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mmseqs2_9-d36de+ds-2_amd64.changes (click to toggle)
Format:1.8
Date:Thu, 25 Jul 2019 03:38:36 +0100
Source:mmseqs2
Binary:mmseqs2 mmseqs2-dbgsym mmseqs2-examples
Architecture:source amd64 all
Version:9-d36de+ds-2
Distribution:unstable
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Shayan Doust <hello@shayandoust.me>
Description:
mmseqs2    - ultra fast and sensitive protein search and clustering
mmseqs2-examples - optional resources for the mmseqs2 package
Changes:
mmseqs2 (9-d36de+ds-2) unstable; urgency=medium

  * Fixed changelog
  * Patch to fix the matrix serialization test
  * Forgot to deallocate within serialization patch
  * Fix test_bestalphabet binary. Now works. This is used within autopkgtest
  * Patch to fix test_alignmentperformance I have excluded this as it takes a
    *very* long time to perform and probably isn't worth it. Probably should be
    used alongside a profiler
  * Patch test_dbreader and include this in the unit test
  * Patch dbreaderserialization test and include in unit test
  * Patch to fix test_dbreaderzstd and include it in the unit test
  * Patch to fix test_indextable
  * This package is only 64 bit, set it as that
  * Append to copyright more entries that were missed out
  * Detect and write more copyright entries using decopy
  * Add more entries to the copyright file
  * Delete some unnecessary lib files and outputs These are used during build
    and serve no purpose to the end users
  * libbz2-dev as a new dependency as mmseqs2 accepts *.bz inputs
  * Copyright edit and changelog append
  * Forgot to set environmental variable
Files:
95bbce9c2b64cb153b923fdec1007e66 2210 science optional mmseqs2_9-d36de+ds-2.dsc
de6c73cdc70e3475daa303c06b72d730 6549700 science optional mmseqs2_9-d36de+ds-2.debian.tar.xz
2705ffcac8a15beefce4bd798c12af48 41526204 debug optional mmseqs2-dbgsym_9-d36de+ds-2_amd64.deb
f075de0e8d6ed222c2c3f92546da0144 6785924 science optional mmseqs2-examples_9-d36de+ds-2_all.deb
d83c3975f351dfdabda8426e651a9be3 7951 science optional mmseqs2_9-d36de+ds-2_amd64.buildinfo
96f5b4dfae257954ab540a769ba6bfc9 5207636 science optional mmseqs2_9-d36de+ds-2_amd64.deb
mmseqs2_9-d36de+ds-2.dsc (click to toggle)
Format:3.0 (quilt)
Source:mmseqs2
Binary:mmseqs2, mmseqs2-examples
Architecture:any-amd64 any-ppc64 any-ia64 arm64 mips64el alpha sparc64 all
Version:9-d36de+ds-2
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Shayan Doust <hello@shayandoust.me>
Homepage:https://github.com/soedinglab/MMseqs2
Standards-Version:4.4.0
Vcs-Browser:https://salsa.debian.org/med-team/mmseqs2
Vcs-Git:https://salsa.debian.org/med-team/mmseqs2.git
Testsuite:autopkgtest
Build-Depends:debhelper (>=12~), cmake, libgzstream-dev, libzstd-dev, zlib1g-dev, libbz2-dev
Package-List:mmseqs2 deb science optional arch=any-amd64,any-ppc64,any-ia64,arm64,mips64el,alpha,sparc64 mmseqs2-examples deb science optional arch=all
Files:
af4532d9e528e6533685018588dbce41 4276540 mmseqs2_9-d36de+ds.orig.tar.xz
de6c73cdc70e3475daa303c06b72d730 6549700 mmseqs2_9-d36de+ds-2.debian.tar.xz
lintian 2.16.0~bpo9+1 check for mmseqs2_9-d36de+ds-2.dsc (click to toggle)
README.source for mmseqs2_9-d36de+ds-2.dsc (click to toggle)
No README.source in this package
control file for mmseqs2_9-d36de+ds-2_amd64.deb (click to toggle)
Package:mmseqs2
Version:9-d36de+ds-2
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:21431
Depends:libbz2-1.0, libc6 (>=2.27), libgcc1 (>=1:3.0), libgomp1 (>=4.9), libgzstream0 (>=1.5+dfsg), libstdc++6 (>=5.2), libzstd1 (>=1.3.8), zlib1g (>=1:1.1.4)
Section:science
Priority:optional
Homepage:https://github.com/soedinglab/MMseqs2
Description:
ultra fast and sensitive protein search and clustering
 MMseqs2 (Many-against-Many sequence searching) is a software suite to
 search and cluster huge proteins/nucleotide sequence sets. MMseqs2 is
 open source GPL-licensed software implemented in C++ for Linux, MacOS,
 and (as beta version, via cygwin) Windows. The software is designed to
 run on multiple cores and servers and exhibits very good scalability.
 MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it
 achieves almost the same sensitivity. It can perform profile searches
 with the same sensitivity as PSI-BLAST at over 400 times its speed.
lintian 2.16.0~bpo9+1 check for mmseqs2_9-d36de+ds-2_amd64.deb (click to toggle)
contents of mmseqs2_9-d36de+ds-2_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2019-07-25 02:38 ./
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/bin/
-rwxr-xr-x root/root   2952072 2019-07-25 02:38 ./usr/bin/mmseqs
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/lib/
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/lib/mmseqs2/
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/lib/mmseqs2/test/
-rw-r--r-- root/root        48 2019-07-25 02:38 ./usr/lib/mmseqs2/test/dataGap
-rw-r--r-- root/root        53 2019-07-25 02:38 ./usr/lib/mmseqs2/test/dataGap.index
-rw-r--r-- root/root        30 2019-07-25 02:38 ./usr/lib/mmseqs2/test/dataLinear
-rw-r--r-- root/root        40 2019-07-25 02:38 ./usr/lib/mmseqs2/test/dataLinear.index
-rwxr-xr-x root/root    780808 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_alignment
-rwxr-xr-x root/root    748040 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_alignmentperformance
-rwxr-xr-x root/root    743944 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_alignmenttraceback
-rwxr-xr-x root/root    596472 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_alp
-rwxr-xr-x root/root    772616 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_backtracetranslator
-rwxr-xr-x root/root    600344 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_bestalphabet
-rwxr-xr-x root/root    432408 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_compositionbias
-rwxr-xr-x root/root    100592 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_counting
-rwxr-xr-x root/root    260336 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_dbreader
-rwxr-xr-x root/root    256240 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_dbreaderindexserialization
-rwxr-xr-x root/root    317680 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_dbreaderzstd
-rwxr-xr-x root/root    469272 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_diagonalscoring
-rwxr-xr-x root/root    448792 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_diagonalscoringperformance
-rwxr-xr-x root/root    665880 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_indextable
-rwxr-xr-x root/root    456984 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_kmergenerator
-rwxr-xr-x root/root    620944 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_kmernucl
-rwxr-xr-x root/root    432408 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_kmerscore
-rwxr-xr-x root/root    768520 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_ksw2
-rwxr-xr-x root/root     18592 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_kwaymerge
-rwxr-xr-x root/root    805384 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_multiplealignment
-rwxr-xr-x root/root    752136 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_profilealignment
-rwxr-xr-x root/root    875016 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_profilestates
-rwxr-xr-x root/root    875016 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_pssm
-rwxr-xr-x root/root    805384 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_pssmprune
-rwxr-xr-x root/root    411928 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_reducematrix
-rwxr-xr-x root/root    411928 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_scorematrixserialization
-rwxr-xr-x root/root    436504 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_sequenceindex
-rwxr-xr-x root/root    444696 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_tantan
-rwxr-xr-x root/root    157936 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_taxonomy
-rwxr-xr-x root/root     39144 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_tinyexpr
-rwxr-xr-x root/root    108904 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_translate
-rwxr-xr-x root/root    100592 2019-07-25 02:38 ./usr/lib/mmseqs2/test/test_util
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/share/
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/share/doc/
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/share/doc/mmseqs2/
-rw-r--r-- root/root      4795 2019-07-20 19:23 ./usr/share/doc/mmseqs2/README.md.gz
-rw-r--r-- root/root       684 2019-07-25 02:38 ./usr/share/doc/mmseqs2/changelog.Debian.gz
-rw-r--r-- root/root     54706 2019-07-25 02:38 ./usr/share/doc/mmseqs2/copyright
-rw-r--r-- root/root   3171441 2019-07-20 19:24 ./usr/share/doc/mmseqs2/userguide.pdf.gz
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/share/man/
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/share/man/man1/
-rw-r--r-- root/root      3355 2019-07-25 02:38 ./usr/share/man/man1/mmseqs.1.gz
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/share/mmseqs2/
-rwxr-xr-x root/root       444 2019-07-20 19:23 ./usr/share/mmseqs2/bash-completion.sh
control file for mmseqs2-dbgsym_9-d36de+ds-2_amd64.deb (click to toggle)
Package:mmseqs2-dbgsym
Source:mmseqs2
Version:9-d36de+ds-2
Auto-Built-Package:debug-symbols
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:43483
Depends:mmseqs2 (=9-d36de+ds-2)
Section:debug
Priority:optional
Description:
debug symbols for mmseqs2
Build-Ids:0bc2c6c12ab01320e6a07a33d9dfc34a2416f862 0dc93cb0ed88dce90fb7f09c2a72e1bb19900864 10c32ef609c2b56efd1cade3292a496df6f6c05c 12a5c56f186c86d54607b28a199c8bddb81b39ac 153cca3c18a2e07738d05016d217120f9e5b4239 1fe7f6f246767b0bceeae2b794297e04175e79f2 24ede0dab375cf92fe2e0452736e7eda717db10c 28d288f2edd41e2206868fc09314276dc303f77b 2ea5526b6791836c0388b4a2d1733b853f1276bf 3a75f85e54d99e48c036567211df808c3c64bbac 47809580bf42676a65be93c81d1908acedecacb5 483152398d8a548a92cc2216ba617c322e08c038 61c586bf00a94c70463ed233326622b21da1226a 6bc1c87425ea5125fbdc4a780800a8b3b05c906c 75e51d58af42bce09581a34683b09ad86da37f17 779d677700cc22e4348f4e6999d1a2048b207986 7c3bcbc246d6ba5432124edc885ac362419657c8 7ed789b34f493f05272975e19b3f50d8fe66fb0c 89220caa220417fafa5dc8e707695ffbe5b32b7f 8a6bdd027b68ea03e904f5f741592bc0d52292ce 9596dac8baf29fce0eea1ca9b69d12725720184a a3fcef82605c5124aec51847c28e22099128a463 adee3f40bbbdb145d7f5343e97665bf6504bf9fc be7dae85585ffdb45f6c11eff71671d93d7d32d5 c2f96e4c03700073402935fb0ed0343ee8a72f58 c73dcd9d56c1584e6826a1e8a0b0e8cae5659597 c9077800ccce851f39aad635586138efd4d9671d c9a0592a17f9cf045e6033d593fa53d177fa87bd d471946f8a6c6047705e851e534629914d50d842 d65fb39159a1154b2872fc907bb3c138a2d2ece9 dcf488456dec7e82b69759a4459c6337153fc92d e590ce25c7a87096cc05f6b2ecdab21c079fec68 fa62afdac3646d05a099d14ae5915e864dae081c
lintian 2.16.0~bpo9+1 check for mmseqs2-dbgsym_9-d36de+ds-2_amd64.deb (click to toggle)
contents of mmseqs2-dbgsym_9-d36de+ds-2_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2019-07-25 02:38 ./
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/lib/
drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/lib/debug/
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drwxr-xr-x root/root         0 2019-07-25 02:38 ./usr/lib/debug/.dwz/
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-rw-r--r-- root/root    878248 2019-07-25 02:38 ./usr/lib/debug/.dwz/x86_64-linux-gnu/mmseqs2.debug
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lrwxrwxrwx root/root         0 2019-07-25 02:38 ./usr/share/doc/mmseqs2-dbgsym -> mmseqs2
control file for mmseqs2-examples_9-d36de+ds-2_all.deb (click to toggle)
Package:mmseqs2-examples
Source:mmseqs2
Version:9-d36de+ds-2
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:6814
Recommends:mmseqs2
Section:science
Priority:optional
Homepage:https://github.com/soedinglab/MMseqs2
Description:
optional resources for the mmseqs2 package
 MMseqs2 (Many-against-Many sequence searching) is a software suite to
 search and cluster huge proteins/nucleotide sequence sets. MMseqs2 is
 open source GPL-licensed software implemented in C++ for Linux, MacOS,
 and (as beta version, via cygwim) Windows. The software is designed to
 run on multiple cores and servers and exhibits very good scalability.
 MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it
 achieves almost the same sensitivity. It can perform profile searches
 with the same sensitivity as PSI-BLAST at over 400 times its speed.
lintian 2.16.0~bpo9+1 check for mmseqs2-examples_9-d36de+ds-2_all.deb (click to toggle)
contents of mmseqs2-examples_9-d36de+ds-2_all.deb (click to toggle)
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Timestamp: 12.08.2019 / 14:02:50 (UTC)