Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
21a0bbbd by Andreas Tille at 2020-02-29T13:45:37+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,72 +1,70 @@
-Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
+Last-Update: Sat, 29 Feb 2020 13:42:03 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------
- dcmtk | 171 | {imaging} |
- orthanc | 92 | {practice,imaging} |
- gdcm | 48 | {imaging-dev} |
- orthanc-wsi | 37 | {imaging,practice,oncology,laboratory,his} |
+ dcmtk | 172 | {imaging} |
+ orthanc | 95 | {practice,imaging} |
+ gdcm | 47 | {imaging-dev} |
+ orthanc-wsi | 37 | {oncology,imaging,his,laboratory,practice} |
+ dcm2niix | 36 | {imaging} |
cfflib | 35 | {imaging-dev} |
- dcm2niix | 34 | {imaging} |
- amide | 32 | {imaging} |
+ amide | 33 | {imaging} |
dicomscope | 26 | {imaging} |
medicalterms | 25 | {tools} |
- dicom3tools | 22 | {imaging} |
- htsjdk | 21 | {bio-dev} |
+ dicom3tools | 23 | {imaging} |
+ htsjdk | 22 | {bio-dev} |
+ gdcm | 17 | {imaging} |
gnumed-server | 17 | {practice} |
- gdcm | 16 | {imaging} |
ngs-sdk | 13 | {bio-dev} |
adun.app | 12 | {bio} |
+ minc-tools | 12 | {imaging} |
pixelmed | 12 | {imaging} |
insighttoolkit4 | 11 | {imaging-dev} |
invesalius | 11 | {imaging} |
- minc-tools | 11 | {imaging} |
- king | 10 | {imaging,typesetting} |
+ king | 11 | {imaging,typesetting} |
+ vtk-dicom | 10 | {imaging} |
jebl2 | 9 | {bio-dev} |
mia | 9 | {imaging} |
- tree-puzzle | 9 | {bio,cloud,bio-phylogeny} |
- vtk-dicom | 9 | {imaging} |
+ plastimatch | 9 | {imaging} |
+ tree-puzzle | 9 | {bio,bio-phylogeny,cloud} |
biojava-live | 8 | {bio-dev} |
gdcm | 8 | {imaging-dev} |
- librg-utils-perl | 8 | {bio} |
obitools | 8 | {bio} |
- plastimatch | 8 | {imaging} |
- fastlink | 7 | {cloud,bio} |
+ fastlink | 7 | {bio,cloud} |
+ librg-utils-perl | 7 | {bio} |
melting | 7 | {bio,cloud} |
ncbi-entrez-direct | 7 | {bio} |
+ openslide | 7 | {imaging} |
psychopy | 7 | {psychology} |
- arden | 6 | {bio,cloud} |
+ arden | 6 | {cloud,bio} |
cgview | 6 | {bio} |
dicompyler | 6 | {oncology} |
jaligner | 6 | {bio} |
maqview | 6 | {bio} |
mipe | 6 | {bio,cloud} |
ncbi-seg | 6 | {bio} |
+ ngs-sdk | 6 | {bio-dev} |
norsp | 6 | {bio} |
- openslide | 6 | {imaging} |
orthanc-webviewer | 6 | {imaging} |
staden | 6 | {bio} |
dazzdb | 5 | {bio} |
embassy-domainatrix | 5 | {cloud,bio} |
estscan | 5 | {bio} |
- gasic | 5 | {cloud,bio} |
+ gasic | 5 | {bio,cloud} |
idba | 5 | {bio,cloud} |
ipig | 5 | {bio} |
king-probe | 5 | {bio} |
lagan | 5 | {bio} |
- libdivsufsort | 5 | {bio-dev} |
mapsembler2 | 5 | {cloud,bio} |
neobio | 5 | {bio,cloud} |
- ngs-sdk | 5 | {bio-dev} |
- openslide | 5 | {imaging-dev} |
+ paml | 5 | {bio} |
radiant | 5 | {bio} |
- sibsim4 | 5 | {bio,cloud} |
- sigma-align | 5 | {bio-phylogeny,cloud,bio} |
+ sibsim4 | 5 | {cloud,bio} |
+ sigma-align | 5 | {bio-phylogeny,bio,cloud} |
sortmerna | 5 | {bio} |
- ampliconnoise | 4 | {cloud,bio} |
+ ampliconnoise | 4 | {bio,cloud} |
anfo | 4 | {bio,cloud} |
biomaj3-cli | 4 | {cloud} |
- bio-tradis | 4 | {bio-dev,bio} |
brig | 4 | {bio} |
cluster3 | 4 | {bio} |
diamond-aligner | 4 | {bio} |
@@ -75,16 +73,18 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
edtsurf | 4 | {bio} |
embassy-domalign | 4 | {bio,cloud} |
embassy-domsearch | 4 | {bio,cloud} |
- fitgcp | 4 | {bio,cloud} |
- freecontact | 4 | {cloud,bio} |
+ fitgcp | 4 | {cloud,bio} |
+ freecontact | 4 | {bio,cloud} |
ghmm | 4 | {bio} |
indelible | 4 | {bio} |
jellyfish1 | 4 | {bio} |
+ libdivsufsort | 4 | {bio-dev} |
+ mauve-aligner | 4 | {bio} |
mhap | 4 | {bio,bio-ngs} |
mlv-smile | 4 | {cloud,bio} |
nutsqlite | 4 | {tools} |
+ openslide | 4 | {imaging-dev} |
orthanc-dicomweb | 4 | {imaging} |
- paml | 4 | {bio} |
phyutility | 4 | {bio,cloud} |
piler | 4 | {bio} |
prime-phylo | 4 | {cloud,bio} |
@@ -94,14 +94,14 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
squizz | 4 | {bio,cloud} |
tracetuner | 4 | {bio} |
transtermhp | 4 | {bio} |
- treeview | 4 | {bio,bio-phylogeny} |
- velvetoptimiser | 4 | {bio} |
- zalign | 4 | {cloud,bio} |
+ treeview | 4 | {bio-phylogeny,bio} |
+ zalign | 4 | {bio,cloud} |
abacas | 3 | {bio} |
assemblytics | 3 | {bio} |
bandage | 3 | {bio} |
beast2-mcmc | 3 | {bio} |
biomaj3-daemon | 3 | {bio} |
+ bio-tradis | 3 | {bio-dev,bio} |
blasr | 3 | {bio,bio-ngs} |
bppsuite | 3 | {bio} |
canu | 3 | {bio} |
@@ -114,7 +114,6 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
libminc | 3 | {imaging-dev} |
libsbml | 3 | {bio-dev} |
lucy | 3 | {bio} |
- mauve-aligner | 3 | {bio} |
microbegps | 3 | {bio} |
mrs | 3 | {bio} |
murasaki | 3 | {bio} |
@@ -122,12 +121,12 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
paraclu | 3 | {cloud,bio} |
parsnp | 3 | {bio} |
pbdagcon | 3 | {bio} |
- perm | 3 | {bio,cloud} |
+ perm | 3 | {cloud,bio} |
phast | 3 | {bio} |
plasmidseeker | 3 | {bio} |
predictprotein | 3 | {bio} |
proalign | 3 | {bio-phylogeny,bio} |
- probabel | 3 | {cloud,bio} |
+ probabel | 3 | {bio,cloud} |
pscan-chip | 3 | {bio} |
pscan-tfbs | 3 | {bio} |
qrisk2 | 3 | {practice} |
@@ -143,7 +142,9 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
seqtools | 3 | {bio} |
spread-phy | 3 | {bio-phylogeny,bio} |
tvc | 3 | {bio} |
+ velvetoptimiser | 3 | {bio} |
yaha | 3 | {bio} |
+ acedb | 2 | {bio,cloud} |
alter-sequence-alignment | 2 | {bio} |
andi | 2 | {bio} |
baitfisher | 2 | {bio} |
@@ -155,8 +156,8 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
centrifuge | 2 | {bio} |
clonalframeml | 2 | {bio} |
clonalorigin | 2 | {bio} |
- cufflinks | 2 | {cloud,bio} |
- daligner | 2 | {bio,bio-ngs} |
+ cufflinks | 2 | {bio,cloud} |
+ daligner | 2 | {bio-ngs,bio} |
dascrubber | 2 | {bio} |
dindel | 2 | {bio} |
dwgsim | 2 | {bio} |
@@ -183,8 +184,7 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
rampler | 2 | {bio} |
rdp-classifier | 2 | {bio} |
relion | 2 | {bio} |
- rtax | 2 | {bio,cloud} |
- runcircos-gui | 2 | {bio} |
+ rtax | 2 | {cloud,bio} |
samblaster | 2 | {bio} |
scythe | 2 | {bio} |
seqtools | 2 | {bio} |
@@ -196,19 +196,18 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
trace2dbest | 2 | {bio} |
transrate-tools | 2 | {bio} |
vsearch | 2 | {bio} |
- acedb | 1 | {bio,cloud} |
atropos | 1 | {bio} |
blimps | 1 | {bio} |
ctn | 1 | {imaging-dev} |
edflib | 1 | {imaging-dev} |
- embassy-phylip | 1 | {cloud,bio} |
+ embassy-phylip | 1 | {bio,cloud} |
emmax | 1 | {bio} |
freebayes | 1 | {bio} |
hunspell-en-med | 1 | {tools} |
kma | 1 | {bio} |
kmerresistance | 1 | {bio} |
- libbio-mage-utils-perl | 1 | {bio-dev} |
libctapimkt | 1 | {practice} |
+ libhmsbeagle | 1 | {bio-dev} |
libsmithwaterman | 1 | {bio-dev} |
libsmithwaterman | 1 | {bio} |
libvistaio | 1 | {imaging-dev} |
@@ -225,10 +224,10 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
qcumber | 1 | {bio} |
relion | 1 | {bio} |
roguenarok | 1 | {bio} |
+ runcircos-gui | 1 | {bio} |
samtools-legacy | 1 | {bio-dev} |
scrm | 1 | {bio} |
seqan | 1 | {bio-dev} |
- seq-gen | 1 | {bio} |
seqmagick | 1 | {bio} |
sga | 1 | {bio} |
sift | 1 | {bio} |
@@ -259,6 +258,7 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
gatb-core | 0 | {bio-dev} |
htscodecs | 0 | {bio-dev} |
libbiod | 0 | {bio-dev} |
+ libbio-mage-utils-perl | 0 | {bio-dev} |
libbioparser-dev | 0 | {bio-dev} |
libbpp-core | 0 | {bio-dev} |
libbpp-phyl | 0 | {bio-dev} |
@@ -271,7 +271,6 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
libdisorder | 0 | {bio-dev} |
libgenome | 0 | {bio-dev} |
libgkarrays | 0 | {bio-dev} |
- libhmsbeagle | 0 | {bio-dev} |
libics | 0 | {imaging-dev} |
libjloda-java | 0 | {bio-dev} |
libmaus2 | 0 | {bio-dev} |
@@ -297,18 +296,19 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
opencfu | 0 | {laboratory} |
opensurgsim | 0 | {imaging-dev} |
orthanc-imagej | 0 | {imaging} |
- oscar | 0 | {data,tools,practice} |
+ oscar | 0 | {data,practice,tools} |
papyrus | 0 | {imaging-dev} |
pbcopper | 0 | {bio-dev} |
pbseqlib | 0 | {bio-dev} |
python-deeptools | 0 | {bio,bio-dev} |
- python-py2bit | 0 | {bio-dev,bio} |
+ python-py2bit | 0 | {bio,bio-dev} |
python-pyani | 0 | {bio-dev} |
- python-tinyalign | 0 | {bio,bio-dev} |
- relion | 0 | {bio} |
+ python-tinyalign | 0 | {bio-dev,bio} |
relion | 0 | {bio-dev} |
+ relion | 0 | {bio} |
sambamba | 0 | {bio} |
sbmltoolbox | 0 | {bio-dev} |
+ seq-gen | 0 | {bio} |
simpleitk | 0 | {imaging-dev} |
skewer | 0 | {bio} |
smrtanalysis | 0 | {bio} |
=====================================
outdated_med-packages.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
+Last-Update: Sat, 29 Feb 2020 13:42:03 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+-----------------------------------------------------------------------------+----------------------+------------------------
@@ -13,6 +13,7 @@ Last-Update: Sat, 29 Feb 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
+ 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
dcm2niix | 1.0.20181125 | 1.0.20190902 | Ghislain Antony Vaillant | Andreas Tille | 2019-01-30 10:04:52+00
ea-utils | 1.1.2 | 1.04.807 | Andreas Tille,Tim Booth | Andreas Tille | 2018-04-26 21:48:01+00
@@ -38,7 +39,7 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
libgclib | 0.11.4 | 0.11.7 | Andreas Tille,Michael R. Crusoe,Steffen Moeller | Michael R. Crusoe | 2020-02-14 13:04:26+00
libics | 1.6.3 | 1.6.4 | Andreas Tille | Andreas Tille | 2019-08-01 12:39:13+00
libjloda-java | 0.0+git20180523.cbaf6d1 | 0.0+git20200227.17134f9 | Andreas Tille | Andreas Tille | 2018-05-25 21:49:43+00
- libmaus2 | 2.0.698 | 2.0.703 | Andreas Tille,Steffen Moeller | Andreas Tille | 2020-02-05 10:04:12+00
+ libmaus2 | 2.0.698 | 2.0.704 | Andreas Tille,Steffen Moeller | Andreas Tille | 2020-02-05 10:04:12+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
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
@@ -47,6 +48,8 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
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 | 13.5.20200221 | 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
nibabel | 2.5.1 | 3.0.1 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-01-20 10:35:09+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
@@ -61,7 +64,7 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
python-cgecore | 1.5.2 | 1.5.3 | Andreas Tille | Steffen Moeller | 2020-01-06 17:05:53+00
python-cobra | 0.14.2 | 0.17.1 | Afif Elghraoui | Liubov Chuprikova | 2019-03-02 06:49:44+00
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+git20200211.116b09f | Andreas Tille | Andreas Tille | 2019-12-19 08:42:03+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-treetime | 0.7.1 | 0.7.4 | Andreas Tille | Steffen Moeller | 2020-01-18 20:52:48+00
q2-feature-classifier | 2019.4.0 | 2019.10.0 | Liubov Chuprikova | Liubov Chuprikova | 2019-11-11 10:00:33+00
@@ -69,6 +72,7 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
resfinder-db | 0.0+git20191001.149209d | 0.0+git20200213.2a8dd7f | Andreas Tille | Andreas Tille | 2019-11-16 23:00:12+00
salmon | 0.12.0 | 1.1.0 | Kevin Murray,Michael R. Crusoe | Andreas Tille | 2018-12-13 19:05:56+00
seaview | 4.7 | 5.0.1 | Andreas Tille,Charles Plessy | Andreas Tille | 2018-05-09 13:43:40+00
+ shapeit4 | 4.1 | 4.1.3 | Dylan Aïssi | Dylan Aïssi | 2019-12-18 22:06:47+00
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
@@ -78,7 +82,7 @@ Last-Update: Sat, 29 Feb 2020 01:42:04 +0000
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
-(76 rows)
+(80 rows)
source | id | severity | title
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/21a0bbbdd1ffc27e453b110c6a32edc057ebc64c
--
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/21a0bbbdd1ffc27e453b110c6a32edc057ebc64c
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