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

Andreas Tille gitlab at salsa.debian.org
Mon May 11 14:46:18 BST 2020



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


Commits:
22024d70 by Andreas Tille at 2020-05-11T13:46:13+00:00
automatic update

- - - - -


2 changed files:

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


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,117 +1,114 @@
-Last-Update: Mon, 11 May 2020 01:42:04 +0000
+Last-Update: Mon, 11 May 2020 13:42:03 +0000
 
  Source                        | Vote   |     Tasks                                           |                                 Tags                                 
 -------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk                         |    187 | {covid-19,imaging}                                  | 
+ dcmtk                         |    188 | {imaging,covid-19}                                  | 
  orthanc                       |     94 | {practice,imaging,covid-19}                         | 
- gdcm                          |     53 | {imaging-dev}                                       | 
- orthanc-wsi                   |     48 | {practice,covid-19,laboratory,imaging,oncology,his} | 
- dicom3tools                   |     35 | {imaging}                                           | 
+ gdcm                          |     52 | {imaging-dev}                                       | 
+ orthanc-wsi                   |     48 | {practice,covid-19,imaging,his,oncology,laboratory} | 
+ dicom3tools                   |     34 | {imaging}                                           | 
  dicomscope                    |     33 | {imaging}                                           | 
- htsjdk                        |     33 | {bio-dev}                                           | 
- gdcm                          |     27 | {imaging,covid-19}                                  | 
- dcm2niix                      |     23 | {imaging}                                           | 
+ htsjdk                        |     32 | {bio-dev}                                           | 
+ dcm2niix                      |     25 | {imaging}                                           | 
+ gdcm                          |     25 | {covid-19,imaging}                                  | 
  pixelmed                      |     20 | {imaging}                                           | 
- minc-tools                    |     18 | {imaging}                                           | 
  openslide                     |     18 | {imaging}                                           | 
  invesalius                    |     17 | {imaging}                                           | 
- plastimatch                   |     17 | {imaging}                                           | 
- king                          |     16 | {imaging,typesetting}                               | 
- gnumed-server                 |     15 | {practice,covid-19}                                 | 
+ minc-tools                    |     17 | {imaging}                                           | 
+ king                          |     16 | {typesetting,imaging}                               | 
+ plastimatch                   |     16 | {imaging}                                           | 
+ gnumed-server                 |     15 | {covid-19,practice}                                 | 
  ngs-sdk                       |     14 | {bio-dev}                                           | 
  vtk-dicom                     |     14 | {imaging}                                           | 
- biosig4c++                    |     13 | {physics,imaging}                                   | 
+ biosig4c++                    |     13 | {imaging,physics}                                   | 
+ gdcm                          |     13 | {imaging-dev}                                       | 
  insighttoolkit4               |     13 | {imaging-dev}                                       | 
  adun.app                      |     12 | {bio}                                               | 
- gdcm                          |     12 | {imaging-dev}                                       | 
- jebl2                         |     11 | {bio-dev}                                           | 
- obitools                      |     11 | {bio}                                               | 
  biojava-live                  |     10 | {bio-dev}                                           | 
+ jebl2                         |     10 | {bio-dev}                                           | 
+ obitools                      |     10 | {bio}                                               | 
+ orthanc-webviewer             |      9 | {imaging}                                           | 
+ librg-utils-perl              |      8 | {bio}                                               | 
  ngs-sdk                       |      8 | {bio-dev}                                           | 
- orthanc-webviewer             |      8 | {imaging}                                           | 
- tree-puzzle                   |      8 | {bio-phylogeny,cloud,bio}                           | 
+ orthanc-dicomweb              |      8 | {covid-19,imaging}                                  | 
+ tree-puzzle                   |      8 | {cloud,bio,bio-phylogeny}                           | 
  cgview                        |      7 | {bio}                                               | 
  ea-utils                      |      7 | {bio}                                               | 
- fastlink                      |      7 | {bio,cloud}                                         | 
+ fastlink                      |      7 | {cloud,bio}                                         | 
  gasic                         |      7 | {bio,cloud}                                         | 
- librg-utils-perl              |      7 | {bio}                                               | 
- mipe                          |      7 | {cloud,bio}                                         | 
- orthanc-dicomweb              |      7 | {covid-19,imaging}                                  | 
+ melting                       |      7 | {bio,cloud}                                         | 
  orthanc-mysql                 |      7 | {imaging}                                           | 
- salmon                        |      7 | {bio}                                               | 
  alter-sequence-alignment      |      6 | {bio}                                               | 
- ampliconnoise                 |      6 | {cloud,bio}                                         | 
  arden                         |      6 | {bio,cloud}                                         | 
- dazzdb                        |      6 | {bio}                                               | 
  indelible                     |      6 | {bio}                                               | 
- jaligner                      |      6 | {bio}                                               | 
  libminc                       |      6 | {imaging-dev}                                       | 
  libsbml                       |      6 | {bio-dev}                                           | 
  maqview                       |      6 | {bio}                                               | 
- melting                       |      6 | {bio,cloud}                                         | 
+ mipe                          |      6 | {bio,cloud}                                         | 
+ nutsqlite                     |      6 | {tools}                                             | 
+ orthanc-postgresql            |      6 | {imaging}                                           | 
  piler                         |      6 | {bio}                                               | 
- seer                          |      6 | {bio}                                               | 
- anfo                          |      5 | {cloud,bio}                                         | 
+ salmon                        |      6 | {bio}                                               | 
+ staden                        |      6 | {bio}                                               | 
+ ampliconnoise                 |      5 | {cloud,bio}                                         | 
+ anfo                          |      5 | {bio,cloud}                                         | 
  bart-view                     |      5 | {imaging}                                           | 
  beast-mcmc                    |      5 | {bio,bio-phylogeny}                                 | 
  biomaj3-cli                   |      5 | {cloud}                                             | 
  bio-rainbow                   |      5 | {bio}                                               | 
- bio-tradis                    |      5 | {bio-dev,bio}                                       | 
+ bio-tradis                    |      5 | {bio,bio-dev}                                       | 
  bppsuite                      |      5 | {bio}                                               | 
  brig                          |      5 | {bio}                                               | 
  cluster3                      |      5 | {bio}                                               | 
- codonw                        |      5 | {bio}                                               | 
+ dazzdb                        |      5 | {bio}                                               | 
  edtsurf                       |      5 | {bio}                                               | 
  embassy-domainatrix           |      5 | {cloud,bio}                                         | 
- embassy-domalign              |      5 | {cloud,bio}                                         | 
- fitgcp                        |      5 | {bio,cloud}                                         | 
+ embassy-domalign              |      5 | {bio,cloud}                                         | 
+ fitgcp                        |      5 | {cloud,bio}                                         | 
  freecontact                   |      5 | {bio,cloud}                                         | 
+ jaligner                      |      5 | {bio}                                               | 
  jellyfish1                    |      5 | {bio}                                               | 
  libgff                        |      5 | {bio-dev}                                           | 
- mhap                          |      5 | {bio-ngs,bio}                                       | 
  ncbi-seg                      |      5 | {bio}                                               | 
  norsp                         |      5 | {bio}                                               | 
- nutsqlite                     |      5 | {tools}                                             | 
- orthanc-postgresql            |      5 | {imaging}                                           | 
- phast                         |      5 | {bio}                                               | 
  psychopy                      |      5 | {psychology}                                        | 
  pymia                         |      5 | {imaging-dev}                                       | 
- sibsim4                       |      5 | {bio,cloud}                                         | 
+ seer                          |      5 | {bio}                                               | 
+ sibsim4                       |      5 | {cloud,bio}                                         | 
  sigma-align                   |      5 | {bio-phylogeny,cloud,bio}                           | 
- spread-phy                    |      5 | {bio,bio-phylogeny}                                 | 
  stacks                        |      5 | {bio}                                               | 
- staden                        |      5 | {bio}                                               | 
  transrate-tools               |      5 | {bio}                                               | 
  transtermhp                   |      5 | {bio}                                               | 
- zalign                        |      5 | {cloud,bio}                                         | 
  abacas                        |      4 | {bio,covid-19}                                      | 
  biomaj3-daemon                |      4 | {bio}                                               | 
  bitseq                        |      4 | {bio}                                               | 
  clonalorigin                  |      4 | {bio}                                               | 
- daligner                      |      4 | {bio,bio-ngs}                                       | 
+ codonw                        |      4 | {bio}                                               | 
+ daligner                      |      4 | {bio-ngs,bio}                                       | 
  ecopcr                        |      4 | {bio}                                               | 
+ elastix                       |      4 | {imaging}                                           | 
  embassy-domsearch             |      4 | {cloud,bio}                                         | 
- freebayes                     |      4 | {bio}                                               | 
  gatb-core                     |      4 | {bio}                                               | 
  harvest-tools                 |      4 | {bio}                                               | 
  ipig                          |      4 | {bio}                                               | 
- jmodeltest                    |      4 | {bio,bio-phylogeny}                                 | 
+ jmodeltest                    |      4 | {bio-phylogeny,bio}                                 | 
  king-probe                    |      4 | {bio}                                               | 
  libdivsufsort                 |      4 | {bio-dev}                                           | 
  libncl                        |      4 | {bio}                                               | 
  libpal-java                   |      4 | {bio-dev}                                           | 
- mapsembler2                   |      4 | {cloud,bio}                                         | 
+ mapsembler2                   |      4 | {bio,cloud}                                         | 
+ mhap                          |      4 | {bio-ngs,bio}                                       | 
  microbegps                    |      4 | {bio}                                               | 
  mrs                           |      4 | {bio}                                               | 
- neobio                        |      4 | {bio,cloud}                                         | 
+ neobio                        |      4 | {cloud,bio}                                         | 
  paml                          |      4 | {bio}                                               | 
- paraclu                       |      4 | {cloud,bio}                                         | 
+ paraclu                       |      4 | {bio,cloud}                                         | 
+ phast                         |      4 | {bio}                                               | 
  phybin                        |      4 | {bio}                                               | 
- phyutility                    |      4 | {cloud,bio}                                         | 
+ phyutility                    |      4 | {bio,cloud}                                         | 
  poretools                     |      4 | {bio}                                               | 
  predictprotein                |      4 | {bio}                                               | 
- prime-phylo                   |      4 | {bio,cloud}                                         | 
- probabel                      |      4 | {cloud,bio}                                         | 
+ probabel                      |      4 | {bio,cloud}                                         | 
  pscan-tfbs                    |      4 | {bio}                                               | 
  radiant                       |      4 | {bio}                                               | 
  rambo-k                       |      4 | {bio}                                               | 
@@ -122,39 +119,37 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  scythe                        |      4 | {bio}                                               | 
  seqtools                      |      4 | {bio}                                               | 
  sickle                        |      4 | {bio}                                               | 
+ spread-phy                    |      4 | {bio,bio-phylogeny}                                 | 
  squizz                        |      4 | {bio,cloud}                                         | 
  srf                           |      4 | {bio-dev}                                           | 
  treeview                      |      4 | {bio-phylogeny,bio}                                 | 
+ zalign                        |      4 | {bio,cloud}                                         | 
  assemblytics                  |      3 | {bio}                                               | 
  baitfisher                    |      3 | {bio}                                               | 
- bandage                       |      3 | {bio}                                               | 
  beads                         |      3 | {bio}                                               | 
  beast2-mcmc                   |      3 | {bio}                                               | 
  canu                          |      3 | {bio}                                               | 
- centrifuge                    |      3 | {bio}                                               | 
  clonalframeml                 |      3 | {covid-19,bio}                                      | 
- cufflinks                     |      3 | {cloud,bio}                                         | 
+ cufflinks                     |      3 | {bio,cloud}                                         | 
  dascrubber                    |      3 | {bio}                                               | 
- delly                         |      3 | {bio,covid-19}                                      | 
  dicompyler                    |      3 | {oncology}                                          | 
  dindel                        |      3 | {bio}                                               | 
- elastix                       |      3 | {imaging}                                           | 
  estscan                       |      3 | {bio}                                               | 
  fastml                        |      3 | {bio}                                               | 
+ freebayes                     |      3 | {bio}                                               | 
  fsm-lite                      |      3 | {bio}                                               | 
  kma                           |      3 | {bio}                                               | 
  lagan                         |      3 | {bio}                                               | 
  librdp-taxonomy-tree-java     |      3 | {bio-dev}                                           | 
- libsmithwaterman              |      3 | {bio}                                               | 
  mauve-aligner                 |      3 | {bio}                                               | 
  murasaki                      |      3 | {bio}                                               | 
- perm                          |      3 | {cloud,bio}                                         | 
+ perm                          |      3 | {bio,cloud}                                         | 
  placnet                       |      3 | {bio}                                               | 
+ prime-phylo                   |      3 | {bio,cloud}                                         | 
  prottest                      |      3 | {bio-phylogeny,bio}                                 | 
  pscan-chip                    |      3 | {bio}                                               | 
  qrisk2                        |      3 | {practice}                                          | 
  rdp-classifier                |      3 | {bio}                                               | 
- relion                        |      3 | {bio}                                               | 
  roguenarok                    |      3 | {bio}                                               | 
  runcircos-gui                 |      3 | {bio}                                               | 
  segemehl                      |      3 | {bio}                                               | 
@@ -164,8 +159,12 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  soapsnp                       |      3 | {bio}                                               | 
  sprai                         |      3 | {bio}                                               | 
  atropos                       |      2 | {bio}                                               | 
+ bandage                       |      2 | {bio}                                               | 
+ biosig4c++                    |      2 | {imaging-dev,physics}                               | 
  biosig4c++                    |      2 | {physics,imaging-dev}                               | 
- blasr                         |      2 | {bio-ngs,bio}                                       | 
+ blasr                         |      2 | {bio,bio-ngs}                                       | 
+ centrifuge                    |      2 | {bio}                                               | 
+ delly                         |      2 | {covid-19,bio}                                      | 
  dwgsim                        |      2 | {bio}                                               | 
  elph                          |      2 | {bio}                                               | 
  getdata                       |      2 | {bio}                                               | 
@@ -174,6 +173,7 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  kmerresistance                |      2 | {bio}                                               | 
  lamarc                        |      2 | {bio}                                               | 
  libctapimkt                   |      2 | {practice}                                          | 
+ libsmithwaterman              |      2 | {bio}                                               | 
  libvistaio                    |      2 | {imaging-dev}                                       | 
  logol                         |      2 | {bio}                                               | 
  maffilter                     |      2 | {bio}                                               | 
@@ -191,6 +191,7 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  python-scitrack               |      2 | {covid-19}                                          | 
  qcumber                       |      2 | {bio}                                               | 
  quorum                        |      2 | {bio}                                               | 
+ relion                        |      2 | {bio}                                               | 
  rtax                          |      2 | {cloud,bio}                                         | 
  samtools-legacy               |      2 | {bio-dev}                                           | 
  scrm                          |      2 | {bio}                                               | 
@@ -205,23 +206,23 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  velvetoptimiser               |      2 | {bio}                                               | 
  vsearch                       |      2 | {bio}                                               | 
  yaha                          |      2 | {bio}                                               | 
- biobambam2                    |      1 | {covid-19,bio-dev,bio}                              | 
+ biobambam2                    |      1 | {bio,covid-19,bio-dev}                              | 
  blimps                        |      1 | {bio}                                               | 
  ctn                           |      1 | {imaging-dev}                                       | 
- embassy-phylip                |      1 | {cloud,bio}                                         | 
+ embassy-phylip                |      1 | {bio,cloud}                                         | 
  emboss-explorer               |      1 | {bio}                                               | 
  emmax                         |      1 | {bio}                                               | 
  gatb-core                     |      1 | {bio-dev}                                           | 
  libbio-mage-utils-perl        |      1 | {bio-dev}                                           | 
  libchado-perl                 |      1 | {bio-dev}                                           | 
- libmaus2                      |      1 | {covid-19,bio-dev}                                  | 
+ libmaus2                      |      1 | {bio-dev,covid-19}                                  | 
  libmialm                      |      1 | {imaging-dev}                                       | 
  libsmithwaterman              |      1 | {bio-dev}                                           | 
  libxdf                        |      1 | {imaging-dev}                                       | 
- multiqc                       |      1 | {bio,covid-19}                                      | 
+ multiqc                       |      1 | {covid-19,bio}                                      | 
  ncbi-vdb                      |      1 | {bio-dev}                                           | 
  opensurgsim                   |      1 | {imaging-dev}                                       | 
- oscar                         |      1 | {data,tools,practice}                               | 
+ oscar                         |      1 | {practice,tools,data}                               | 
  pal2nal                       |      1 | {bio}                                               | 
  papyrus                       |      1 | {imaging-dev}                                       | 
  pbdagcon                      |      1 | {bio}                                               | 
@@ -234,15 +235,15 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  simpleitk                     |      1 | {imaging-dev}                                       | 
  skesa                         |      1 | {bio}                                               | 
  spaln                         |      1 | {covid-19,bio}                                      | 
- stringtie                     |      1 | {bio,covid-19}                                      | 
+ stringtie                     |      1 | {covid-19,bio}                                      | 
  sweed                         |      1 | {bio}                                               | 
  trace2dbest                   |      1 | {bio}                                               | 
- tree-puzzle                   |      1 | {cloud,bio,bio-phylogeny}                           | 
+ tree-puzzle                   |      1 | {bio,bio-phylogeny,cloud}                           | 
  tvc                           |      1 | {bio}                                               | 
- varscan                       |      1 | {bio,covid-19}                                      | 
+ varscan                       |      1 | {covid-19,bio}                                      | 
  volpack                       |      1 | {imaging-dev}                                       | 
  acedb                         |      0 | {bio,cloud}                                         | 
- augur                         |      0 | {covid-19,bio}                                      | 
+ augur                         |      0 | {bio,covid-19}                                      | 
  bambamc                       |      0 | {bio-dev}                                           | 
  bbmap                         |      0 | {covid-19}                                          | 
  biojava4-live                 |      0 | {bio-dev}                                           | 
@@ -251,7 +252,7 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  camp                          |      0 | {imaging-dev}                                       | 
  fis-gtm                       |      0 | {his}                                               | 
  freecontact                   |      0 | {bio-dev}                                           | 
- htscodecs                     |      0 | {covid-19,bio-dev}                                  | 
+ htscodecs                     |      0 | {bio-dev,covid-19}                                  | 
  libbigwig                     |      0 | {bio-dev}                                           | 
  libbiod                       |      0 | {bio-dev}                                           | 
  libbioparser-dev              |      0 | {bio-dev}                                           | 
@@ -266,7 +267,7 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  libgenome                     |      0 | {bio-dev}                                           | 
  libgkarrays                   |      0 | {bio-dev}                                           | 
  libhmsbeagle                  |      0 | {bio-dev}                                           | 
- libics                        |      0 | {imaging-dev,covid-19}                              | 
+ libics                        |      0 | {covid-19,imaging-dev}                              | 
  libjloda-java                 |      0 | {bio-dev}                                           | 
  libmems                       |      0 | {bio-dev}                                           | 
  libmuscle                     |      0 | {bio-dev}                                           | 
@@ -279,7 +280,7 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  metastudent-data              |      0 | {bio}                                               | 
  metastudent-data-2            |      0 | {bio}                                               | 
  miaviewit                     |      0 | {imaging-dev}                                       | 
- milib                         |      0 | {bio-dev,covid-19}                                  | 
+ milib                         |      0 | {covid-19,bio-dev}                                  | 
  mssstest                      |      0 | {tools}                                             | 
  murasaki                      |      0 | {bio}                                               | 
  opencfu                       |      0 | {laboratory}                                        | 
@@ -288,19 +289,19 @@ Last-Update: Mon, 11 May 2020 01:42:04 +0000
  pbseqlib                      |      0 | {bio-dev}                                           | 
  pilercr                       |      0 | {bio}                                               | 
  pycoqc                        |      0 | {covid-19,bio}                                      | 
- python-py2bit                 |      0 | {bio,bio-dev}                                       | 
+ python-py2bit                 |      0 | {bio-dev,bio}                                       | 
  relion                        |      0 | {bio-dev}                                           | 
  relion                        |      0 | {bio}                                               | 
  sambamba                      |      0 | {bio}                                               | 
  sbmltoolbox                   |      0 | {bio-dev}                                           | 
  seq-gen                       |      0 | {bio}                                               | 
  skewer                        |      0 | {bio}                                               | 
- smrtanalysis                  |      0 | {bio,covid-19}                                      | 
+ smrtanalysis                  |      0 | {covid-19,bio}                                      | 
  solvate                       |      0 | {bio}                                               | 
  thesias                       |      0 | {covid-19,bio}                                      | 
  varna                         |      0 | {bio}                                               | 
  vtk-dicom                     |      0 | {imaging-dev}                                       | 
  wtdbg2                        |      0 | {covid-19}                                          | 
  bustools                      |     -1 | {bio}                                               | 
-(329 rows)
+(330 rows)
 


=====================================
outdated_med-packages.txt
=====================================
The diff for this file was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/22024d70deae61f5e49af441ab2d24a87ba55359

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