Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
7d653b30 by Andreas Tille at 2020-04-07T13:44:31+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,72 +1,89 @@
-Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
+Last-Update: Tue, 07 Apr 2020 13:42:04 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk | 165 | {imaging,covid-19} |
- orthanc | 94 | {practice,imaging,covid-19} |
- gdcm | 47 | {imaging-dev} |
+ dcmtk | 164 | {imaging,covid-19} |
+ orthanc | 93 | {practice,imaging,covid-19} |
+ gdcm | 46 | {imaging-dev} |
orthanc-wsi | 39 | {practice,his,laboratory,imaging,oncology,covid-19} |
+ amide | 30 | {imaging} |
htsjdk | 30 | {bio-dev} |
- amide | 29 | {imaging} |
dcm2niix | 26 | {imaging} |
dicomscope | 24 | {imaging} |
- dicom3tools | 22 | {imaging} |
+ dicom3tools | 23 | {imaging} |
gdcm | 21 | {covid-19,imaging} |
gnumed-server | 18 | {covid-19,practice} |
ngs-sdk | 17 | {bio-dev} |
- invesalius | 14 | {imaging} |
- king | 14 | {typesetting,imaging} |
- minc-tools | 14 | {imaging} |
- ncbi-entrez-direct | 13 | {bio} |
- pixelmed | 13 | {imaging} |
- insighttoolkit4 | 12 | {imaging-dev} |
+ minc-tools | 15 | {imaging} |
+ ncbi-entrez-direct | 14 | {bio} |
+ invesalius | 13 | {imaging} |
+ king | 13 | {typesetting,imaging} |
+ adun.app | 12 | {bio} |
+ pixelmed | 12 | {imaging} |
vtk-dicom | 12 | {imaging} |
- adun.app | 11 | {bio} |
biojava-live | 11 | {bio-dev} |
cgview | 11 | {bio} |
+ insighttoolkit4 | 11 | {imaging-dev} |
openslide | 11 | {imaging} |
psychopy | 11 | {psychology} |
+ staden | 11 | {bio} |
+ ea-utils | 10 | {bio} |
+ gasic | 10 | {cloud,bio} |
+ hunspell-en-med | 10 | {tools} |
jebl2 | 10 | {bio-dev} |
+ king-probe | 10 | {bio} |
mia | 10 | {imaging} |
obitools | 10 | {bio} |
- staden | 10 | {bio} |
- ea-utils | 9 | {bio} |
- hunspell-en-med | 9 | {tools} |
- king-probe | 9 | {bio} |
+ dazzdb | 9 | {bio} |
+ gdcm | 9 | {imaging-dev} |
+ mipe | 9 | {bio,cloud} |
ngs-sdk | 9 | {bio-dev} |
+ paml | 9 | {bio} |
+ arden | 8 | {bio,cloud} |
biosig4c++ | 8 | {imaging,physics} |
- dazzdb | 8 | {bio} |
- gasic | 8 | {cloud,bio} |
- gdcm | 8 | {imaging-dev} |
- mipe | 8 | {bio,cloud} |
+ bppsuite | 8 | {bio} |
+ fitgcp | 8 | {cloud,bio} |
+ lagan | 8 | {bio} |
+ parsnp | 8 | {bio} |
+ phast | 8 | {bio} |
plastimatch | 8 | {imaging} |
radiant | 8 | {bio} |
seqsero | 8 | {bio} |
tree-puzzle | 8 | {cloud,bio,bio-phylogeny} |
abacas | 7 | {bio} |
alter-sequence-alignment | 7 | {bio} |
- bppsuite | 7 | {bio} |
+ anfo | 7 | {cloud,bio} |
+ biomaj3-cli | 7 | {cloud} |
+ daligner | 7 | {bio-ngs,bio} |
diamond-aligner | 7 | {bio,covid-19} |
+ embassy-domainatrix | 7 | {bio,cloud} |
fastlink | 7 | {bio,cloud} |
+ freecontact | 7 | {bio,cloud} |
librg-utils-perl | 7 | {bio} |
ncbi-seg | 7 | {bio} |
neobio | 7 | {cloud,bio} |
norsp | 7 | {bio} |
- paml | 7 | {bio} |
- parsnp | 7 | {bio} |
- phast | 7 | {bio} |
- anfo | 6 | {cloud,bio} |
- arden | 6 | {bio,cloud} |
- biomaj3-cli | 6 | {cloud} |
+ prime-phylo | 7 | {bio,cloud} |
+ seqtools | 7 | {bio} |
+ tracetuner | 7 | {bio} |
+ ampliconnoise | 6 | {cloud,bio} |
+ bandage | 6 | {bio} |
+ beads | 6 | {bio} |
+ biomaj3-daemon | 6 | {bio} |
+ bio-rainbow | 6 | {bio} |
+ bitseq | 6 | {bio} |
cluster3 | 6 | {bio} |
- daligner | 6 | {bio-ngs,bio} |
+ codonw | 6 | {bio} |
ecopcr | 6 | {bio} |
- embassy-domainatrix | 6 | {bio,cloud} |
+ edtsurf | 6 | {bio} |
+ embassy-domalign | 6 | {cloud,bio} |
embassy-domsearch | 6 | {bio,cloud} |
- fitgcp | 6 | {cloud,bio} |
- freecontact | 6 | {bio,cloud} |
+ estscan | 6 | {bio} |
+ freebayes | 6 | {bio} |
+ gatb-core | 6 | {bio} |
+ ghmm | 6 | {bio} |
jaligner | 6 | {bio} |
- lagan | 6 | {bio} |
+ jellyfish1 | 6 | {bio} |
maqview | 6 | {bio} |
melting | 6 | {cloud,bio} |
orthanc-webviewer | 6 | {imaging} |
@@ -74,35 +91,30 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
piler | 6 | {bio} |
placnet | 6 | {bio} |
predictprotein | 6 | {bio} |
- prime-phylo | 6 | {bio,cloud} |
+ pscan-chip | 6 | {bio} |
pscan-tfbs | 6 | {bio} |
pymia | 6 | {imaging-dev} |
+ rambo-k | 6 | {bio} |
rdp-readseq | 6 | {bio} |
salmon | 6 | {bio} |
seqtools | 6 | {bio} |
sibsim4 | 6 | {bio,cloud} |
sigma-align | 6 | {cloud,bio-phylogeny,bio} |
sumatra | 6 | {bio} |
- tracetuner | 6 | {bio} |
- ampliconnoise | 5 | {cloud,bio} |
- andi | 5 | {bio} |
- bandage | 5 | {bio} |
- beads | 5 | {bio} |
- biomaj3-daemon | 5 | {bio} |
- bio-rainbow | 5 | {bio} |
- bitseq | 5 | {bio} |
+ baitfisher | 5 | {bio} |
+ bio-tradis | 5 | {bio,bio-dev} |
brig | 5 | {bio} |
- canu | 5 | {bio} |
- codonw | 5 | {bio} |
- edtsurf | 5 | {bio} |
- embassy-domalign | 5 | {cloud,bio} |
- estscan | 5 | {bio} |
- freebayes | 5 | {bio} |
- gatb-core | 5 | {bio} |
- ghmm | 5 | {bio} |
+ centrifuge | 5 | {bio} |
+ clonalframeml | 5 | {bio,covid-19} |
+ clonalorigin | 5 | {bio} |
+ dascrubber | 5 | {bio} |
+ dwgsim | 5 | {bio} |
+ elph | 5 | {bio} |
+ fastml | 5 | {bio} |
+ harvest-tools | 5 | {bio} |
+ hinge | 5 | {bio} |
indelible | 5 | {bio} |
ipig | 5 | {bio} |
- jellyfish1 | 5 | {bio} |
lamarc | 5 | {bio} |
libdivsufsort | 5 | {bio-dev} |
lucy | 5 | {bio} |
@@ -110,73 +122,60 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
mauve-aligner | 5 | {bio} |
microbegps | 5 | {bio} |
mlv-smile | 5 | {cloud,bio} |
- openslide | 5 | {imaging-dev} |
paraclu | 5 | {bio,cloud} |
perm | 5 | {bio,cloud} |
poretools | 5 | {bio} |
proalign | 5 | {bio,bio-phylogeny} |
probabel | 5 | {cloud,bio} |
- pscan-chip | 5 | {bio} |
quorum | 5 | {bio} |
- rambo-k | 5 | {bio} |
rdp-alignment | 5 | {bio} |
+ repeatmasker-recon | 5 | {bio} |
saint | 5 | {bio} |
+ seer | 5 | {bio} |
seqtools | 5 | {bio} |
sickle | 5 | {bio} |
+ sprai | 5 | {bio} |
spread-phy | 5 | {bio,bio-phylogeny} |
squizz | 5 | {cloud,bio} |
transtermhp | 5 | {bio} |
treeview | 5 | {bio,bio-phylogeny} |
vsearch | 5 | {bio} |
- baitfisher | 4 | {bio} |
+ assemblytics | 4 | {bio} |
bart-view | 4 | {imaging} |
beast2-mcmc | 4 | {bio} |
beast-mcmc | 4 | {bio,bio-phylogeny} |
- bio-tradis | 4 | {bio,bio-dev} |
- centrifuge | 4 | {bio} |
- clonalframeml | 4 | {bio,covid-19} |
- clonalorigin | 4 | {bio} |
- dascrubber | 4 | {bio} |
- dwgsim | 4 | {bio} |
- elph | 4 | {bio} |
- fastml | 4 | {bio} |
- harvest-tools | 4 | {bio} |
- hinge | 4 | {bio} |
+ blasr | 4 | {bio,bio-ngs} |
+ canu | 4 | {bio} |
+ delly | 4 | {bio,covid-19} |
+ dindel | 4 | {bio} |
+ fsm-lite | 4 | {bio} |
jmodeltest | 4 | {bio,bio-phylogeny} |
+ libncl | 4 | {bio} |
libpal-java | 4 | {bio-dev} |
librdp-taxonomy-tree-java | 4 | {bio-dev} |
logol | 4 | {bio} |
+ mencal | 4 | {tools} |
mhap | 4 | {bio,bio-ngs} |
+ mrs | 4 | {bio} |
+ murasaki | 4 | {bio} |
+ openslide | 4 | {imaging-dev} |
patman | 4 | {bio} |
+ pbdagcon | 4 | {bio} |
prottest | 4 | {bio-phylogeny,bio} |
rdp-classifier | 4 | {bio} |
relion | 4 | {bio} |
- repeatmasker-recon | 4 | {bio} |
samblaster | 4 | {covid-19,bio} |
scythe | 4 | {bio} |
- seer | 4 | {bio} |
- seqtools | 4 | {bio} |
soapsnp | 4 | {bio} |
- sprai | 4 | {bio} |
- assemblytics | 3 | {bio} |
- blasr | 3 | {bio,bio-ngs} |
- delly | 3 | {bio,covid-19} |
- dindel | 3 | {bio} |
- fsm-lite | 3 | {bio} |
+ dicompyler | 3 | {oncology} |
libminc | 3 | {imaging-dev} |
- libncl | 3 | {bio} |
libsbml | 3 | {bio-dev} |
maffilter | 3 | {bio} |
- mencal | 3 | {tools} |
metaphlan2 | 3 | {bio} |
mptp | 3 | {bio} |
- mrs | 3 | {bio} |
- murasaki | 3 | {bio} |
- ngs-sdk | 3 | {bio-dev} |
nutsqlite | 3 | {tools} |
orthanc-dicomweb | 3 | {covid-19,imaging} |
orthanc-mysql | 3 | {imaging} |
- pbdagcon | 3 | {bio} |
phipack | 3 | {bio} |
phybin | 3 | {bio} |
pilon | 3 | {bio} |
@@ -186,6 +185,7 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
roguenarok | 3 | {bio} |
rtax | 3 | {cloud,bio} |
runcircos-gui | 3 | {bio} |
+ segemehl | 3 | {bio} |
seqmagick | 3 | {covid-19,bio} |
sga | 3 | {bio} |
soapaligner | 3 | {bio} |
@@ -194,13 +194,13 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
surankco | 3 | {bio} |
sweed | 3 | {bio} |
tnseq-transit | 3 | {bio,covid-19} |
+ transrate-tools | 3 | {bio} |
tvc | 3 | {bio} |
varscan | 3 | {bio} |
yaha | 3 | {bio} |
zalign | 3 | {cloud,bio} |
biosig4c++ | 2 | {physics,imaging-dev} |
cufflinks | 2 | {bio,cloud} |
- dicompyler | 2 | {oncology} |
elastix | 2 | {imaging} |
getdata | 2 | {bio} |
igor | 2 | {bio} |
@@ -208,16 +208,16 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
kmerresistance | 2 | {bio} |
libgff | 2 | {bio-dev} |
libsmithwaterman | 2 | {bio} |
+ ngs-sdk | 2 | {bio-dev} |
+ pal2nal | 2 | {bio} |
qcumber | 2 | {bio} |
qrisk2 | 2 | {practice} |
scrm | 2 | {bio} |
- segemehl | 2 | {bio} |
skesa | 2 | {bio} |
snap-aligner | 2 | {bio} |
spaced | 2 | {bio} |
srf | 2 | {bio-dev} |
thesias | 2 | {bio,covid-19} |
- transrate-tools | 2 | {bio} |
velvetoptimiser | 2 | {bio} |
atropos | 1 | {bio} |
biosig4c++ | 1 | {physics,imaging-dev} |
@@ -231,7 +231,6 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
opencfu | 1 | {laboratory} |
opensurgsim | 1 | {imaging-dev} |
orthanc-postgresql | 1 | {imaging} |
- pal2nal | 1 | {bio} |
papyrus | 1 | {imaging-dev} |
pilercr | 1 | {bio} |
python-questplus | 1 | {covid-19} |
@@ -293,6 +292,7 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
miaviewit | 0 | {imaging-dev} |
milib | 0 | {bio-dev,covid-19} |
mssstest | 0 | {tools} |
+ multiqc | 0 | {bio} |
murasaki | 0 | {bio} |
ncbi-vdb | 0 | {bio-dev} |
orthanc-imagej | 0 | {imaging} |
=====================================
outdated_med-packages.txt
=====================================
@@ -1,15 +1,17 @@
-Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
+Last-Update: Tue, 07 Apr 2020 13:42:04 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+-----------------------------------------------------------------------------+----------------------+------------------------
atropos | 1.1.24 | 2.0.0-alpha.4 | Andreas Tille | Steffen Moeller | 2019-11-30 12:19:31+00
baitfisher | 1.2.7+git20180107.e92dbf2 | 1.2.7+git20190123.241d060 | Olivier Sallou | Andreas Tille | 2018-09-24 13:04:18+00
+ bbmap | 38.79 | 38.80 | Andreas Tille | Andreas Tille | 2020-02-27 11:08:04+00
biobambam2 | 2.0.160 | 2.0.162+ds | Andreas Tille | Andreas Tille | 2020-03-27 10:34:45+00
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 | 2.0.2 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-03-02 08:38:37+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
daligner | 1.0+git20200115.c2b47da | 1.0+git20200322.477d5b9 | Andreas Tille | Andreas Tille | 2020-01-28 10:34:12+00
dazzdb | 1.0+git20200115.d8adde7 | 1.0+git20200322.ba88d76 | Andreas Tille | Andreas Tille | 2020-01-23 16:34:35+00
discosnp | 2.4.3 | 4.4.4 | Andreas Tille,Olivier Sallou | Andreas Tille | 2020-01-27 15:19:13+00
@@ -25,6 +27,7 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
jebl2 | 0.1+git20180418.653eb83 | 0.1+git20190308.a98448e | Andreas Tille | Andreas Tille | 2018-07-05 12:05:57+00
kineticstools | 0.6.1+git20180425.27a1878 | 0.6.1+git20200325.3558942 | Andreas Tille | Andreas Tille | 2019-02-14 13:26:09+00
king-probe | 2.16.160404+git20180613.a09b012 | 2.16.160404+git20200121.9b198c1 | Andreas Tille,Malihe Asemani,Michael Prisant | Andreas Tille | 2018-07-16 07:34:48+00
+ kissplice | 2.4.0-p1 | 2.5.0 | Andreas Tille,David Parsons | Saira Hussain | 2019-08-14 21:04:51+00
kma | 1.2.21 | 1.2.22 | Andreas Tille | Steffen Moeller | 2020-01-17 22:54:10+00
libgclib | 0.11.4 | 0.11.7 | Andreas Tille,Michael R. Crusoe,Steffen Moeller | Michael R. Crusoe | 2020-02-14 13:04:26+00
libjloda-java | 0.0+git20180523.cbaf6d1 | 0.0+git20200330.cb91494 | Andreas Tille | Andreas Tille | 2018-05-25 21:49:43+00
@@ -48,9 +51,6 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
python-schema-salad | 5.0.20200220195218 | 5.0.20200302192450 | Michael R. Crusoe | Michael R. Crusoe | 2020-02-27 19:19:53+00
python-skbio | 0.5.5 | 0.5.6 | Andreas Tille,Kevin Murray,Tim Booth | Michael R. Crusoe | 2020-02-28 14:48:20+00
python-xopen | 0.8.4 | 0.9.0 | Andreas Tille | Steffen Moeller | 2019-11-05 15:34:45+00
- q2-demux | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2020-01-26 07:34:40+00
- q2-feature-classifier | 2019.4.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2019-11-11 10:00:33+00
- q2-metadata | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Andreas Tille | 2020-02-03 08:42:28+00
q2-types | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2019-12-23 20:39:42+00
qiime | 2019.10.0 | 2020.2.0 | Andreas Tille,Liubov Chuprikova,Steffen Moeller | Liubov Chuprikova | 2019-12-16 09:51:27+00
resfinder-db | 0.0+git20191001.149209d | 0.0+git20200318.d6f36d3 | Andreas Tille | Andreas Tille | 2019-11-16 23:00:12+00
@@ -58,11 +58,11 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
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
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 | 2.10.5 | Andreas Tille,Charles Plessy | Steffen Moeller | 2018-10-23 20:40:02+00
stacks | 2.52 | 2.53 | Andreas Tille,Tim Booth | Steffen Moeller | 2020-03-26 02:50:13+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
- 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
(62 rows)
@@ -124,7 +124,6 @@ Last-Update: Tue, 07 Apr 2020 01:42:04 +0000
falcon | 902132 | serious | falcon: FTBFS since python-networkx version 2.1-1; fails in test suite
falcon | 936503 | serious | falcon: Python2 removal in sid/bullseye
fastlink | 909713 | minor | fastlink: Please provide autopkgtest
- fastqc | 950311 | normal | fastqc: FAIL strings in output - what does this mean?
garli | 907905 | normal | garli: FTBFS randomly (failing tests)
gatb-core | 929564 | normal | gatb-core-testdata: broken symlink: /usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit
gdcm | 731435 | normal | warning: iteration 55823u invokes undefined behavior [-Waggressive-loop-optimizations]
@@ -268,5 +267,5 @@ Last-Update: Tue, 07 Apr 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
-(199 rows)
+(198 rows)
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/7d653b302e82a417ec008d613098dda5e6d0fac2
--
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