Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
7220631f by Andreas Tille at 2020-04-09T13:44:33+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,43 +1,44 @@
-Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
+Last-Update: Thu, 09 Apr 2020 13:42:04 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk | 167 | {imaging,covid-19} |
- orthanc | 94 | {practice,imaging,covid-19} |
- gdcm | 44 | {imaging-dev} |
- orthanc-wsi | 40 | {practice,imaging,oncology,laboratory,covid-19,his} |
+ dcmtk | 170 | {imaging,covid-19} |
+ orthanc | 95 | {imaging,covid-19,practice} |
+ gdcm | 43 | {imaging-dev} |
+ orthanc-wsi | 41 | {imaging,laboratory,covid-19,practice,oncology,his} |
amide | 30 | {imaging} |
htsjdk | 29 | {bio-dev} |
dcm2niix | 26 | {imaging} |
dicom3tools | 24 | {imaging} |
dicomscope | 24 | {imaging} |
- gdcm | 22 | {imaging,covid-19} |
- gnumed-server | 18 | {covid-19,practice} |
- ngs-sdk | 18 | {bio-dev} |
- minc-tools | 15 | {imaging} |
- ncbi-entrez-direct | 13 | {bio} |
+ gdcm | 22 | {covid-19,imaging} |
+ gnumed-server | 19 | {covid-19,practice} |
+ ngs-sdk | 17 | {bio-dev} |
+ minc-tools | 14 | {imaging} |
+ ncbi-entrez-direct | 14 | {bio} |
adun.app | 12 | {bio} |
invesalius | 12 | {imaging} |
- king | 12 | {imaging,typesetting} |
+ king | 12 | {typesetting,imaging} |
vtk-dicom | 12 | {imaging} |
hunspell-en-med | 11 | {tools} |
- insighttoolkit4 | 11 | {imaging-dev} |
pixelmed | 11 | {imaging} |
- psychopy | 11 | {psychology} |
cgview | 10 | {bio} |
ea-utils | 10 | {bio} |
+ insighttoolkit4 | 10 | {imaging-dev} |
mia | 10 | {imaging} |
- ngs-sdk | 10 | {bio-dev} |
openslide | 10 | {imaging} |
+ psychopy | 10 | {psychology} |
staden | 10 | {bio} |
gasic | 9 | {bio,cloud} |
gdcm | 9 | {imaging-dev} |
jebl2 | 9 | {bio-dev} |
king-probe | 9 | {bio} |
+ ngs-sdk | 9 | {bio-dev} |
obitools | 9 | {bio} |
biojava-live | 8 | {bio-dev} |
biosig4c++ | 8 | {physics,imaging} |
dazzdb | 8 | {bio} |
+ librg-utils-perl | 8 | {bio} |
mipe | 8 | {bio,cloud} |
paml | 8 | {bio} |
parsnp | 8 | {bio} |
@@ -45,22 +46,21 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
arden | 7 | {cloud,bio} |
biomaj3-cli | 7 | {cloud} |
bppsuite | 7 | {bio} |
- diamond-aligner | 7 | {bio,covid-19} |
- fitgcp | 7 | {bio,cloud} |
+ diamond-aligner | 7 | {covid-19,bio} |
+ fitgcp | 7 | {cloud,bio} |
lagan | 7 | {bio} |
- librg-utils-perl | 7 | {bio} |
phast | 7 | {bio} |
radiant | 7 | {bio} |
salmon | 7 | {bio} |
- tree-puzzle | 7 | {cloud,bio-phylogeny,bio} |
+ tree-puzzle | 7 | {bio,cloud,bio-phylogeny} |
abacas | 6 | {bio} |
anfo | 6 | {cloud,bio} |
biomaj3-daemon | 6 | {bio} |
cluster3 | 6 | {bio} |
ecopcr | 6 | {bio} |
- embassy-domainatrix | 6 | {cloud,bio} |
+ embassy-domainatrix | 6 | {bio,cloud} |
fastlink | 6 | {cloud,bio} |
- freecontact | 6 | {bio,cloud} |
+ freecontact | 6 | {cloud,bio} |
ncbi-seg | 6 | {bio} |
neobio | 6 | {bio,cloud} |
norsp | 6 | {bio} |
@@ -73,7 +73,7 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
seqtools | 6 | {bio} |
tracetuner | 6 | {bio} |
alter-sequence-alignment | 5 | {bio} |
- ampliconnoise | 5 | {bio,cloud} |
+ ampliconnoise | 5 | {cloud,bio} |
bandage | 5 | {bio} |
bio-rainbow | 5 | {bio} |
bitseq | 5 | {bio} |
@@ -81,7 +81,7 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
codonw | 5 | {bio} |
daligner | 5 | {bio-ngs,bio} |
edtsurf | 5 | {bio} |
- embassy-domalign | 5 | {bio,cloud} |
+ embassy-domalign | 5 | {cloud,bio} |
embassy-domsearch | 5 | {bio,cloud} |
estscan | 5 | {bio} |
fastml | 5 | {bio} |
@@ -92,11 +92,9 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
indelible | 5 | {bio} |
jaligner | 5 | {bio} |
jellyfish1 | 5 | {bio} |
- libdivsufsort | 5 | {bio-dev} |
maqview | 5 | {bio} |
melting | 5 | {cloud,bio} |
- openslide | 5 | {imaging-dev} |
- phyutility | 5 | {cloud,bio} |
+ phyutility | 5 | {bio,cloud} |
placnet | 5 | {bio} |
predictprotein | 5 | {bio} |
pscan-chip | 5 | {bio} |
@@ -104,17 +102,17 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
seer | 5 | {bio} |
seqtools | 5 | {bio} |
sibsim4 | 5 | {bio,cloud} |
- sigma-align | 5 | {cloud,bio-phylogeny,bio} |
+ sigma-align | 5 | {cloud,bio,bio-phylogeny} |
sumatra | 5 | {bio} |
vsearch | 5 | {bio} |
baitfisher | 4 | {bio} |
bart-view | 4 | {imaging} |
beads | 4 | {bio} |
- beast-mcmc | 4 | {bio-phylogeny,bio} |
- bio-tradis | 4 | {bio-dev,bio} |
+ beast-mcmc | 4 | {bio,bio-phylogeny} |
+ bio-tradis | 4 | {bio,bio-dev} |
brig | 4 | {bio} |
centrifuge | 4 | {bio} |
- clonalframeml | 4 | {bio,covid-19} |
+ clonalframeml | 4 | {covid-19,bio} |
dascrubber | 4 | {bio} |
delly | 4 | {bio,covid-19} |
dindel | 4 | {bio} |
@@ -124,18 +122,20 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
hinge | 4 | {bio} |
ipig | 4 | {bio} |
lamarc | 4 | {bio} |
+ libdivsufsort | 4 | {bio-dev} |
libncl | 4 | {bio} |
- mapsembler2 | 4 | {cloud,bio} |
+ mapsembler2 | 4 | {bio,cloud} |
mencal | 4 | {tools} |
microbegps | 4 | {bio} |
mlv-smile | 4 | {bio,cloud} |
mrs | 4 | {bio} |
murasaki | 4 | {bio} |
+ openslide | 4 | {imaging-dev} |
paraclu | 4 | {cloud,bio} |
perm | 4 | {bio,cloud} |
poretools | 4 | {bio} |
proalign | 4 | {bio-phylogeny,bio} |
- probabel | 4 | {bio,cloud} |
+ probabel | 4 | {cloud,bio} |
quorum | 4 | {bio} |
rdp-alignment | 4 | {bio} |
rdp-readseq | 4 | {bio} |
@@ -143,16 +143,17 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
repeatmasker-recon | 4 | {bio} |
saint | 4 | {bio} |
sprai | 4 | {bio} |
- spread-phy | 4 | {bio,bio-phylogeny} |
- squizz | 4 | {cloud,bio} |
+ spread-phy | 4 | {bio-phylogeny,bio} |
+ squizz | 4 | {bio,cloud} |
transtermhp | 4 | {bio} |
treeview | 4 | {bio-phylogeny,bio} |
assemblytics | 3 | {bio} |
beast2-mcmc | 3 | {bio} |
- blasr | 3 | {bio,bio-ngs} |
+ blasr | 3 | {bio-ngs,bio} |
canu | 3 | {bio} |
dicompyler | 3 | {oncology} |
- jmodeltest | 3 | {bio,bio-phylogeny} |
+ jmodeltest | 3 | {bio-phylogeny,bio} |
+ libgff | 3 | {bio-dev} |
libminc | 3 | {imaging-dev} |
libpal-java | 3 | {bio-dev} |
librdp-taxonomy-tree-java | 3 | {bio-dev} |
@@ -168,7 +169,7 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
orthanc-mysql | 3 | {imaging} |
patman | 3 | {bio} |
pbdagcon | 3 | {bio} |
- prottest | 3 | {bio,bio-phylogeny} |
+ prottest | 3 | {bio-phylogeny,bio} |
rdp-classifier | 3 | {bio} |
samblaster | 3 | {covid-19,bio} |
scythe | 3 | {bio} |
@@ -179,13 +180,12 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
stacks | 3 | {bio} |
transrate-tools | 3 | {bio} |
biosig4c++ | 2 | {imaging-dev,physics} |
- cufflinks | 2 | {cloud,bio} |
+ cufflinks | 2 | {bio,cloud} |
elastix | 2 | {imaging} |
getdata | 2 | {bio} |
igor | 2 | {bio} |
- libgff | 2 | {bio-dev} |
libsmithwaterman | 2 | {bio} |
- mhap | 2 | {bio-ngs,bio} |
+ mhap | 2 | {bio,bio-ngs} |
ngs-sdk | 2 | {bio-dev} |
pal2nal | 2 | {bio} |
phipack | 2 | {bio} |
@@ -197,10 +197,10 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
rampler | 2 | {bio} |
relion | 2 | {bio} |
roguenarok | 2 | {bio} |
- rtax | 2 | {cloud,bio} |
+ rtax | 2 | {bio,cloud} |
runcircos-gui | 2 | {bio} |
scrm | 2 | {bio} |
- seqmagick | 2 | {covid-19,bio} |
+ seqmagick | 2 | {bio,covid-19} |
snap-aligner | 2 | {bio} |
soapaligner | 2 | {bio} |
spaced | 2 | {bio} |
@@ -208,17 +208,17 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
suitename | 2 | {bio} |
surankco | 2 | {bio} |
sweed | 2 | {bio} |
- thesias | 2 | {covid-19,bio} |
+ thesias | 2 | {bio,covid-19} |
tnseq-transit | 2 | {covid-19,bio} |
tvc | 2 | {bio} |
varscan | 2 | {bio} |
yaha | 2 | {bio} |
- zalign | 2 | {cloud,bio} |
+ zalign | 2 | {bio,cloud} |
atropos | 1 | {bio} |
biosig4c++ | 1 | {imaging-dev,physics} |
blimps | 1 | {bio} |
ctn | 1 | {imaging-dev} |
- embassy-phylip | 1 | {bio,cloud} |
+ embassy-phylip | 1 | {cloud,bio} |
kma | 1 | {bio} |
kmerresistance | 1 | {bio} |
libchado-perl | 1 | {bio-dev} |
@@ -234,9 +234,9 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
samtools-legacy | 1 | {bio-dev} |
sift | 1 | {bio} |
skesa | 1 | {bio} |
- stringtie | 1 | {bio,covid-19} |
+ stringtie | 1 | {covid-19,bio} |
trace2dbest | 1 | {bio} |
- tree-puzzle | 1 | {cloud,bio,bio-phylogeny} |
+ tree-puzzle | 1 | {bio-phylogeny,bio,cloud} |
velvetoptimiser | 1 | {bio} |
volpack | 1 | {imaging-dev} |
acedb | 0 | {cloud,bio} |
@@ -250,11 +250,11 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
camp | 0 | {imaging-dev} |
emboss-explorer | 0 | {bio} |
emmax | 0 | {bio} |
- fasta3 | 0 | {covid-19,bio} |
+ fasta3 | 0 | {bio,covid-19} |
fis-gtm | 0 | {his} |
freecontact | 0 | {bio-dev} |
gatb-core | 0 | {bio-dev} |
- htscodecs | 0 | {covid-19,bio-dev} |
+ htscodecs | 0 | {bio-dev,covid-19} |
libbigwig | 0 | {bio-dev} |
libbiod | 0 | {bio-dev} |
libbio-mage-utils-perl | 0 | {bio-dev} |
@@ -289,14 +289,14 @@ Last-Update: Thu, 09 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} |
multiqc | 0 | {bio} |
murasaki | 0 | {bio} |
ncbi-vdb | 0 | {bio-dev} |
opencfu | 0 | {laboratory} |
orthanc-imagej | 0 | {imaging} |
- oscar | 0 | {data,practice,tools} |
+ oscar | 0 | {practice,data,tools} |
pbcopper | 0 | {bio-dev} |
pbseqlib | 0 | {bio-dev} |
python-py2bit | 0 | {bio-dev,bio} |
@@ -315,6 +315,7 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
varna | 0 | {bio} |
vtk-dicom | 0 | {imaging-dev} |
bustools | -1 | {bio} |
+ relion | -1 | {bio} |
wtdbg2 | -1 | {covid-19} |
-(344 rows)
+(345 rows)
=====================================
outdated_med-packages.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
+Last-Update: Thu, 09 Apr 2020 13:42:04 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+-------------------------------------------------------------------------+----------------------+------------------------
@@ -22,7 +22,7 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
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
htsjdk | 2.18.2 | 2.21.3 | Andreas Tille,Charles Plessy,Olivier Sallou,Vincent Danjean | Andreas Tille | 2019-03-01 22:19:40+00
- igdiscover | 0.11 | 0.12.3 | Steffen Moeller | Andreas Tille | 2019-09-06 07:04:02+00
+ hyphy | 2.5.1 | 2.5.8 | Andreas Tille | Andreas Tille | 2020-01-07 21:19:50+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
jebl2 | 0.1+git20180418.653eb83 | 0.1+git20190308.a98448e | Andreas Tille | Andreas Tille | 2018-07-05 12:05:57+00
@@ -39,11 +39,10 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
metaphlan2 | 2.9.22 | 2.96.1 | Andreas Tille | Andreas Tille | 2019-11-08 07:19:11+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
- ncbi-vdb | 2.10.3 | 2.10.5 | Andreas Tille | Andreas Tille | 2020-02-24 21:12:17+00
plink2 | 2.00~a3-200217 | 200328 | Dylan Aïssi | Dylan Aïssi | 2020-02-19 06:19:18+00
pynn | 0.7.5 | 0.9.5 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-04-03 16:34:56+00
python-avro | 1.9.1 | 1.9.2 | Afif Elghraoui | Andreas Tille | 2019-12-18 08:41:55+00
- python-bids-validator | 1.2.4 | 1.5.0 | Yaroslav Halchenko | Yaroslav Halchenko | 2019-08-17 19:00:11+00
+ python-bids-validator | 1.2.4 | 1.5.1 | Yaroslav Halchenko | Yaroslav Halchenko | 2019-08-17 19:00:11+00
python-cgecore | 1.5.3 | 1.5.4 | Andreas Tille | Steffen Moeller | 2020-03-17 12:49:52+00
python-colormap | 1.0.2 | 1.0.3 | Andreas Tille | Andreas Tille | 2019-12-06 16:51:43+00
python-pbcore | 1.7.1+git20200313.41ba394 | 1.7.1+git20200326.ea0808a | Andreas Tille | Steffen Moeller | 2020-03-21 19:39:08+00
@@ -52,7 +51,7 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
python-xopen | 0.8.4 | 0.9.0 | Andreas Tille | Steffen Moeller | 2019-11-05 15:34:45+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
+ resfinder-db | 0.0+git20191001.149209d | 0.0+git20200408.0322c0d | Andreas Tille | Andreas Tille | 2019-11-16 23:00:12+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
simpleitk | 1.0.1 | 1.2.0 | Ghislain Antony Vaillant | Andreas Tille | 2019-01-30 10:06:08+00
@@ -65,7 +64,7 @@ Last-Update: Thu, 09 Apr 2020 01:42:03 +0000
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 | 4.2.0-1 | Afif Elghraoui,Andreas Tille | Adrian Bunk | 2019-02-06 07:34:42+00
xmedcon | 0.16.1 | 0.16.2 | Andreas Tille,Roland Marcus Rutschmann | Andreas Tille | 2019-01-25 18:23:59+00
-(63 rows)
+(62 rows)
source | id | severity | title
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/7220631fac8da64eb9cdd461c38bfb66f7c892b6
--
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