Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
a0573b0f by Andreas Tille at 2020-04-01T13:44:22+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,47 +1,47 @@
-Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
+Last-Update: Wed, 01 Apr 2020 13:42:04 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk | 165 | {covid-19,imaging} |
- orthanc | 94 | {imaging,practice,covid-19} |
- gdcm | 46 | {imaging-dev} |
- orthanc-wsi | 40 | {oncology,his,imaging,practice,covid-19,laboratory} |
- htsjdk | 33 | {bio-dev} |
- amide | 32 | {imaging} |
+ dcmtk | 166 | {covid-19,imaging} |
+ orthanc | 95 | {covid-19,practice,imaging} |
+ gdcm | 45 | {imaging-dev} |
+ orthanc-wsi | 40 | {practice,covid-19,laboratory,his,oncology,imaging} |
+ htsjdk | 32 | {bio-dev} |
+ amide | 30 | {imaging} |
dcm2niix | 27 | {imaging} |
- dicomscope | 26 | {imaging} |
+ dicomscope | 24 | {imaging} |
dicom3tools | 23 | {imaging} |
- gdcm | 19 | {imaging,covid-19} |
- gnumed-server | 19 | {covid-19,practice} |
+ gdcm | 19 | {covid-19,imaging} |
+ gnumed-server | 18 | {practice,covid-19} |
minc-tools | 17 | {imaging} |
ngs-sdk | 17 | {bio-dev} |
- pixelmed | 17 | {imaging} |
+ pixelmed | 16 | {imaging} |
ncbi-entrez-direct | 14 | {bio} |
openslide | 14 | {imaging} |
- vtk-dicom | 14 | {imaging} |
biojava-live | 13 | {bio-dev} |
insighttoolkit4 | 13 | {imaging-dev} |
invesalius | 13 | {imaging} |
king | 13 | {typesetting,imaging} |
+ vtk-dicom | 13 | {imaging} |
+ mia | 12 | {imaging} |
cgview | 11 | {bio} |
ea-utils | 11 | {bio} |
- mia | 11 | {imaging} |
psychopy | 11 | {psychology} |
adun.app | 10 | {bio} |
diamond-aligner | 10 | {covid-19,bio} |
jebl2 | 10 | {bio-dev} |
king-probe | 10 | {bio} |
+ ngs-sdk | 10 | {bio-dev} |
radiant | 10 | {bio} |
staden | 10 | {bio} |
dazzdb | 9 | {bio} |
- ngs-sdk | 9 | {bio-dev} |
obitools | 9 | {bio} |
plastimatch | 9 | {imaging} |
pscan-tfbs | 9 | {bio} |
- tree-puzzle | 9 | {bio,bio-phylogeny,cloud} |
- biosig4c++ | 8 | {physics,imaging} |
+ tree-puzzle | 9 | {bio-phylogeny,cloud,bio} |
+ biosig4c++ | 8 | {imaging,physics} |
bppsuite | 8 | {bio} |
- fastlink | 8 | {bio,cloud} |
+ fastlink | 8 | {cloud,bio} |
gdcm | 8 | {imaging-dev} |
hunspell-en-med | 8 | {tools} |
librg-utils-perl | 8 | {bio} |
@@ -50,17 +50,19 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
phast | 8 | {bio} |
prime-phylo | 8 | {cloud,bio} |
seqsero | 8 | {bio} |
- sigma-align | 8 | {cloud,bio-phylogeny,bio} |
+ sigma-align | 8 | {bio,cloud,bio-phylogeny} |
abacas | 7 | {bio} |
- ampliconnoise | 7 | {bio,cloud} |
- anfo | 7 | {cloud,bio} |
- arden | 7 | {bio,cloud} |
+ ampliconnoise | 7 | {cloud,bio} |
+ anfo | 7 | {bio,cloud} |
+ arden | 7 | {cloud,bio} |
biomaj3-cli | 7 | {cloud} |
daligner | 7 | {bio-ngs,bio} |
ecopcr | 7 | {bio} |
embassy-domainatrix | 7 | {bio,cloud} |
embassy-domsearch | 7 | {bio,cloud} |
+ fitgcp | 7 | {cloud,bio} |
freecontact | 7 | {bio,cloud} |
+ gasic | 7 | {cloud,bio} |
jaligner | 7 | {bio} |
maqview | 7 | {bio} |
melting | 7 | {bio,cloud} |
@@ -70,24 +72,23 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
phyutility | 7 | {cloud,bio} |
piler | 7 | {bio} |
saint | 7 | {bio} |
- sibsim4 | 7 | {bio,cloud} |
- bio-tradis | 6 | {bio,bio-dev} |
+ sibsim4 | 7 | {cloud,bio} |
+ bio-tradis | 6 | {bio-dev,bio} |
bitseq | 6 | {bio} |
codonw | 6 | {bio} |
edtsurf | 6 | {bio} |
embassy-domalign | 6 | {cloud,bio} |
estscan | 6 | {bio} |
- fitgcp | 6 | {cloud,bio} |
freebayes | 6 | {bio} |
- gasic | 6 | {bio,cloud} |
lagan | 6 | {bio} |
lamarc | 6 | {bio} |
+ logol | 6 | {bio} |
lucy | 6 | {bio} |
- mauve-aligner | 6 | {bio} |
microbegps | 6 | {bio} |
- mlv-smile | 6 | {bio,cloud} |
+ mlv-smile | 6 | {cloud,bio} |
+ openslide | 6 | {imaging-dev} |
orthanc-webviewer | 6 | {imaging} |
- paraclu | 6 | {bio,cloud} |
+ paraclu | 6 | {cloud,bio} |
perm | 6 | {bio,cloud} |
placnet | 6 | {bio} |
poretools | 6 | {bio} |
@@ -99,10 +100,10 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
scythe | 6 | {bio} |
seqtools | 6 | {bio} |
sickle | 6 | {bio} |
- spread-phy | 6 | {bio,bio-phylogeny} |
- squizz | 6 | {cloud,bio} |
+ spread-phy | 6 | {bio-phylogeny,bio} |
+ squizz | 6 | {bio,cloud} |
tracetuner | 6 | {bio} |
- treeview | 6 | {bio,bio-phylogeny} |
+ treeview | 6 | {bio-phylogeny,bio} |
alter-sequence-alignment | 5 | {bio} |
andi | 5 | {bio} |
baitfisher | 5 | {bio} |
@@ -128,10 +129,9 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
libdivsufsort | 5 | {bio-dev} |
libminc | 5 | {imaging-dev} |
librdp-taxonomy-tree-java | 5 | {bio-dev} |
- logol | 5 | {bio} |
- mapsembler2 | 5 | {cloud,bio} |
+ mapsembler2 | 5 | {bio,cloud} |
+ mauve-aligner | 5 | {bio} |
murasaki | 5 | {bio} |
- openslide | 5 | {imaging-dev} |
parsnp | 5 | {bio} |
predictprotein | 5 | {bio} |
proalign | 5 | {bio,bio-phylogeny} |
@@ -139,20 +139,22 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
quorum | 5 | {bio} |
rdp-classifier | 5 | {bio} |
repeatmasker-recon | 5 | {bio} |
+ samblaster | 5 | {covid-19,bio} |
seer | 5 | {bio} |
seqtools | 5 | {bio} |
sprai | 5 | {bio} |
sumatra | 5 | {bio} |
transtermhp | 5 | {bio} |
vsearch | 5 | {bio} |
- zalign | 5 | {cloud,bio} |
+ zalign | 5 | {bio,cloud} |
assemblytics | 4 | {bio} |
- beast-mcmc | 4 | {bio,bio-phylogeny} |
+ bart-view | 4 | {imaging} |
+ beast-mcmc | 4 | {bio-phylogeny,bio} |
dwgsim | 4 | {bio} |
elastix | 4 | {imaging} |
fastml | 4 | {bio} |
hinge | 4 | {bio} |
- jmodeltest | 4 | {bio-phylogeny,bio} |
+ jmodeltest | 4 | {bio,bio-phylogeny} |
libncl | 4 | {bio} |
libpal-java | 4 | {bio-dev} |
libsbml | 4 | {bio-dev} |
@@ -162,37 +164,36 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
mrs | 4 | {bio} |
patman | 4 | {bio} |
phipack | 4 | {bio} |
- prottest | 4 | {bio-phylogeny,bio} |
+ prottest | 4 | {bio,bio-phylogeny} |
rampler | 4 | {bio} |
rdp-alignment | 4 | {bio} |
relion | 4 | {bio} |
roguenarok | 4 | {bio} |
- samblaster | 4 | {bio,covid-19} |
sga | 4 | {bio} |
soapsnp | 4 | {bio} |
sweed | 4 | {bio} |
tvc | 4 | {bio} |
- bart-view | 3 | {imaging} |
- blasr | 3 | {bio-ngs,bio} |
- delly | 3 | {covid-19,bio} |
+ blasr | 3 | {bio,bio-ngs} |
+ delly | 3 | {bio,covid-19} |
dicompyler | 3 | {oncology} |
dindel | 3 | {bio} |
fsm-lite | 3 | {bio} |
metaphlan2 | 3 | {bio} |
- orthanc-dicomweb | 3 | {imaging,covid-19} |
+ orthanc-dicomweb | 3 | {covid-19,imaging} |
orthanc-mysql | 3 | {imaging} |
pbdagcon | 3 | {bio} |
phybin | 3 | {bio} |
pilon | 3 | {bio} |
plasmidseeker | 3 | {bio} |
relion | 3 | {bio} |
- rtax | 3 | {cloud,bio} |
+ rtax | 3 | {bio,cloud} |
runcircos-gui | 3 | {bio} |
seqmagick | 3 | {bio,covid-19} |
snap-aligner | 3 | {bio} |
soapaligner | 3 | {bio} |
+ stacks | 3 | {bio} |
suitename | 3 | {bio} |
- sumaclust | 3 | {covid-19,bio} |
+ sumaclust | 3 | {bio,covid-19} |
surankco | 3 | {bio} |
tnseq-transit | 3 | {bio,covid-19} |
transrate-tools | 3 | {bio} |
@@ -200,7 +201,7 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
velvetoptimiser | 3 | {bio} |
yaha | 3 | {bio} |
biosig4c++ | 2 | {imaging-dev,physics} |
- cufflinks | 2 | {bio,cloud} |
+ cufflinks | 2 | {cloud,bio} |
getdata | 2 | {bio} |
igor | 2 | {bio} |
kma | 2 | {bio} |
@@ -217,14 +218,12 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
skesa | 2 | {bio} |
spaced | 2 | {bio} |
srf | 2 | {bio-dev} |
- stacks | 2 | {bio} |
- thesias | 2 | {covid-19,bio} |
+ thesias | 2 | {bio,covid-19} |
tree-puzzle | 2 | {bio,bio-phylogeny,cloud} |
- volpack | 2 | {imaging-dev} |
atropos | 1 | {bio} |
biosig4c++ | 1 | {physics,imaging-dev} |
ctn | 1 | {imaging-dev} |
- embassy-phylip | 1 | {bio,cloud} |
+ embassy-phylip | 1 | {cloud,bio} |
libbio-mage-utils-perl | 1 | {bio-dev} |
libchado-perl | 1 | {bio-dev} |
libctapimkt | 1 | {practice} |
@@ -239,13 +238,14 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
papyrus | 1 | {imaging-dev} |
pilercr | 1 | {bio} |
qrisk2 | 1 | {practice} |
- stringtie | 1 | {covid-19,bio} |
+ stringtie | 1 | {bio,covid-19} |
trace2dbest | 1 | {bio} |
+ volpack | 1 | {imaging-dev} |
acedb | 0 | {cloud,bio} |
augur | 0 | {covid-19,bio} |
bambamc | 0 | {bio-dev} |
bbmap | 0 | {covid-19} |
- biobambam2 | 0 | {covid-19,bio,bio-dev} |
+ biobambam2 | 0 | {bio,bio-dev,covid-19} |
biojava4-live | 0 | {bio-dev} |
biosig4c++ | 0 | {physics} |
biosyntax | 0 | {bio} |
@@ -253,7 +253,7 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
camp | 0 | {imaging-dev} |
emboss-explorer | 0 | {bio} |
emmax | 0 | {bio} |
- fasta3 | 0 | {bio,covid-19} |
+ fasta3 | 0 | {covid-19,bio} |
fis-gtm | 0 | {his} |
freecontact | 0 | {bio-dev} |
gatb-core | 0 | {bio-dev} |
@@ -274,7 +274,7 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
libhmsbeagle | 0 | {bio-dev} |
libics | 0 | {covid-19,imaging-dev} |
libjloda-java | 0 | {bio-dev} |
- libmaus2 | 0 | {covid-19,bio-dev} |
+ libmaus2 | 0 | {bio-dev,covid-19} |
libmems | 0 | {bio-dev} |
libmialm | 0 | {imaging-dev} |
libmuscle | 0 | {bio-dev} |
@@ -289,7 +289,7 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
metastudent-data-2 | 0 | {bio} |
mia | 0 | {imaging-dev} |
miaviewit | 0 | {imaging-dev} |
- milib | 0 | {covid-19,bio-dev} |
+ milib | 0 | {bio-dev,covid-19} |
mssstest | 0 | {tools} |
murasaki | 0 | {bio} |
ncbi-vdb | 0 | {bio-dev} |
@@ -310,9 +310,9 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
sift | 0 | {bio} |
simpleitk | 0 | {imaging-dev} |
skewer | 0 | {bio} |
- smrtanalysis | 0 | {covid-19,bio} |
+ smrtanalysis | 0 | {bio,covid-19} |
solvate | 0 | {bio} |
- spaln | 0 | {covid-19,bio} |
+ spaln | 0 | {bio,covid-19} |
trim-galore | 0 | {bio} |
varna | 0 | {bio} |
vtk-dicom | 0 | {imaging-dev} |
=====================================
outdated_med-packages.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
+Last-Update: Wed, 01 Apr 2020 13:42:04 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+-------------------------------------------------------------------------+----------------------+------------------------
@@ -8,6 +8,7 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
biobambam2 | 2.0.160 | 2.0.162+ds | Andreas Tille | Andreas Tille | 2020-03-27 10:34:45+00
biomaj3-process | 3.0.15 | 3.0.16 | Olivier Sallou | Olivier Sallou | 2019-11-12 11:20:38+00
biosig4c++ | 1.9.5 | 2.0.2 | 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 | 3.0.20200324120055 | Michael R. Crusoe | Michael R. Crusoe | 2020-02-26 12:07:54+00
cyvcf2 | 0.11.6 | 0.11.7 | Liubov Chuprikova,Steffen Moeller | Andreas Tille | 2020-03-30 09:03:56+00
@@ -17,9 +18,10 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
ea-utils | 1.1.2 | 1.04.807 | Andreas Tille,Tim Booth | Andreas Tille | 2018-04-26 21:48:01+00
falcon | 1.8.8 | 2.1.4 | Afif Elghraoui | Afif Elghraoui | 2017-12-16 08:49:13+00
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
+ gatb-core | 1.4.1+git20191209.9398f28 | 1.4.1+git20200330.e99c5d7 | Andreas Tille,Nadiya Sitdykova | Michael R. Crusoe | 2020-02-17 14:52:30+00
gmap | 2019-09-12 | 2020-03-12 | Alexandre Mestiashvili,Andreas Tille,Shaun Jackman | Steffen Moeller | 2019-12-30 12:37:15+00
hdmf | 1.5.4 | 1.6.1 | Yaroslav Halchenko | Yaroslav Halchenko | 2020-02-03 03:01:25+00
+ htseq | 0.11.3 | 0.11.4 | Andreas Tille,Diane Trout | Diane Trout | 2020-03-04 07:04:25+00
igdiscover | 0.11 | 0.12.3 | Steffen Moeller | Andreas Tille | 2019-09-06 07:04:02+00
igv | 2.4.17 | 2.8.2 | Andreas Tille,Olivier Sallou | Andreas Tille | 2019-01-30 15:11:57+00
imagej | 1.52r | 1.52u | David Miguel Susano Pinto | Andreas Tille | 2019-12-04 14:55:11+00
@@ -32,14 +34,15 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
libmaus2 | 2.0.713 | 2.0.714 | Andreas Tille,Steffen Moeller | Andreas Tille | 2020-03-27 09:34:39+00
libsis-base-java | 18.09~pre1+git20180827.fe4953e | 18.09~pre1+git20180928.45fbd31 | Andreas Tille,Olivier Sallou,Tim Booth | Andreas Tille | 2018-09-26 08:35:30+00
libthread-pool | 2.0.1 | 2.0.2 | Andreas Tille | Andreas Tille | 2019-11-19 21:21:23+00
- libundead | 1.0.10 | 1.1.1 | Andreas Tille | Andreas Tille | 2019-09-13 21:06:10+00
metaphlan2 | 2.9.22 | 2.96.1 | Andreas Tille | Andreas Tille | 2019-11-08 07:19:11+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 | 13.5.20200326 | Aaron M. Ucko | Aaron M. Ucko | 2020-02-03 03:53:53+00
nibabel | 3.0.1 | 3.0.2 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-03-03 14:58:34+00
pbcopper | 1.3.0 | 1.4.0 | Andreas Tille | Andreas Tille | 2020-01-29 08:51:15+00
+ pbgenomicconsensus | 2.3.2 | 2.3.3 | Andreas Tille | Liubov Chuprikova | 2019-04-07 15:33:36+00
plink2 | 2.00~a3-200217 | 200328 | Dylan Aïssi | Dylan Aïssi | 2020-02-19 06:19:18+00
+ proteinortho | 6.0.14 | 6.0.15 | Andreas Tille | Michael R. Crusoe | 2020-02-17 14:53:34+00
pydicom | 1.4.1 | 1.4.2 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-01-23 12:34:53+00
pynn | 0.7.5 | 0.9.5 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-03-20 11:00:12+00
python-bids-validator | 1.2.4 | 1.4.4 | Yaroslav Halchenko | Yaroslav Halchenko | 2019-08-17 19:00:11+00
@@ -54,7 +57,6 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
resfinder-db | 0.0+git20191001.149209d | 0.0+git20200318.d6f36d3 | Andreas Tille | Andreas Tille | 2019-11-16 23:00:12+00
scrm | 1.7.3 | 1.7.4 | Kevin Murray | Andreas Tille | 2018-12-17 13:05:34+00
seaview | 4.7 | 5.0.2 | Andreas Tille,Charles Plessy | Andreas Tille | 2018-05-09 13:43:40+00
- simka | 1.5.1 | 1.5.2 | Shayan Doust | Andreas Tille | 2020-01-12 18:49:47+00
skesa | 2.3.0 | 2.4.0 | Andreas Tille | Andreas Tille | 2019-08-20 14:49:33+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
sra-sdk | 2.9.3 | 2.10.4 | Andreas Tille,Charles Plessy | Steffen Moeller | 2018-10-23 20:40:02+00
@@ -65,7 +67,7 @@ Last-Update: Wed, 01 Apr 2020 01:42:03 +0000
unanimity | 3.3.0 | 4.2.0-1 | 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
-(63 rows)
+(65 rows)
source | id | severity | title
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/a0573b0f228f6f0837400175b4a56ddade92bdc6
--
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