blocks_finder
  • bin/Linux/blalign
  • bin/Linux/blastdat
  • bin/Linux/bldist
  • bin/Linux/blimps
  • bin/Linux/blk2mot
  • bin/Linux/blk2pssm
  • bin/Linux/blk2slx
  • bin/Linux/blkprob
  • bin/Linux/blksort
  • bin/Linux/block_vis
  • bin/Linux/blocks_search
  • bin/Linux/blosum
  • bin/Linux/blweight
  • bin/Linux/cobbler
  • bin/Linux/codehop
  • bin/Linux/coduse
  • bin/Linux/fastaseqs
  • bin/Linux/find_biassed_blocks
  • bin/Linux/format_block
  • bin/Linux/getblock
  • bin/Linux/getseq
  • bin/Linux/htmlize-LAMA
  • bin/Linux/htmlize-codehop
  • bin/Linux/interpro
  • bin/Linux/lisblk
  • bin/Linux/mablock
  • bin/Linux/makeblockmap
  • bin/Linux/makelis
  • bin/Linux/makelogob
  • bin/Linux/matrix_logob
  • bin/Linux/motifj
  • bin/Linux/motomat
  • bin/Linux/multimat
  • bin/Linux/narrow
  • bin/Linux/oligo_melt
  • bin/Linux/papssm
  • bin/Linux/prints2blocks
  • bin/Linux/pssmBL
  • bin/Linux/pssmdist
  • bin/Linux/rank_matrix
  • bin/Linux/retblock
  • bin/Linux/show_aligned_blocks
  • bin/Linux/uextract
  • bin/Sun_intel/LAMA
  • bin/Sun_intel/LAMA_search
  • bin/Sun_intel/addseqs
  • bin/Sun_intel/biassed_blocks_finder
  • bin/Sun_intel/blalign
  • bin/Sun_intel/blastdat
  • bin/Sun_intel/bldist
  • bin/Sun_intel/blimps
  • bin/Sun_intel/blk2mot
  • bin/Sun_intel/blk2pssm
  • bin/Sun_intel/blk2slx
  • bin/Sun_intel/blkprob
  • bin/Sun_intel/blksort
  • bin/Sun_intel/block_vis
  • bin/Sun_intel/blocks_search
  • bin/Sun_intel/blosum
  • bin/Sun_intel/blweight
  • bin/Sun_intel/cobbler
  • bin/Sun_intel/codehop
  • bin/Sun_intel/coduse
  • bin/Sun_intel/fastaseqs
  • bin/Sun_intel/find_biassed_blocks
  • bin/Sun_intel/format_block
  • bin/Sun_intel/getblock
  • bin/Sun_intel/getseq
  • bin/Sun_intel/htmlize-LAMA
  • bin/Sun_intel/htmlize-codehop
  • bin/Sun_intel/interpro
  • bin/Sun_intel/lisblk
  • bin/Sun_intel/mablock
  • bin/Sun_intel/makeblockmap
  • bin/Sun_intel/makelis
  • bin/Sun_intel/makelogob
  • bin/Sun_intel/matrix_logob
  • bin/Sun_intel/motifj
  • bin/Sun_intel/motomat
  • bin/Sun_intel/multimat
  • bin/Sun_intel/narrow
  • bin/Sun_intel/oligo_melt
  • bin/Sun_intel/papssm
  • bin/Sun_intel/prints2blocks
  • bin/Sun_intel/pssmBL
  • bin/Sun_intel/pssmdist
  • bin/Sun_intel/rank_matrix
  • bin/Sun_intel/retblock
  • bin/Sun_intel/show_aligned_blocks
  • bin/Sun_intel/uextract
  • bin/Sun_sparc/LAMA
  • bin/Sun_sparc/LAMA_search
  • bin/Sun_sparc/addseqs
  • bin/Sun_sparc/biassed_blocks_finder
  • bin/Sun_sparc/blalign
  • bin/Sun_sparc/blastdat
  • bin/Sun_sparc/bldist
  • bin/Sun_sparc/blimps
  • bin/Sun_sparc/blk2lis
  • bin/Sun_sparc/blk2mot
  • bin/Sun_sparc/blk2pssm
  • bin/Sun_sparc/blk2slx
  • bin/Sun_sparc/blkprob
  • bin/Sun_sparc/blksort
  • bin/Sun_sparc/block_vis
  • bin/Sun_sparc/blocks_search
  • bin/Sun_sparc/blosum
  • bin/Sun_sparc/blweight
  • bin/Sun_sparc/cobbler
  • bin/Sun_sparc/codehop
  • bin/Sun_sparc/coduse
  • bin/Sun_sparc/fastaseqs
  • bin/Sun_sparc/find_biassed_blocks
  • bin/Sun_sparc/format_block
  • bin/Sun_sparc/getblock
  • bin/Sun_sparc/getseq
  • bin/Sun_sparc/htmlize-LAMA
  • bin/Sun_sparc/htmlize-codehop
  • bin/Sun_sparc/interpro
  • bin/Sun_sparc/lisblk
  • bin/Sun_sparc/lislis
  • bin/Sun_sparc/mablock
  • bin/Sun_sparc/makeblockmap
  • bin/Sun_sparc/makelis
  • bin/Sun_sparc/makelogob
  • bin/Sun_sparc/matrix_logob
  • bin/Sun_sparc/motifj
  • bin/Sun_sparc/motmisc.o
  • bin/Sun_sparc/motomat
  • bin/Sun_sparc/multimat
  • bin/Sun_sparc/narrow
  • bin/Sun_sparc/oligo_melt
  • bin/Sun_sparc/papssm
  • bin/Sun_sparc/prints2blocks
  • bin/Sun_sparc/protxblk
  • bin/Sun_sparc/pssmBL
  • bin/Sun_sparc/pssmdist
  • bin/Sun_sparc/rank_matrix
  • bin/Sun_sparc/retblock
  • bin/Sun_sparc/show_aligned_blocks
  • bin/Sun_sparc/uextract
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/blimps.git
  • vcs-git https://anonscm.debian.org/git/debian-med/blimps.git

blimps-examples

• X duplicate-files
  • usr/share/doc/blimps-examples/examples/processor/distribution/fasta.in.seqs usr/share/doc/blimps-examples/examples/processor/distribution/stockholm.in.seqs
• X package-contains-no-arch-dependent-files

blimps-utils

• X duplicate-files
  • usr/share/doc/blimps-utils/html/biased_blocks.html usr/share/doc/blimps-utils/html/biassed_blocks.html
• I hardening-no-bindnow
  • usr/bin/fastaseqs
• W privacy-breach-generic
  • usr/share/doc/blimps-utils/html/thanks.html [<img src="http://www.nigms.nih.gov/nigms.nih.gov/images/banner_nigms.gif" height="45" width="300">] (http://www.nigms.nih.gov/nigms.nih.gov/images/banner_nigms.gif)
• W zero-byte-file-in-doc-directory
  • usr/share/doc/blimps-utils/html/bin/marks
  • usr/share/doc/blimps-utils/html/bin/wave

blimps-utils-dbgsym

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/b3/1fe833082cf677db5fb84acfdb8765e4ad9dcf.debug

libblimps3

• I hardening-no-bindnow
  • usr/lib/libblimps.so.3.0.0
• I no-symbols-control-file
  • usr/lib/libblimps.so.3.0.0
• X shlib-calls-exit
  • usr/lib/libblimps.so.3.0.0
• I spelling-error-in-binary
  • usr/lib/libblimps.so.3.0.0 nam name
  • usr/lib/libblimps.so.3.0.0 occured occurred
  • usr/lib/libblimps.so.3.0.0 outputing outputting
  • usr/lib/libblimps.so.3.0.0 retur return

libblimps3-dbgsym

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/d7/e047413df8095339461122e593b24b553cf656.debug

• P debian-watch-does-not-check-gpg-signature

bolt-lmm (2.3.2+dfsg-2+b1; main)

• I spelling-error-in-binary
  • usr/bin/bolt helpFull helpful

• I debian-rules-contains-unnecessary-get-orig-source-target
• I debian-rules-parses-dpkg-parsechangelog
  • (line 11)
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 130)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
  • (line 45)
• P package-uses-old-debhelper-compat-version
  • 9
• W spelling-error-in-patch-description
  • debian/patches/gcc-64bit.patch unfortunatly unfortunately
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/viewvc/debian-med/trunk/packages/bowtie/trunk/
  • vcs-svn svn://anonscm.debian.org/debian-med/trunk/packages/bowtie/trunk/
• I vcs-field-uses-insecure-uri
  • vcs-svn svn://anonscm.debian.org/debian-med/trunk/packages/bowtie/trunk/

bowtie-examples

• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/LGPL

• P debian-watch-does-not-check-gpg-signature
• I override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
  • (line 46)
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

bowtie

• O binary-without-manpage
  • usr/bin/bowtie-align-l
  • usr/bin/bowtie-align-l-debug
  • usr/bin/bowtie-align-s
  • usr/bin/bowtie-align-s-debug
  • usr/bin/bowtie-build-l
  • usr/bin/bowtie-build-l-debug
  • usr/bin/bowtie-build-s
  • usr/bin/bowtie-build-s-debug
  • usr/bin/bowtie-inspect-l
  • usr/bin/bowtie-inspect-l-debug
  • usr/bin/bowtie-inspect-s
  • usr/bin/bowtie-inspect-s-debug
• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)
• X duplicate-files
  • usr/share/doc/bowtie/tests/example1.out usr/share/doc/bowtie/tests/example3.out usr/share/doc/bowtie/tests/example8.out
  • usr/share/doc/bowtie/tests/example6.out usr/share/doc/bowtie/tests/example9.out

• W ancient-standards-version
  • 3.9.6 (released 2014-09-17) (current is 4.2.0)
• I debian-rules-contains-unnecessary-get-orig-source-target
• I debian-rules-parses-dpkg-parsechangelog
  • (line 3)
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 131)
  • debian/changelog (line 132)
  • debian/changelog (line 138)
  • debian/changelog (line 145)
  • debian/changelog (line 152)
  • debian/changelog (line 153)
  • debian/changelog (line 170)
  • debian/changelog (line 29)
  • debian/changelog (line 71)
  • debian/changelog (line 72)
  • debian/changelog (line 73)
  • debian/changelog (line 79)
  • debian/changelog (line 90)
  • debian/control (line 24)
  • debian/control (line 25)
  • debian/control (line 26)
  • debian/control (line 27)
  • debian/control (line 30)
  • debian/control (line 39)
  • debian/control (line 40)
  • debian/control (line 41)
  • debian/control (line 42)
  • debian/control (line 45)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 9
• W patch-file-present-but-not-mentioned-in-series
  • fix_makefile_machine_detection.patch
• W unnecessary-testsuite-autopkgtest-field
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/bowtie2.git
  • vcs-git git://anonscm.debian.org/debian-med/bowtie2.git
• I vcs-field-uses-insecure-uri
  • vcs-git git://anonscm.debian.org/debian-med/bowtie2.git

bowtie2-examples

• E wrong-path-for-interpreter
  • usr/share/doc/bowtie2/examples/scripts/debug_wrapper.pl (#!/usr/bin/env != /usr/bin/perl)

• P debian-watch-does-not-check-gpg-signature

bowtie2

• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)
• W privacy-breach-generic
  • usr/share/doc/bowtie2/manual.html [<script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js">] (//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js)
• E wrong-path-for-interpreter
  • usr/bin/bowtie2 (#!/usr/bin/env != /usr/bin/perl)

• P debian-watch-does-not-check-gpg-signature
• P package-uses-old-debhelper-compat-version
  • 10
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/boxshade.git
  • vcs-git https://anonscm.debian.org/git/debian-med/boxshade.git

boxshade

• X binary-file-built-without-LFS-support
  • usr/lib/boxshade/boxshade

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 61)
  • debian/rules (line 12)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing

bppphyview

• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
  • usr/share/common-licenses/GPL
• I extended-description-is-probably-too-short

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 143)
  • debian/changelog (line 38)
  • debian/changelog (line 44)
• I testsuite-autopkgtest-missing

bppsuite

• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
  • usr/share/common-licenses/GPL
• I hardening-no-fortify-functions
  • usr/bin/bppdist
  • usr/bin/bppdist
  • usr/bin/bppmixedlikelihoods
  • usr/bin/bppmixedlikelihoods
  • usr/bin/bpppopstats
  • usr/bin/bpppopstats
• I spelling-error-in-binary
  • usr/bin/bppalnscore occurence occurrence
  • usr/bin/bppalnscore occurence occurrence
  • usr/bin/bppancestor particularily particularly
  • usr/bin/bppancestor particularily particularly
  • usr/bin/bppmixedlikelihoods particularily particularly
  • usr/bin/bppmixedlikelihoods particularily particularly
  • usr/bin/bppml particularily particularly
  • usr/bin/bppml particularily particularly
  • usr/bin/bpppopstats ouptut output
  • usr/bin/bpppopstats ouptut output
  • usr/bin/bppseqgen begining beginning
  • usr/bin/bppseqgen begining beginning
  • usr/bin/bpptreedraw controler controller
  • usr/bin/bpptreedraw controler controller

bppsuite-examples

• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
• X duplicate-files
  • usr/share/doc/bppsuite-examples/examples/MaximumLikelihood/Nucleotides/Homogeneous/Ancestor.bpp usr/share/doc/bppsuite-examples/examples/MaximumLikelihood/Nucleotides/NonHomogeneousGeneral/Ancestor.bpp

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I out-of-date-standards-version
  • 4.1.4 (released 2018-04-05) (current is 4.2.0)
• P source-contains-empty-directory
  • bin/
  • lib/
• I testsuite-autopkgtest-missing

brig

• W bad-jar-name
  • usr/share/java/BRIG-0.95.jar
  • usr/share/java/BRIG-0.95.jar
• W binary-without-manpage
  • usr/bin/brig
  • usr/bin/brig
• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
  • usr/share/common-licenses/GPL

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 178)
  • debian/changelog (line 29)
  • debian/changelog (line 31)
  • debian/changelog (line 33)
  • debian/control (line 52)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/bwa.git
  • vcs-git https://anonscm.debian.org/git/debian-med/bwa.git

bwa

• I spelling-error-in-manpage
  • usr/share/man/man1/bwa.1.gz extentions extensions
  • usr/share/man/man1/bwa.1.gz occurence occurrence
  • usr/share/man/man1/bwa.1.gz openning opening
  • usr/share/man/man1/bwa.1.gz ouptut output
  • usr/share/man/man1/bwa.1.gz overriden overridden
• E wrong-path-for-interpreter
  • usr/share/bwa/qualfa2fq.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/bwa/xa2multi.pl (#!/usr/bin/env != /usr/bin/perl)

• I debian-rules-parses-dpkg-parsechangelog
  • (line 9)
• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 7)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I testsuite-autopkgtest-missing

cain

• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)
• I desktop-entry-lacks-keywords-entry
  • usr/share/applications/cain.desktop
• I package-contains-documentation-outside-usr-share-doc
  • usr/include/cain/loki/readme.txt

cain-examples

• I package-contains-documentation-outside-usr-share-doc
  • usr/share/cain/examples/cain/dsmts23/Readme.txt
  • usr/share/cain/examples/sbml/dsmts31/README.txt

• P debian-watch-does-not-check-gpg-signature
• P package-does-not-install-examples
  • sdk/libraries/qtpropertybrowser/examples/
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 2

libcamitk-dev

• X development-package-ships-elf-binary-in-path
  • usr/bin/camitk-cepgenerator
  • usr/bin/camitk-cepgenerator
  • usr/bin/camitk-testactions
  • usr/bin/camitk-testactions
  • usr/bin/camitk-testcomponents
  • usr/bin/camitk-testcomponents
  • usr/bin/camitk-wizard
  • usr/bin/camitk-wizard
• I hardening-no-fortify-functions
  • usr/bin/camitk-testcomponents
  • usr/bin/camitk-testcomponents
• I spelling-error-in-binary
  • usr/bin/camitk-wizard exemple example
  • usr/bin/camitk-wizard exemple example
  • usr/bin/camitk-wizard wether whether
  • usr/bin/camitk-wizard wether whether
• I unstripped-static-library
  • usr/lib/camitk-4.1/liblmlschema.a(Acceleration.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(AppliedTo.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(DirState.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(Direction.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(Force.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(Load.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(Loads.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(Pressure.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(Rotation.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(Transition.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(Translation.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(Units.cxx.o)
  • usr/lib/camitk-4.1/liblmlschema.a(ValueEvent.cxx.o)

libcamitk4

• I no-symbols-control-file
  • usr/lib/libcamitkcore.so.4.1.2
  • usr/lib/libcamitkcore.so.4.1.2
  • usr/lib/libmonitoring.so.4.1.2
  • usr/lib/libmonitoring.so.4.1.2
• O package-name-doesnt-match-sonames
  • libcamitkcore4 libmonitoring4
  • libcamitkcore4 libmonitoring4
• I spelling-error-in-binary
  • usr/lib/camitk-4.1/actions/libmml.so.4.1.2 Pres Press
  • usr/lib/camitk-4.1/components/libdicom.so.4.1.2 Serie Series
  • usr/lib/camitk-4.1/components/libdicom.so.4.1.2 Serie Series
  • usr/lib/libcamitkcore.so.4.1.2 Substract Subtract
  • usr/lib/libcamitkcore.so.4.1.2 Substract Subtract
  • usr/lib/libmonitoring.so.4.1.2 Pres Press
  • usr/lib/libmonitoring.so.4.1.2 ment meant

libcamitk4-data

• I duplicated-compressed-file
  • usr/share/camitk-4.1/testdata/BigEndianCompressed.img.gz

libqtpropertybrowser4

• I no-symbols-control-file
  • usr/lib/libqtpropertybrowser.so.4.1.2
  • usr/lib/libqtpropertybrowser.so.4.1.2

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 24)
  • debian/changelog (line 27)
  • debian/changelog (line 4)
  • debian/rules (line 18)
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing

libcamp0.8

• I no-symbols-control-file
  • usr/lib/i386-linux-gnu/libcamp.so.0.8.2
  • usr/lib/x86_64-linux-gnu/libcamp.so.0.8.2

• P debian-watch-does-not-check-gpg-signature
• I testsuite-autopkgtest-missing

canu

• I spelling-error-in-binary
  • usr/lib/canu/bin/alignGFA misformed malformed
  • usr/lib/canu/bin/bogart beacuse because
  • usr/lib/canu/bin/estimate-mer-threshold endianess endianness
  • usr/lib/canu/bin/existDB endianess endianness
  • usr/lib/canu/bin/existDB existance existence
  • usr/lib/canu/bin/gatekeeperCreate nam name
  • usr/lib/canu/bin/leaff endianess endianness
  • usr/lib/canu/bin/maskMers endianess endianness
  • usr/lib/canu/bin/merTrim endianess endianness
  • usr/lib/canu/bin/meryl endianess endianness
  • usr/lib/canu/bin/overlapInCore wHE when
  • usr/lib/canu/bin/overlapInCorePartition interally internally
  • usr/lib/canu/bin/positionDB endianess endianness
  • usr/lib/canu/bin/simple endianess endianness
  • usr/lib/canu/bin/simple-dump endianess endianness
  • usr/lib/canu/bin/splitReads ouput output
  • usr/lib/canu/bin/trimReads ouput output
• E wrong-path-for-interpreter
  • usr/lib/canu/bin/canu (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/canu/bin/trioCanu (#!/usr/bin/env != /usr/bin/perl)

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 10)
  • debian/changelog (line 12)
  • debian/changelog (line 25)
  • debian/changelog (line 31)
  • debian/changelog (line 64)
  • debian/changelog (line 71)
  • debian/changelog (line 77)
  • debian/rules (line 13)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I out-of-date-standards-version
  • 4.1.0 (released 2017-08-21) (current is 4.2.0)
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/cassiopee.git
  • vcs-git https://anonscm.debian.org/git/debian-med/cassiopee.git

libcassie-doc

• X duplicate-files
  • usr/share/doc/cassiopee/html/search/all_2.js usr/share/doc/cassiopee/html/search/variables_2.js
  • usr/share/doc/cassiopee/html/search/all_3.js usr/share/doc/cassiopee/html/search/functions_1.js
  • usr/share/doc/cassiopee/html/search/all_4.js usr/share/doc/cassiopee/html/search/functions_2.js
  • usr/share/doc/cassiopee/html/search/all_6.js usr/share/doc/cassiopee/html/search/functions_4.js
  • usr/share/doc/cassiopee/html/search/all_8.js usr/share/doc/cassiopee/html/search/variables_5.js
  • usr/share/doc/cassiopee/html/search/all_9.js usr/share/doc/cassiopee/html/search/functions_5.js
  • usr/share/doc/cassiopee/html/search/all_b.js usr/share/doc/cassiopee/html/search/functions_6.js

libcassie1v5

• I no-symbols-control-file
  • usr/lib/libcassie.so.1.0.0
  • usr/lib/libcassie.so.1.0.0
• I wrong-section-according-to-package-name
  • libcassie1v5 => libs
  • libcassie1v5 => libs

• I debian-rules-parses-dpkg-parsechangelog
  • (line 12)
  • (line 13)
• P debian-watch-does-not-check-gpg-signature
• I file-contains-fixme-placeholder
  • debian/rules:71 FIXME
• P file-contains-trailing-whitespace
  • debian/changelog (line 87)
  • debian/control (line 26)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I out-of-date-standards-version
  • 3.9.8 (released 2016-04-06) (current is 4.2.0)
• P package-uses-old-debhelper-compat-version
  • 9
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/cd-hit.git
  • vcs-git https://anonscm.debian.org/git/debian-med/cd-hit.git

cd-hit

• X binary-file-built-without-LFS-support
  • usr/lib/cd-hit/cd-hit
  • usr/lib/cd-hit/cd-hit-2d
  • usr/lib/cd-hit/cd-hit-454
  • usr/lib/cd-hit/cd-hit-div
  • usr/lib/cd-hit/cd-hit-est
  • usr/lib/cd-hit/cd-hit-est-2d
• W binary-without-manpage
  • usr/bin/cdhit
  • usr/bin/cdhit
  • usr/bin/cdhit-2d
  • usr/bin/cdhit-2d
  • usr/bin/cdhit-454
  • usr/bin/cdhit-454
  • usr/bin/cdhit-est
  • usr/bin/cdhit-est
  • usr/bin/cdhit-est-2d
  • usr/bin/cdhit-est-2d
  • usr/bin/clstr2tree
  • usr/bin/clstr2tree
  • usr/bin/clstr_merge
  • usr/bin/clstr_merge
  • usr/bin/clstr_merge_noorder
  • usr/bin/clstr_merge_noorder
  • usr/bin/clstr_reduce
  • usr/bin/clstr_reduce
  • usr/bin/clstr_renumber
  • usr/bin/clstr_renumber
  • usr/bin/clstr_rev
  • usr/bin/clstr_rev
  • usr/bin/clstr_sort_by
  • usr/bin/clstr_sort_by
  • usr/bin/clstr_sort_prot_by
  • usr/bin/clstr_sort_prot_by
  • usr/bin/make_multi_seq
  • usr/bin/make_multi_seq
• I spelling-error-in-binary
  • usr/lib/cd-hit/cd-hit-div writen written
  • usr/lib/cd-hit/cd-hit-div writen written
• I spelling-error-in-manpage
  • usr/share/man/man1/cd-hit-2d-para.1.gz requred required
  • usr/share/man/man1/cd-hit-2d-para.1.gz requred required
  • usr/share/man/man1/cd-hit-para.1.gz requred required
  • usr/share/man/man1/cd-hit-para.1.gz requred required

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 33)
  • debian/changelog (line 41)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• W spelling-error-in-patch-description
  • debian/patches/workaround-lintian-false-positive gramatically grammatically
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/cdbfasta.git
  • vcs-git https://anonscm.debian.org/git/debian-med/cdbfasta.git

cdbfasta

• I hardening-no-fortify-functions
  • usr/bin/cdbfasta
  • usr/bin/cdbfasta
  • usr/bin/cdbyank
  • usr/bin/cdbyank

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/centrifuge.git
  • vcs-git https://anonscm.debian.org/git/debian-med/centrifuge.git

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/centrifuge.git
  • vcs-git https://anonscm.debian.org/git/debian-med/centrifuge.git

centrifuge

• P copyright-refers-to-symlink-license
  • usr/share/common-licenses/GPL
• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)
• I hardening-no-fortify-functions
  • usr/lib/centrifuge/centrifuge-build-bin
  • usr/lib/centrifuge/centrifuge-class
  • usr/lib/centrifuge/centrifuge-inspect-bin
• I package-contains-documentation-outside-usr-share-doc
  • usr/lib/centrifuge/share/centrifuge/doc/README
• I possible-documentation-but-no-doc-base-registration
• W script-not-executable
  • usr/lib/centrifuge/share/centrifuge/doc/strip_markdown.pl
• E wrong-path-for-interpreter
  • usr/lib/centrifuge/centrifuge (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/centrifuge/centrifuge-BuildSharedSequence.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/centrifuge/centrifuge-RemoveEmptySequence.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/centrifuge/centrifuge-RemoveN.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/centrifuge/centrifuge-compress.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/centrifuge/centrifuge-kreport (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/centrifuge/centrifuge-sort-nt.pl (#!/usr/bin/env != /usr/bin/perl)
  • usr/lib/centrifuge/share/centrifuge/doc/strip_markdown.pl (#!/usr/bin/env != /usr/bin/perl)
• W zero-byte-file-in-doc-directory
  • usr/share/doc/centrifuge/html/manual.inc.html

• W build-depends-on-python-sphinx-only
• P debian-watch-does-not-check-gpg-signature
• I out-of-date-standards-version
  • 4.1.4 (released 2018-04-05) (current is 4.2.0)
• W python-foo-but-no-python3-foo
  • python-cfflib
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing

• P debian-watch-does-not-check-gpg-signature
• P insane-line-length-in-source-file
  • src/ca/ualberta/stothard/cgview/includes/overlib.js line length is 562 characters (>512)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• P source-contains-empty-directory
  • ca/ualberta/stothard/cgview/
  • lib/
• P source-contains-prebuilt-javascript-object
  • src/ca/ualberta/stothard/cgview/includes/overlib.js line length is 562 characters (>512)
• O source-is-missing
  • src/ca/ualberta/stothard/cgview/includes/overlib.js line length is 562 characters (>512)
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/cgview.git
  • vcs-git https://anonscm.debian.org/git/debian-med/cgview.git

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 9
• W patch-file-present-but-not-mentioned-in-series
  • charls_add_cmake_install_target.patch
  • charls_add_sharedlib_soname.patch
  • charls_fix_tests.patch
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/charls.git
  • vcs-git https://anonscm.debian.org/git/debian-med/charls.git

• P debian-watch-does-not-check-gpg-signature

• P debian-watch-does-not-check-gpg-signature

• P debian-watch-does-not-check-gpg-signature

libcifti0

• I hardening-no-fortify-functions
  • usr/lib/i386-linux-gnu/libCifti.so.1.5
  • usr/lib/x86_64-linux-gnu/libCifti.so.1.5
• I no-symbols-control-file
  • usr/lib/i386-linux-gnu/libCifti.so.1.5
  • usr/lib/x86_64-linux-gnu/libCifti.so.1.5

• P debian-watch-does-not-check-gpg-signature
• I override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
  • (line 11)
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/circlator.git
  • vcs-git https://anonscm.debian.org/git/debian-med/circlator.git

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://circos.ca/software/download
• P file-contains-trailing-whitespace
  • debian/changelog (line 114)
  • debian/changelog (line 120)
  • debian/changelog (line 126)
  • debian/changelog (line 45)
  • debian/changelog (line 84)
  • debian/changelog (line 90)
  • debian/rules (line 9)
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/circos.git
  • vcs-git https://anonscm.debian.org/git/debian-med/circos.git

circos

• X duplicate-files
  • usr/share/doc/circos/examples/data/heatmap.hs.mm.10e6.txt.gz usr/share/doc/circos/examples/data/heatmap.hs.rn.10e6.txt.gz
  • usr/share/doc/circos/examples/data/heatmap.hs.mm.20e6.txt.gz usr/share/doc/circos/examples/data/heatmap.hs.rn.20e6.txt.gz
  • usr/share/doc/circos/examples/data/heatmap.hs.mm.50e6.txt usr/share/doc/circos/examples/data/heatmap.hs.rn.50e6.txt
  • usr/share/doc/circos/examples/data/heatmap.hs.mm.5e6.txt.gz usr/share/doc/circos/examples/data/heatmap.hs.rn.5e6.txt.gz
  • usr/share/doc/circos/examples/data/karyotype/karyotype.arabidopsis.tair10.txt usr/share/doc/circos/examples/data/karyotype/karyotype.arabidopsis.txt
  • usr/share/doc/circos/examples/data/karyotype/karyotype.chimp.pt4.txt.gz usr/share/doc/circos/examples/data/karyotype/karyotype.chimp.txt.gz
  • usr/share/doc/circos/examples/data/karyotype/karyotype.drosophila.lowres.dm3.txt.gz usr/share/doc/circos/examples/data/karyotype/karyotype.drosophila.txt.gz
  • usr/share/doc/circos/examples/data/karyotype/karyotype.human.hg19.txt.gz usr/share/doc/circos/examples/data/karyotype/karyotype.human.txt.gz
  • usr/share/doc/circos/examples/data/karyotype/karyotype.mouse.mm10.txt.gz usr/share/doc/circos/examples/data/karyotype/karyotype.mouse.txt.gz
  • usr/share/doc/circos/examples/data/karyotype/karyotype.rat.rn4.txt.gz usr/share/doc/circos/examples/data/karyotype/karyotype.rat.txt.gz
  • usr/share/doc/circos/examples/data/karyotype/karyotype.rm.3.txt usr/share/doc/circos/examples/data/karyotype/karyotype.rm.txt
• W manpage-has-bad-whatis-entry
  • usr/share/man/man1/circos.1.gz
• I spelling-error-in-manpage
  • usr/share/man/man1/circos.1.gz overide override
  • usr/share/man/man1/circos.1.gz unuseable unusable
• E wrong-path-for-interpreter
  • etc/circos/makehuesteps (#!/usr/bin/env != /usr/bin/perl)
  • usr/bin/circos (#!/usr/bin/env != /usr/bin/perl)

fonts-circos-symbols

• I font-outside-font-dir
  • usr/share/circos/fonts/symbols/circossymbols.otf

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://circos.ca/software/download
• P file-contains-trailing-whitespace
  • debian/changelog (line 41)
  • debian/changelog (line 48)
  • debian/changelog (line 55)
  • debian/changelog (line 61)
  • debian/rules (line 3)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• P source-contains-empty-directory
  • tools/binlinks/doc/
  • tools/resample/etc/
• I testsuite-autopkgtest-missing
• X upstream-metadata-file-is-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/circos-tools.git
  • vcs-git https://anonscm.debian.org/git/debian-med/circos-tools.git

circos-tools

• I package-contains-documentation-outside-usr-share-doc
  • usr/share/circos/tools/clustal2link/README
  • usr/share/circos/tools/connectogram/README
  • usr/share/circos/tools/tableviewer/README
• I package-contains-empty-directory
  • usr/share/circos/tools/binlinks/doc/
  • usr/share/circos/tools/resample/etc/
• E wrong-path-for-interpreter
  • usr/share/circos/tools/binlinks/bin/binlinks (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/binlinks/data/toplinks (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/bundlelinks/bin/bundlelinks (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/calcdatarange/bin/calcdatarange (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/categoryviewer/bin/parse-category (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/categoryviewer/data/makedata (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/clustal2link/bin/clustal2link (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/colorinterpolate/bin/colorinterpolate (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/connectogram/parsemap (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/convertlinks/bin/convertlinks (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/filterlinks/bin/filterlinks (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/maketutorialimages/bin/make_tutorial_images (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/matrix/matrix (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/matrix/unmatrix (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/orderchr/bin/orderchr (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/randomdata/bin/randomdata (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/randomlinks/bin/randomlinks (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/resample/bin/resample (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/tableviewer/bin/make-conf (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/tableviewer/bin/make-table (#!/usr/bin/env != /usr/bin/perl)
  • usr/share/circos/tools/tableviewer/bin/parse-table (#!/usr/bin/env != /usr/bin/perl)

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://bioinformatics.hungry.com/clearcut/clearcut-([0-9.]+).tar.gz
• P file-contains-trailing-whitespace
  • debian/control (line 20)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/clearcut.git
  • vcs-git https://anonscm.debian.org/git/debian-med/clearcut.git

clearcut

• X binary-file-built-without-LFS-support
  • usr/bin/clearcut
• I hardening-no-bindnow
  • usr/bin/clearcut
  • usr/bin/clearcut
• I hardening-no-fortify-functions
  • usr/bin/clearcut
  • usr/bin/clearcut

clearcut-dbgsym

• W debug-file-with-no-debug-symbols
  • usr/lib/debug/.build-id/27/39b8faf2cf1b2e3f92a3d5bef9516958dc4b91.debug
  • usr/lib/debug/.build-id/61/a68f85b73b4ef89dfe30a0766b9df0a4099782.debug

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
• P file-contains-trailing-whitespace
  • debian/rules (line 27)
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/clonalframe.git
  • vcs-git https://anonscm.debian.org/git/debian-med/clonalframe.git

clonalframe

• X binary-file-built-without-LFS-support
  • usr/bin/ClonalFrame
• I hardening-no-fortify-functions
  • usr/bin/ClonalFrame
  • usr/bin/ClonalFrame

• P debian-watch-does-not-check-gpg-signature
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/clonalframeml.git
  • vcs-git https://anonscm.debian.org/git/debian-med/clonalframeml.git

clonalframeml

• I hardening-no-fortify-functions
  • usr/bin/ClonalFrameML
  • usr/bin/ClonalFrameML

• P debian-watch-does-not-check-gpg-signature
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/clonalorigin.git
  • vcs-git https://anonscm.debian.org/git/debian-med/clonalorigin.git

clonalorigin

• X binary-file-built-without-LFS-support
  • usr/bin/warg
• W binary-without-manpage
  • usr/bin/blocksplit
  • usr/bin/blocksplit
  • usr/bin/computeMedians
  • usr/bin/computeMedians
  • usr/bin/makeMauveWargFile
  • usr/bin/makeMauveWargFile
• I spelling-error-in-binary
  • usr/bin/warg lik link
  • usr/bin/warg lik link

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://www.clustal.org/omega/clustal-omega-(.*)\.tar\.gz
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

clustalo

• X binary-file-built-without-LFS-support
  • usr/bin/clustalo
• I spelling-error-in-binary
  • usr/bin/clustalo exceded exceeded
  • usr/bin/clustalo exceded exceeded
  • usr/bin/clustalo occured occurred
  • usr/bin/clustalo occured occurred

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://www.clustal.org/download/current/clustalw-([\.\d]*).tar.gz
• P file-contains-trailing-whitespace
  • debian/changelog (line 123)
  • debian/changelog (line 155)
  • debian/changelog (line 202)
  • debian/changelog (line 274)
  • debian/changelog (line 345)
  • debian/changelog (line 377)
  • debian/changelog (line 385)
  • debian/control (line 33)
  • debian/rules (line 19)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1

clustalw

• X binary-file-built-without-LFS-support
  • usr/bin/clustalw

• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://www.clustal.org/download/current/clustalx-([\.\d]*).tar.gz
• P file-contains-trailing-whitespace
  • debian/changelog (line 213)
  • debian/changelog (line 284)
  • debian/changelog (line 316)
  • debian/changelog (line 324)
• P package-uses-old-debhelper-compat-version
  • 9
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/clustalx.git
  • vcs-git https://anonscm.debian.org/git/debian-med/clustalx.git

clustalx

• X binary-file-built-without-LFS-support
  • usr/bin/clustalx
• I desktop-entry-lacks-keywords-entry
  • usr/share/applications/clustalx.desktop
  • usr/share/applications/clustalx.desktop
• I hardening-no-fortify-functions
  • usr/bin/clustalx
  • usr/bin/clustalx

• I debian-rules-contains-unnecessary-get-orig-source-target
• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm
• P file-contains-trailing-whitespace
  • debian/changelog (line 23)
  • debian/changelog (line 41)
  • debian/changelog (line 46)
  • debian/changelog (line 50)
  • debian/changelog (line 65)
  • debian/rules (line 23)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I missing-explanation-for-contrib-or-non-free-package
• P package-uses-old-debhelper-compat-version
  • 10
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/cluster3.git
  • vcs-git https://anonscm.debian.org/git/debian-med/cluster3.git

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 23)
  • debian/rules (line 43)
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I testsuite-autopkgtest-missing

cnvkit

• W binary-without-manpage
  • usr/bin/cnvkit-cnv_annotate
  • usr/bin/cnvkit-cnv_expression_correlate
  • usr/bin/cnvkit-cnv_updater
  • usr/bin/cnvkit-cnv_ztest
  • usr/bin/cnvkit-guess_baits
  • usr/bin/cnvkit-skg_convert
  • usr/bin/cnvkit-snpfilter.sh
  • usr/bin/snpfilter.sh
• W executable-not-elf-or-script
  • usr/bin/cnvkit-cnv_expression_correlate
• W manpage-has-errors-from-man
  • usr/share/man/man1/cnvkit.1.gz 8: warning [p 1, 1.7i]: cannot adjust line
• W script-with-language-extension
  • usr/bin/cnvkit-snpfilter.sh
  • usr/bin/snpfilter.sh
• I spelling-error-in-manpage
  • usr/share/man/man1/cnvkit-batch.1.gz excecutable executable
  • usr/share/man/man1/cnvkit-segment.1.gz excecutable executable

• O debian-watch-does-not-check-gpg-signature
• I out-of-date-standards-version
  • 4.1.4 (released 2018-04-05) (current is 4.2.0)
• P package-uses-deprecated-source-override-location
• I testsuite-autopkgtest-missing

codonw

• X binary-file-built-without-LFS-support
  • usr/bin/codonw
• I hardening-no-bindnow
  • usr/bin/codonw
  • usr/bin/codonw

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 5)
  • debian/changelog (line 6)
  • debian/changelog (line 80)
  • debian/rules (line 12)
  • debian/rules (line 28)
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/coils.git
  • vcs-git https://anonscm.debian.org/git/debian-med/coils.git

ncoils

• X binary-file-built-without-LFS-support
  • usr/bin/ncoils
• I hardening-no-fortify-functions
  • usr/bin/ncoils
  • usr/bin/ncoils

• P debian-watch-does-not-check-gpg-signature
• O debian-watch-file-should-mangle-version
  • line 3
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• P source-contains-empty-directory
  • bin/
  • lib/

concavity

• X binary-file-built-without-LFS-support
  • usr/bin/concavity

• P debian-watch-does-not-check-gpg-signature
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• X upstream-metadata-file-is-missing

• P debian-watch-does-not-check-gpg-signature
• P file-contains-trailing-whitespace
  • debian/changelog (line 20)
  • debian/changelog (line 23)
  • debian/rules (line 55)
• P package-uses-old-debhelper-compat-version
  • 10
• P unknown-runtime-tests-restriction
  • allow-stderr paragraph starting at line 1
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/conservation-code.git
  • vcs-git https://anonscm.debian.org/git/debian-med/conservation-code.git

conservation-code

• X dependency-on-python-version-marked-for-end-of-life
  • (Depends: python)

• W changelog-should-mention-nmu
• P debian-watch-does-not-check-gpg-signature
• I debian-watch-uses-insecure-uri
  • http://gforge.inria.fr/frs/?group_id=3008
• P insecure-copyright-format-uri
  • http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
• I out-of-date-standards-version
  • 3.9.8 (released 2016-04-06) (current is 4.2.0)
• P package-uses-old-debhelper-compat-version
  • 9
• W source-nmu-has-incorrect-version-number
  • 2.5.0+dfsg-2
• I testsuite-autopkgtest-missing
• W vcs-deprecated-in-debian-infrastructure
  • vcs-browser https://anonscm.debian.org/cgit/debian-med/crac.git
  • vcs-git https://anonscm.debian.org/git/debian-med/crac.git

crac

• W binary-without-manpage
  • usr/bin/crac-client
  • usr/bin/crac-index
• W manpage-has-bad-whatis-entry
  • usr/share/man/man1/crac.1.gz
• I spelling-error-in-binary
  • usr/bin/crac Erorr Error
  • usr/bin/crac alignement alignment
  • usr/bin/crac informations information
  • usr/bin/crac-index informations information
• I spelling-error-in-manpage
  • usr/share/man/man1/crac.1.gz alignement alignment
  • usr/share/man/man1/crac.1.gz differents different
  • usr/share/man/man1/crac.1.gz informations information
  • usr/share/man/man1/crac.1.gz informations information
  • usr/share/man/man1/crac.1.gz informations information
  • usr/share/man/man1/crac.1.gz softwares software