[med-svn] [Git][med-team/community/helper-scripts][master] automatic update

Andreas Tille gitlab at salsa.debian.org
Fri Mar 6 13:45:07 GMT 2020



Andreas Tille pushed to branch master at Debian Med / community / helper-scripts


Commits:
f0bb75b8 by Andreas Tille at 2020-03-06T13:45:02+00:00
automatic update

- - - - -


2 changed files:

- debian-med-tests.txt
- outdated_med-packages.txt


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,52 +1,51 @@
-Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
+Last-Update: Fri, 06 Mar 2020 13:42:03 +0000
 
  Source                        | Vote   | Tasks                                      |                                 Tags                                 
 -------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------
- dcmtk                         |    175 | {imaging}                                  | 
- orthanc                       |     95 | {practice,imaging}                         | 
- gdcm                          |     45 | {imaging-dev}                              | 
+ dcmtk                         |    178 | {imaging}                                  | 
+ orthanc                       |     97 | {practice,imaging}                         | 
+ gdcm                          |     47 | {imaging-dev}                              | 
+ dcm2niix                      |     40 | {imaging}                                  | 
  orthanc-wsi                   |     38 | {oncology,laboratory,imaging,his,practice} | 
- dcm2niix                      |     37 | {imaging}                                  | 
- amide                         |     35 | {imaging}                                  | 
- dicomscope                    |     29 | {imaging}                                  | 
- dicom3tools                   |     26 | {imaging}                                  | 
+ amide                         |     37 | {imaging}                                  | 
+ dicomscope                    |     30 | {imaging}                                  | 
+ dicom3tools                   |     29 | {imaging}                                  | 
  medicalterms                  |     26 | {tools}                                    | 
- htsjdk                        |     24 | {bio-dev}                                  | 
- gdcm                          |     18 | {imaging}                                  | 
- gnumed-server                 |     17 | {practice}                                 | 
+ htsjdk                        |     25 | {bio-dev}                                  | 
+ gdcm                          |     20 | {imaging}                                  | 
+ gnumed-server                 |     18 | {practice}                                 | 
+ pixelmed                      |     16 | {imaging}                                  | 
  invesalius                    |     15 | {imaging}                                  | 
- pixelmed                      |     14 | {imaging}                                  | 
- ngs-sdk                       |     13 | {bio-dev}                                  | 
+ king                          |     14 | {imaging,typesetting}                      | 
+ ngs-sdk                       |     14 | {bio-dev}                                  | 
+ minc-tools                    |     13 | {imaging}                                  | 
  adun.app                      |     12 | {bio}                                      | 
- minc-tools                    |     12 | {imaging}                                  | 
  insighttoolkit4               |     11 | {imaging-dev}                              | 
- king                          |     11 | {imaging,typesetting}                      | 
  vtk-dicom                     |     11 | {imaging}                                  | 
- gdcm                          |     10 | {imaging-dev}                              | 
+ biosig4c++                    |     10 | {imaging,physics}                          | 
  jebl2                         |     10 | {bio-dev}                                  | 
- mia                           |      9 | {imaging}                                  | 
- tree-puzzle                   |      9 | {bio,bio-phylogeny,cloud}                  | 
- biosig4c++                    |      8 | {imaging,physics}                          | 
+ mia                           |     10 | {imaging}                                  | 
+ openslide                     |     10 | {imaging}                                  | 
+ tree-puzzle                   |     10 | {bio,bio-phylogeny,cloud}                  | 
+ gdcm                          |      9 | {imaging-dev}                              | 
+ plastimatch                   |      9 | {imaging}                                  | 
  librg-utils-perl              |      8 | {bio}                                      | 
+ ncbi-entrez-direct            |      8 | {bio}                                      | 
  ngs-sdk                       |      8 | {bio-dev}                                  | 
- openslide                     |      8 | {imaging}                                  | 
- plastimatch                   |      8 | {imaging}                                  | 
- psychopy                      |      8 | {psychology}                               | 
  biojava-live                  |      7 | {bio-dev}                                  | 
+ dicompyler                    |      7 | {oncology}                                 | 
  fastlink                      |      7 | {cloud,bio}                                | 
  melting                       |      7 | {bio,cloud}                                | 
- ncbi-entrez-direct            |      7 | {bio}                                      | 
  obitools                      |      7 | {bio}                                      | 
+ psychopy                      |      7 | {psychology}                               | 
+ sortmerna                     |      7 | {bio}                                      | 
+ staden                        |      7 | {bio}                                      | 
  arden                         |      6 | {cloud,bio}                                | 
- dicompyler                    |      6 | {oncology}                                 | 
+ cgview                        |      6 | {bio}                                      | 
  maqview                       |      6 | {bio}                                      | 
  mipe                          |      6 | {bio,cloud}                                | 
  ncbi-seg                      |      6 | {bio}                                      | 
  norsp                         |      6 | {bio}                                      | 
- sortmerna                     |      6 | {bio}                                      | 
- staden                        |      6 | {bio}                                      | 
- cgview                        |      5 | {bio}                                      | 
- cluster3                      |      5 | {bio}                                      | 
  estscan                       |      5 | {bio}                                      | 
  gasic                         |      5 | {cloud,bio}                                | 
  idba                          |      5 | {bio,cloud}                                | 
@@ -66,7 +65,9 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  anfo                          |      4 | {cloud,bio}                                | 
  biomaj3-cli                   |      4 | {cloud}                                    | 
  bio-tradis                    |      4 | {bio-dev,bio}                              | 
+ cluster3                      |      4 | {bio}                                      | 
  dazzdb                        |      4 | {bio}                                      | 
+ diamond-aligner               |      4 | {bio}                                      | 
  ea-utils                      |      4 | {bio}                                      | 
  ecopcr                        |      4 | {bio}                                      | 
  edtsurf                       |      4 | {bio}                                      | 
@@ -79,6 +80,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  ipig                          |      4 | {bio}                                      | 
  jellyfish1                    |      4 | {bio}                                      | 
  libdivsufsort                 |      4 | {bio-dev}                                  | 
+ libsbml                       |      4 | {bio-dev}                                  | 
  mapsembler2                   |      4 | {bio,cloud}                                | 
  mauve-aligner                 |      4 | {bio}                                      | 
  paml                          |      4 | {bio}                                      | 
@@ -90,6 +92,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  proalign                      |      4 | {bio-phylogeny,bio}                        | 
  probabel                      |      4 | {bio,cloud}                                | 
  relion                        |      4 | {bio}                                      | 
+ salmon                        |      4 | {bio}                                      | 
  seqtools                      |      4 | {bio}                                      | 
  squizz                        |      4 | {bio,cloud}                                | 
  tracetuner                    |      4 | {bio}                                      | 
@@ -106,7 +109,6 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  canu                          |      3 | {bio}                                      | 
  codonw                        |      3 | {bio}                                      | 
  delly                         |      3 | {bio}                                      | 
- diamond-aligner               |      3 | {bio}                                      | 
  elph                          |      3 | {bio}                                      | 
  gatb-core                     |      3 | {bio}                                      | 
  getdata                       |      3 | {bio}                                      | 
@@ -115,7 +117,6 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  libgff                        |      3 | {bio-dev}                                  | 
  libminc                       |      3 | {imaging-dev}                              | 
  libncl                        |      3 | {bio}                                      | 
- libsbml                       |      3 | {bio-dev}                                  | 
  lucy                          |      3 | {bio}                                      | 
  mhap                          |      3 | {bio-ngs,bio}                              | 
  microbegps                    |      3 | {bio}                                      | 
@@ -129,12 +130,10 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  prime-phylo                   |      3 | {cloud,bio}                                | 
  pscan-chip                    |      3 | {bio}                                      | 
  pscan-tfbs                    |      3 | {bio}                                      | 
- qrisk2                        |      3 | {practice}                                 | 
  quorum                        |      3 | {bio}                                      | 
  rdp-alignment                 |      3 | {bio}                                      | 
  rdp-readseq                   |      3 | {bio}                                      | 
  saint                         |      3 | {bio}                                      | 
- salmon                        |      3 | {bio}                                      | 
  seer                          |      3 | {bio}                                      | 
  segemehl                      |      3 | {bio}                                      | 
  seqsero                       |      3 | {bio}                                      | 
@@ -144,6 +143,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  yaha                          |      3 | {bio}                                      | 
  abacas                        |      2 | {bio}                                      | 
  acedb                         |      2 | {bio,cloud}                                | 
+ alter-sequence-alignment      |      2 | {bio}                                      | 
  andi                          |      2 | {bio}                                      | 
  baitfisher                    |      2 | {bio}                                      | 
  bart-view                     |      2 | {imaging}                                  | 
@@ -155,6 +155,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  blasr                         |      2 | {bio-ngs,bio}                              | 
  centrifuge                    |      2 | {bio}                                      | 
  clonalorigin                  |      2 | {bio}                                      | 
+ ctn                           |      2 | {imaging-dev}                              | 
  cufflinks                     |      2 | {bio,cloud}                                | 
  daligner                      |      2 | {bio-ngs,bio}                              | 
  dascrubber                    |      2 | {bio}                                      | 
@@ -165,6 +166,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  hinge                         |      2 | {bio}                                      | 
  igor                          |      2 | {bio}                                      | 
  lamarc                        |      2 | {bio}                                      | 
+ libpal-java                   |      2 | {bio-dev}                                  | 
  librdp-taxonomy-tree-java     |      2 | {bio-dev}                                  | 
  maffilter                     |      2 | {bio}                                      | 
  mptp                          |      2 | {bio}                                      | 
@@ -175,7 +177,9 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  phipack                       |      2 | {bio}                                      | 
  phybin                        |      2 | {bio}                                      | 
  poretools                     |      2 | {bio}                                      | 
+ prottest                      |      2 | {bio-phylogeny,bio}                        | 
  qcumber                       |      2 | {bio}                                      | 
+ qrisk2                        |      2 | {practice}                                 | 
  rambo-k                       |      2 | {bio}                                      | 
  rampler                       |      2 | {bio}                                      | 
  rdp-classifier                |      2 | {bio}                                      | 
@@ -195,11 +199,9 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  trace2dbest                   |      2 | {bio}                                      | 
  transrate-tools               |      2 | {bio}                                      | 
  tvc                           |      2 | {bio}                                      | 
- alter-sequence-alignment      |      1 | {bio}                                      | 
  biosig4c++                    |      1 | {physics,imaging-dev}                      | 
  blimps                        |      1 | {bio}                                      | 
  clonalframeml                 |      1 | {bio}                                      | 
- ctn                           |      1 | {imaging-dev}                              | 
  edflib                        |      1 | {imaging-dev}                              | 
  elastix                       |      1 | {imaging}                                  | 
  embassy-phylip                |      1 | {cloud,bio}                                | 
@@ -213,20 +215,20 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  libbio-mage-utils-perl        |      1 | {bio-dev}                                  | 
  libctapimkt                   |      1 | {practice}                                 | 
  libhmsbeagle                  |      1 | {bio-dev}                                  | 
- libpal-java                   |      1 | {bio-dev}                                  | 
- libsmithwaterman              |      1 | {bio}                                      | 
  libsmithwaterman              |      1 | {bio-dev}                                  | 
+ libsmithwaterman              |      1 | {bio}                                      | 
  libvistaio                    |      1 | {imaging-dev}                              | 
  logol                         |      1 | {bio}                                      | 
  maxflow                       |      1 | {imaging-dev}                              | 
  medicalterms                  |      1 | {tools}                                    | 
  mencal                        |      1 | {tools}                                    | 
  metaphlan2                    |      1 | {bio}                                      | 
+ opencfu                       |      1 | {laboratory}                               | 
  orthanc-mysql                 |      1 | {imaging}                                  | 
  orthanc-postgresql            |      1 | {imaging}                                  | 
  pal2nal                       |      1 | {bio}                                      | 
+ papyrus                       |      1 | {imaging-dev}                              | 
  pilercr                       |      1 | {bio}                                      | 
- prottest                      |      1 | {bio-phylogeny,bio}                        | 
  python-tinyalign              |      1 | {bio-dev,bio}                              | 
  roguenarok                    |      1 | {bio}                                      | 
  samtools-legacy               |      1 | {bio-dev}                                  | 
@@ -249,6 +251,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  tree-puzzle                   |      1 | {cloud,bio-phylogeny,bio}                  | 
  varscan                       |      1 | {bio}                                      | 
  volpack                       |      1 | {imaging-dev}                              | 
+ vtk-dicom                     |      1 | {imaging-dev}                              | 
  atropos                       |      0 | {bio}                                      | 
  bambamc                       |      0 | {bio-dev}                                  | 
  biobambam2                    |      0 | {bio,bio-dev}                              | 
@@ -296,11 +299,9 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  murasaki                      |      0 | {bio}                                      | 
  ncbi-vdb                      |      0 | {bio-dev}                                  | 
  ngs-sdk                       |      0 | {bio-dev}                                  | 
- opencfu                       |      0 | {laboratory}                               | 
  opensurgsim                   |      0 | {imaging-dev}                              | 
  orthanc-imagej                |      0 | {imaging}                                  | 
  oscar                         |      0 | {tools,data,practice}                      | 
- papyrus                       |      0 | {imaging-dev}                              | 
  pbcopper                      |      0 | {bio-dev}                                  | 
  pbseqlib                      |      0 | {bio-dev}                                  | 
  python-deeptools              |      0 | {bio-dev,bio}                              | 
@@ -318,6 +319,5 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  spaln                         |      0 | {bio}                                      | 
  trim-galore                   |      0 | {bio}                                      | 
  varna                         |      0 | {bio}                                      | 
- vtk-dicom                     |      0 | {imaging-dev}                              | 
 (347 rows)
 


=====================================
outdated_med-packages.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
+Last-Update: Fri, 06 Mar 2020 13:42:03 +0000
 
  source                        |             version             |        upstream_version         |                       uploaders                                             | Last uploader         |     Last uploaded      
 -------------------------------+---------------------------------+---------------------------------+-----------------------------------------------------------------------------+-----------------------+------------------------
@@ -14,7 +14,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  biomaj3-core                  | 3.0.19                          | 3.0.22                          | Olivier Sallou                                                              | Olivier Sallou        | 2019-11-12 11:20:23+00
  biomaj3-download              | 3.1.0                           | 3.1.2                           | Olivier Sallou                                                              | Olivier Sallou        | 2019-11-12 13:19:24+00
  biomaj3-process               | 3.0.15                          | 3.0.16                          | Olivier Sallou                                                              | Olivier Sallou        | 2019-11-12 11:20:38+00
- biosig4c++                    | 1.9.5                           | 2.0.1                           | Michael Hanke,Yaroslav Halchenko                                            | Andreas Tille         | 2020-03-02 08:38:37+00
+ biosig4c++                    | 1.9.5                           | 2.0.2                           | Michael Hanke,Yaroslav Halchenko                                            | Andreas Tille         | 2020-03-02 08:38:37+00
  bowtie2                       | 2.3.5.1                         | 2.4.1                           | Alexandre Mestiashvili,Andreas Tille                                        | Michael R. Crusoe     | 2019-12-19 16:34:16+00
  charls                        | 2.0.0                           | 2.1.0                           | Andreas Tille                                                               | Andreas Tille         | 2019-01-10 20:10:56+00
  cwltool                       | 2.0.20200224214940              | 2.0.20200303141624              | Michael R. Crusoe                                                           | Michael R. Crusoe     | 2020-02-26 12:07:54+00
@@ -26,7 +26,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  fis-gtm                       | 6.3-007                         | 6.3-010                         | Amul Shah,Andreas Tille                                                     | Amul Shah             | 2019-02-28 14:12:19+00
  gatb-core                     | 1.4.1+git20191209.9398f28       | 1.4.1+git20200118.1dc23ff       | Andreas Tille,Nadiya Sitdykova                                              | Michael R. Crusoe     | 2020-02-17 14:52:30+00
  gdcm                          | 3.0.4                           | 3.0.5                           | Gert Wollny,Sébastien Jodogne,Steve M. Robbins                             | Gert Wollny           | 2019-11-07 11:49:02+00
- hdmf                          | 1.5.4                           | 1.6.0                           | Yaroslav Halchenko                                                          | Yaroslav Halchenko    | 2020-02-03 03:01:25+00
+ hdmf                          | 1.5.4                           | 1.6.1                           | Yaroslav Halchenko                                                          | Yaroslav Halchenko    | 2020-02-03 03:01:25+00
  htsjdk                        | 2.18.2                          | 2.21.2                          | Andreas Tille,Charles Plessy,Olivier Sallou,Vincent Danjean                 | Andreas Tille         | 2019-03-01 22:19:40+00
  hyphy                         | 2.5.1                           | 2.5.5                           | Andreas Tille                                                               | Andreas Tille         | 2020-01-07 21:19:50+00
  igdiscover                    | 0.11                            | 0.12.2                          | Steffen Moeller                                                             | Andreas Tille         | 2019-09-06 07:04:02+00
@@ -50,6 +50,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  mothur                        | 1.42.1                          | 1.43.0                          | Andreas Tille,Steffen Moeller,Tomasz Buchert                                | Andreas Tille         | 2019-08-01 19:09:05+00
  mummer                        | 3.23                            | 4.0.0~beta2                     | Andreas Tille,Charles Plessy,Steffen Moeller                                | Andreas Tille         | 2018-06-11 07:19:31+00
  ncbi-blast+                   | 2.9.0                           | 2.10.0                          | Aaron M. Ucko,Andreas Tille,Olivier Sallou                                  | Aaron M. Ucko         | 2020-02-17 01:50:53+00
+ ncbi-entrez-direct            | 12.0.20190816                   | 13.5.20200304                   | Aaron M. Ucko                                                               | Aaron M. Ucko         | 2020-02-03 03:53:53+00
  ncbi-vdb                      | 2.10.3                          | 2.10.4                          | Andreas Tille                                                               | Andreas Tille         | 2020-02-24 21:12:17+00
  ngs-sdk                       | 2.10.2                          | 2.10.4                          | Andreas Tille,Olivier Sallou,Vincent Danjean                                | Michael R. Crusoe     | 2020-02-17 15:36:45+00
  pbcopper                      | 1.3.0                           | 1.4.0                           | Andreas Tille                                                               | Andreas Tille         | 2020-01-29 08:51:15+00
@@ -67,6 +68,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  python-colormap               | 1.0.2                           | 1.0.3                           | Andreas Tille                                                               | Andreas Tille         | 2019-12-06 16:51:43+00
  python-pbcommand              | 1.1.1+git20191122.ec024c3       | 1.1.1+git20200227.663a4d9       | Andreas Tille                                                               | Andreas Tille         | 2019-12-19 08:42:03+00
  python-pymummer               | 0.10.3                          | 0.11.0                          | Afif Elghraoui                                                              | Andreas Tille         | 2019-01-07 09:06:07+00
+ python-schema-salad           | 5.0.20200220195218              | 5.0.20200302192450              | Michael R. Crusoe                                                           | Michael R. Crusoe     | 2020-02-27 19:19:53+00
  python-treetime               | 0.7.1                           | 0.7.4                           | Andreas Tille                                                               | Steffen Moeller       | 2020-01-18 20:52:48+00
  q2cli                         | 2019.10.0                       | 2020.2.0                        | Liubov Chuprikova                                                           | Liubov Chuprikova     | 2019-12-16 10:20:08+00
  q2-cutadapt                   | 2019.10.0                       | 2020.2.0                        | Liubov Chuprikova                                                           | Liubov Chuprikova     | 2020-01-26 07:34:32+00
@@ -85,13 +87,14 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  simka                         | 1.5.1                           | 1.5.2                           | Shayan Doust                                                                | Andreas Tille         | 2020-01-12 18:49:47+00
  simpleitk                     | 1.0.1                           | 1.2.0                           | Ghislain Antony Vaillant                                                    | Andreas Tille         | 2019-01-30 10:06:08+00
  spades                        | 3.13.1                          | 3.14.0                          | Alexandre Mestiashvili,Andreas Tille,Michael R. Crusoe,Sascha Steinbiss     | Andreas Tille         | 2019-11-22 10:05:04+00
+ spoa                          | 3.0.1                           | 3.0.2                           | Andreas Tille                                                               | Andreas Tille         | 2019-09-16 11:53:05+00
  sra-sdk                       | 2.9.3                           | 2.10.4                          | Andreas Tille,Charles Plessy                                                | Steffen Moeller       | 2018-10-23 20:40:02+00
  sumatra                       | 1.0.31                          | 1.0.34                          | Andreas Tille,Tim Booth                                                     | Andreas Tille         | 2018-10-16 10:06:33+00
  t-coffee                      | 12.00.7fb08c2                   | 13.41.0.28bdc39                 | Andreas Tille,Steffen Moeller                                               | Andreas Tille         | 2019-02-15 07:57:10+00
  unanimity                     | 3.3.0                           | 4.2.0                           | Afif Elghraoui,Andreas Tille                                                | Adrian Bunk           | 2019-02-06 07:34:42+00
  vsearch                       | 2.14.1                          | 2.14.2                          | Andreas Tille,Tim Booth                                                     | Andreas Tille         | 2019-12-17 10:07:09+00
  xmedcon                       | 0.16.1                          | 0.16.2                          | Andreas Tille,Roland Marcus Rutschmann                                      | Andreas Tille         | 2019-01-25 18:23:59+00
-(89 rows)
+(92 rows)
 
 
  source                        |   id   | severity  |                                                                                                                                                                                                                           title                                                                                                                                                                                                                           
@@ -237,6 +240,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  prokka                        | 924128 | normal    | prokka: creates world writable directory tree /var/lib/prokka/*
  psychopy                      | 730810 | normal    | psychopy: Movie support suboptimal
  psychopy                      | 829424 | normal    | psychopy: ioHub uses inappropriate PID file location
+ psychopy                      | 937330 | normal    | psychopy: Python2 removal in sid/bullseye
  psychopy                      | 953052 | important | psychopy: python2 dependencies
  psychopy                      | 953053 | important | psychopy: missing python3 dependencies
  pynast                        | 937488 | normal    | pynast: Python2 removal in sid/bullseye
@@ -290,5 +294,5 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
  xmedcon                       | 671828 | normal    | xmedcon: Cannot open file with YBR photometric interpretation
  xmedcon                       | 779707 | normal    | Errors when reading dicomdir file: "No images found" / "Loading: DICM Error reading file"
  xmedcon                       | 924017 | normal    | desktop entry
-(194 rows)
+(195 rows)
 



View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/f0bb75b897d46feb37b50d8d9a718a27af38f546

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