Debian Package Tracker

general

source: bcbio (main)
version: 1.1.5-1
maintainer: Debian Med Packaging Team (archive) (DMD) (LowNMU)
uploaders: Steffen Moeller [DMD]
arch: all
std-ver: 4.3.0
VCS: Git (Browse, QA)

versions [more versions can be listed by madison] [old versions available from snapshot.debian.org]

[pool directory]

stable: 1.1.2-3
testing: 1.1.2-3
unstable: 1.1.5-1
NEW/unstable: 1.1.7-1

versioned links

1.1.2-3: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
1.1.5-1: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]

binaries

bcbio
bcbio-doc
python3-bcbio

action needed

A new upstream version is available: 1.1.7 high

A new upstream version 1.1.7 is available, you should consider packaging it.

Created: 2019-10-13 Last update: 2019-10-20 15:03

The package has not entered testing even though the delay is over normal

The package has not entered testing even though the 5-day delay is over. Check why.

Created: 2019-08-20 Last update: 2019-10-20 16:02

version in VCS is newer than in repository, is it time to upload? normal

vcswatch reports that this package seems to have a new changelog entry (version 1.1.7-1, distribution unstable) and new commits in its VCS. You should consider whether it's time to make an upload.

Here are the relevant commit messages:

commit c8f9eac5127fe3bdaa65fb13c779509c9756d863
Merge: 5ff0ae1 5429a03
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Oct 19 14:20:58 2019 +0200

    Merge branch 'master' of salsa.debian.org:med-team/bcbio

commit 5ff0ae1bda71d145b9bf35a93075fc37a901d839
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Oct 19 14:20:26 2019 +0200

    Added ref to conda

commit fa26f1975965ae230a8c0d5861aca90a8754382a
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Oct 19 14:13:27 2019 +0200

    Avoid lintian errors because of missing -x flags

commit 37c2bb77d12e684efaff6d00a5ad2af597ea5a74
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Oct 19 14:09:48 2019 +0200

    Directing bcbio to contrib

commit 1bfdb9f4fc73b24f67644ed0c6b73884554edec8
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Oct 19 14:04:23 2019 +0200

    Prepare for new upstream release.

commit dd4280b1fcd16341abf7a4806b9f29820a0648ff
Merge: 5c52226 b50e6f1
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Oct 19 14:02:04 2019 +0200

    Update upstream source from tag 'upstream/1.1.7'
    
    Update to upstream version '1.1.7'
    with Debian dir 687a566dcf2fc239ec1c51afd05eb2b1f6d5e08e

commit b50e6f19c716aa9563e93645a3c2cd48194c2820
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Oct 19 14:01:29 2019 +0200

    New upstream version 1.1.7

commit 5429a03ecebe644d6cfbb1dd30c6c3cd58f53fc4
Author: Andreas Tille <tille@debian.org>
Date:   Mon Sep 23 08:03:32 2019 +0200

    Fix typo

commit 6cba0d9e1b9766c4c8a6a71c37d491b1140c2e36
Author: Steffen Möller <moeller@debian.org>
Date:   Wed Sep 18 12:22:53 2019 +0000

    Added ref to conda

commit 1e5c05c402d8e7a25c7a71834491c3d016b24154
Author: Steffen Möller <moeller@debian.org>
Date:   Wed Sep 11 21:50:04 2019 +0000

    Update TODO - cthreadpool accepted, viennarna progressed

commit 5c522268ba0f1e338baea96f2d4181dc506f5795
Author: Steffen Möller <moeller@debian.org>
Date:   Mon Aug 26 16:03:08 2019 +0200

    MultiQC in new, -> contrib

commit fe5b70a2ae6238dd12d25d9d9e74c23f9b710398
Author: Steffen Möller <moeller@debian.org>
Date:   Fri Aug 23 17:47:06 2019 +0200

    Updates.
    
    python-dateutils no longer required by seqcluster

commit 88d4ecdcc9e3a0366c92d3155c78c282b8d22e3c
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Aug 22 08:22:59 2019 +0200

    pytutilib builds now

commit d92738f5b890fc501a7f83ca53e85c3fa0187f11
Author: Steffen Möller <moeller@debian.org>
Date:   Wed Aug 14 16:15:58 2019 +0200

    tophat-recondition was accepted

commit bb99c885b46d11323758cc061c761dfd74903099
Author: Steffen Möller <moeller@debian.org>
Date:   Wed Aug 14 16:12:13 2019 +0200

    More towards "it", not there, yet.

commit 8570c34d4c715a20a6e1aa53cbcce5012e287def
Author: Steffen Möller <moeller@debian.org>
Date:   Wed Aug 14 16:07:57 2019 +0200

    Two more transitioned to unstable

commit be386cdfcf010bd6c85ccc23538e9779889ddb82
Author: Steffen Möller <moeller@debian.org>
Date:   Tue Aug 13 14:43:30 2019 +0200

    apropos was accepted

commit d02adbfb352d3a3a957c0ab7bd04bba305440b5f
Author: Steffen Möller <moeller@debian.org>
Date:   Tue Aug 13 14:25:34 2019 +0200

    gffread is in the distribution

commit 7cee64ad75f23d4a1bd6c680098791c6708ea262
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Aug 3 16:34:01 2019 +0200

    Update, mention crash space

commit e07605b598378934e116c207dbcf43775177c1db
Author: Steffen Möller <moeller@debian.org>
Date:   Fri Aug 2 18:19:28 2019 +0200

    Updates while appearing on crash space

commit ccf718303ca042801f427714d9c480df2d79b69b
Author: Steffen Möller <moeller@debian.org>
Date:   Wed Jul 24 18:09:54 2019 +0200

    Uploaded ViennaRNA-dependency 'cthreadpool' which itself is a seqcluster dep

commit 8aef932733e9f717f77cf32c6df0b7b43203e590
Author: Steffen Möller <moeller@debian.org>
Date:   Fri Jul 19 14:59:33 2019 +0200

    Update for seqcluster and ViennaRNA

commit b5831fd60db7a3b4f3382c5e84c98af925253378
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Jul 11 06:59:59 2019 +0200

    python3-geneimpacts got accepted

commit 8949f2be90a5bacef52ea999e0e82a4b4ffe64fa
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Jul 11 06:51:39 2019 +0200

    wham accepted as wham-align in main

commit eb801de1f564c23dc962cad7d7b12e39c9ef83c5
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Jun 27 15:21:04 2019 +0200

    Scribl in new queue

commit ec6be7565d7ee33bca8bb1203e654049e4e1f2f8
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Jun 27 12:58:04 2019 +0200

    update seqcluster loses amcharts

commit 4b7d837dd941866a31f5e646b93820a1769c0ab6
Author: Andreas Tille <tille@debian.org>
Date:   Wed Jun 26 13:44:06 2019 +0200

    python3-pytz ----> packaged but under the name python3-tz

commit f778732eed48351d8285bc9a967871ec4370957c
Author: Andreas Tille <tille@debian.org>
Date:   Wed Jun 26 11:37:10 2019 +0200

    r-bioc-DEGreport - all pre-depends except edgeR are in new

commit 7db28bc2f1c5da96528aca6da281914501807da5
Author: Andreas Tille <tille@debian.org>
Date:   Wed Jun 26 09:55:10 2019 +0200

    r-bioc-isomiRs - (needs r-bioc-DEGreport) Andreas volunteering to package pre-depends as for r-bioc-DEGreport

commit 1b6ac36472207f7ca572d0e110c9b14d8819f5ee
Author: Andreas Tille <tille@debian.org>
Date:   Wed Jun 26 09:00:06 2019 +0200

    r-bioc-DEGreport - all pre-depends except edgeR are in new

commit 3cd75c44bdabd4e4150a7ebd75eaa83b839ad78b
Author: Andreas Tille <tille@debian.org>
Date:   Mon Jun 24 21:58:22 2019 +0200

    Andreas volunteers for official BioConductor packages

commit ce7a2658d980cc9af0179214c46870202294c69b
Author: Steffen Möller <moeller@debian.org>
Date:   Mon Jun 24 16:58:16 2019 +0200

    seqcluster keeps making trouble

commit b6021c6d96f2e15cc8f9751fc2506382b54ae6c6
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Jun 22 10:28:37 2019 +0200

    Steffen addresses ViennaRNA

commit 506471e5de07d60fcc77991bfe7eb9417068dacd
Author: Andreas Tille <tille@debian.org>
Date:   Thu Jun 20 14:12:54 2019 +0200

    Update pyomo and its dependency

commit 0cd543d3cc66fa1bc70dc90a9b82b894478c2eac
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Jun 20 12:13:05 2019 +0200

    seqcluster needs ViennaRNA

commit a785f732a7d94ddc1c350a36736216724fab29d3
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Jun 20 00:28:49 2019 +0200

    Wording, Steffen revisits seqcluster

commit 2e244db1de811660f590c8d9c3820819b7021d42
Author: Andreas Tille <tille@debian.org>
Date:   Sat Jun 15 07:45:49 2019 +0200

    Update TODO

commit 3975d052b2f40110b87c667bbc0fef2bf147d43b
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Jun 8 20:30:17 2019 +0200

    Reordering for importance

commit e32bd3ad1024ac7989732c7e547b63f0b0062d32
Author: Steffen Möller <moeller@debian.org>
Date:   Fri Jun 7 11:50:17 2019 +0200

    pizzly is in new queue, general updates

commit 86669a52ae53c3cf475c4b5d3dba6de8c6740836
Author: Steffen Möller <moeller@debian.org>
Date:   Tue Jun 4 00:58:10 2019 +0200

    Update on pizzly packaging

commit 86cdb51ceb37ac51305573d5382165c295f33541
Author: Steffen Möller <moeller@debian.org>
Date:   Mon Jun 3 18:25:32 2019 +0200

    Update of d/TODO, d/control

commit 22e2db16f9988b7a310700970b3faf7d6a0fca8b
Author: Steffen Möller <moeller@debian.org>
Date:   Sat Jun 1 17:35:43 2019 +0200

    Few updates on bcbio packaging and deps

commit ac98dabfa20bd51f15591ae4ca4911e0ae01c8ec
Author: Steffen Möller <moeller@debian.org>
Date:   Tue May 28 10:40:40 2019 +0200

    Updated TODO - will address geneimpacts

commit c27247126fe04bd8d18542d3204c6bbabc26fbf9
Author: Steffen Möller <moeller@debian.org>
Date:   Fri May 24 18:47:17 2019 +0200

    New upstream version.

commit 0df836e78b3829c02d3ff248b609bcc4135a82cc
Merge: a15afab 4016ff0
Author: Steffen Möller <moeller@debian.org>
Date:   Fri May 24 18:41:00 2019 +0200

    Update upstream source from tag 'upstream/1.1.5'
    
    Update to upstream version '1.1.5'
    with Debian dir a0525dd819b71479a92efedcb8f9b18da0656bd2

commit 4016ff058ea96bdb5999731d4add1cd2d9dcaf2d
Author: Steffen Möller <moeller@debian.org>
Date:   Fri May 24 18:40:28 2019 +0200

    New upstream version 1.1.5

commit a15afab377b43a4736374a9114f5aeecb5fa8499
Author: Steffen Möller <moeller@debian.org>
Date:   Fri May 24 18:38:31 2019 +0200

    Update of TODO, bits here and there

commit c96b034925066b9d42b618be9235267830e8f58b
Author: Andreas Tille <tille@debian.org>
Date:   Thu May 16 09:49:46 2019 +0200

    Recommends: umis (accepted to unstable)

commit 43c6515dbb528e1487da0b13658db62df9c0b451
Author: Andreas Tille <tille@debian.org>
Date:   Fri May 10 17:42:43 2019 +0200

    r-other-wasabi in new queue

commit 6d70b08dbdc68156880bf99086e0397f83039213
Author: Andreas Tille <tille@debian.org>
Date:   Sat Apr 27 07:56:17 2019 +0200

    Beginn of packaging is in Salsa

commit 92d1434e0ea8784ddc7c52475ef06236c2c9dfc8
Author: Andreas Tille <tille@debian.org>
Date:   Sat Apr 27 07:54:53 2019 +0200

    r-other-wasabi and oncufuse injected into Salsa (both not finished)

commit d8902ed2a6b6f74f65053aed76549b4a51587b75
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Apr 18 17:46:53 2019 +0200

    Updates to bcbio's TODO list

commit ea18afc57fbb62ae4265098af1bad5a101e97f6d
Author: Andreas Tille <tille@debian.org>
Date:   Thu Apr 18 12:47:23 2019 +0200

    Initial packaging skeleton at https://salsa.debian.org/med-team/gffread

commit f01b74ddb3edc28ff831904d42f135edfe1f03ae
Author: Andreas Tille <tille@debian.org>
Date:   Thu Apr 18 11:10:39 2019 +0200

    Qalimap packaging is in Git but some code depencency lost

commit 70ff04377ad64e9a7e134ec6b8eb90ca0a14d8f3
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Apr 18 01:03:21 2019 +0200

    build tests bring more dependencies

commit 224914aca1acac67c345d1ad2492850aa5686e86
Merge: bab609c 3be210d
Author: Steffen Möller <moeller@debian.org>
Date:   Wed Apr 17 20:56:46 2019 +0200

    Merge branch 'master' of salsa.debian.org:med-team/bcbio

commit bab609c608db094e5c2ad0cf43f2ff46e84271a8
Author: Steffen Möller <moeller@debian.org>
Date:   Wed Apr 17 20:56:35 2019 +0200

    Added Lumpy and Manta to TODO list for bcbio

commit 3be210d092009a7b0a6cf08af67b6b46b4dc0c76
Author: Andreas Tille <tille@debian.org>
Date:   Wed Apr 17 11:01:53 2019 +0200

    Rudimentary packaging for vcfanno pushed to Salsa

commit 94e816873954e01492d7ed42a4bb6554f9f9a36d
Merge: 189397a da67169
Author: Steffen Möller <moeller@debian.org>
Date:   Sun Apr 14 16:42:11 2019 +0200

    Merge branch 'master' of salsa.debian.org:med-team/bcbio

commit 189397abcc6f67c2df35292c483d3b263e53c77a
Author: Steffen Möller <moeller@debian.org>
Date:   Sun Apr 14 16:41:16 2019 +0200

    Uploaded .14 new upstream version
    
    Work on tests needs to be completed.

commit da6716984c75348e92aab043a53eca28ffcb4112
Author: Andreas Tille <tille@debian.org>
Date:   Sun Apr 14 06:26:42 2019 +0200

    https://github.com/indraniel/OptiType is just a fork of an old version of optitype

commit be590c259698f3968011b198d1c4ac119a97a9bb
Author: Andreas Tille <tille@debian.org>
Date:   Sat Apr 13 19:52:47 2019 +0200

    Update TODO

commit 5c3c0fc06a6babaddcf333af6a047d0f176c18e2
Author: Andreas Tille <tille@debian.org>
Date:   Sat Apr 13 10:49:10 2019 +0200

    Update TODO

commit 18ee7b3cfcbaf1b60f23f66210fa352b19890949
Author: Andreas Tille <tille@debian.org>
Date:   Sat Apr 13 07:47:59 2019 +0200

    Update TODO

commit bc10e237464aa8c6638c361fbdd08b5102a27425
Author: Andreas Tille <tille@debian.org>
Date:   Fri Apr 12 13:44:46 2019 +0200

    Rudimentary packaging for atropos

commit 73d036672fd93440ecdb387fa60e4d7c6dff25bc
Author: Andreas Tille <tille@debian.org>
Date:   Fri Apr 12 10:58:56 2019 +0200

    Rudimentary packaging of biobambam2

commit 55e88e34a586a6f6743cbf6b7eb2be5271c56069
Author: Andreas Tille <tille@debian.org>
Date:   Thu Apr 11 21:43:12 2019 +0200

    Update TODO

commit d7b53059f326dc800095abc65b7ad8728058ae75
Merge: 31c8df2 7e68a1c
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Apr 11 12:56:14 2019 +0200

    Update upstream source from tag 'upstream/1.1.4'
    
    Update to upstream version '1.1.4'
    with Debian dir 3a7e136e3d6bf67998442cc491be453fc411f09f

commit 7e68a1c2b85360ecaab4e1abd57faf298fbcb64b
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Apr 11 12:55:17 2019 +0200

    New upstream version 1.1.4

commit 31c8df20f037d292d8699d635affa0fae9be86de
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Apr 11 12:54:37 2019 +0200

    Updated control, TODO

commit 3a5bfc9a55a5a782d22f7ee5d498e616a6fbb55b
Author: Andreas Tille <tille@debian.org>
Date:   Thu Mar 21 16:31:35 2019 +0100

    Some metadata for kallisto

commit 47e02d0edfb02ca0e92db779d7743ac0905b26fd
Author: Andreas Tille <tille@debian.org>
Date:   Thu Mar 21 15:51:26 2019 +0100

    Add some URLs

commit e52b151133c3af226fb80401eb54497bfa1c4e87
Author: Steffen Möller <moeller@debian.org>
Date:   Thu Mar 21 14:01:44 2019 +0100

    Update for newly packaged StringTie

commit 7b98f981e77e80d109e7b14e4cacc2e544a480a1
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 01:16:54 2019 -0800

    Add recommendations discovered through testing
    
    and make a list of software that needs packaging

commit f188722ae030378ed2cdbff7d63f1484da185827
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 01:02:41 2019 -0800

    python3-bcbio: section is "python"

commit 63353604fecedcfef1690e3af5d6ee589a6a44ea
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 01:00:59 2019 -0800

    add pytest to enable running the tests

commit 0b8fbcfe450a32be6bf300faa6a07e26e4ccab0d
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 00:56:04 2019 -0800

    fixes a few spelling errors

commit b2ff8b839bb06eaf2f08ae27388c2c31fe25a3bd
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 00:48:02 2019 -0800

    add ${sphinxdoc:Built-Using} to -doc

commit 5d78e887138135274bbb4989af2f60c704934b38
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 00:45:24 2019 -0800

    debian/patches/python3.patch: removed, applied upstream

commit 8d2a4655c9667033197722fbe20102582fee6398
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 00:42:51 2019 -0800

    new upstream release

commit d44333413b59d7e3e2517665c89a168944750d8d
Merge: 5e2407d d9e2b21
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 00:41:40 2019 -0800

    Update upstream source from tag 'upstream/1.1.3'
    
    Update to upstream version '1.1.3'
    with Debian dir 66b4b7739104633ad67c5c4511f4d60bbbd50333

commit d9e2b213d053cd3071fde18f521f7130cd609da0
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 00:40:50 2019 -0800

    New upstream version 1.1.3

commit 5e2407d63b681f9fa7949220147f279132213c62
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Date:   Sun Feb 10 00:36:48 2019 -0800

    bcbio-doc: mark as "Multi-Arch: foreign"

Created: 2019-01-23 Last update: 2019-10-19 14:18

lintian reports 17 warnings normal

Lintian reports 17 warnings about this package. You should make the package lintian clean getting rid of them.

Created: 2019-08-13 Last update: 2019-08-13 04:35

Standards version of the package is outdated. wishlist

The package should be updated to follow the last version of Debian Policy (Standards-Version 4.4.1 instead of 4.3.0).

Created: 2019-07-08 Last update: 2019-09-29 23:41

testing migrations

excuses:
- Migrates after: wham-align
- Migration status for bcbio (1.1.2-3 to 1.1.5-1): BLOCKED: Rejected/violates migration policy/introduces a regression
- Issues preventing migration:
- Not built on buildd: arch all binaries uploaded by moeller, a new source-only upload is needed to allow migration
- Additional info:
- Piuparts tested OK - https://piuparts.debian.org/sid/source/b/bcbio.html
- 66 days old (needed 5 days)
- Not considered

news

[rss feed]

[2019-08-14] Accepted bcbio 1.1.5-1 (source all) into unstable (Steffen Moeller)
[2019-04-14] Accepted bcbio 1.1.4-1 (source all) into unstable (Steffen Moeller)
[2019-03-21] Accepted bcbio 1.1.3-1 (source all) into unstable (Michael R. Crusoe) (signed by: Steffen Moeller)
[2019-01-29] bcbio 1.1.2-3 MIGRATED to testing (Debian testing watch)
[2019-01-23] Accepted bcbio 1.1.2-1 (source all) into unstable, unstable (Steffen Moeller)
[2019-01-23] Accepted bcbio 1.1.2-3 (source all) into unstable, unstable (Steffen Moeller)
[2019-01-23] Accepted bcbio 1.1.2-2 (source all) into unstable, unstable (Steffen Moeller)

bugs [bug history graph]

all: 1
RC: 0
I&N: 1
M&W: 0
F&P: 0
patch: 0

links

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version: 1.1.5-1