Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
f0bb75b8 by Andreas Tille at 2020-03-06T13:45:02+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,52 +1,51 @@
-Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
+Last-Update: Fri, 06 Mar 2020 13:42:03 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------
- dcmtk | 175 | {imaging} |
- orthanc | 95 | {practice,imaging} |
- gdcm | 45 | {imaging-dev} |
+ dcmtk | 178 | {imaging} |
+ orthanc | 97 | {practice,imaging} |
+ gdcm | 47 | {imaging-dev} |
+ dcm2niix | 40 | {imaging} |
orthanc-wsi | 38 | {oncology,laboratory,imaging,his,practice} |
- dcm2niix | 37 | {imaging} |
- amide | 35 | {imaging} |
- dicomscope | 29 | {imaging} |
- dicom3tools | 26 | {imaging} |
+ amide | 37 | {imaging} |
+ dicomscope | 30 | {imaging} |
+ dicom3tools | 29 | {imaging} |
medicalterms | 26 | {tools} |
- htsjdk | 24 | {bio-dev} |
- gdcm | 18 | {imaging} |
- gnumed-server | 17 | {practice} |
+ htsjdk | 25 | {bio-dev} |
+ gdcm | 20 | {imaging} |
+ gnumed-server | 18 | {practice} |
+ pixelmed | 16 | {imaging} |
invesalius | 15 | {imaging} |
- pixelmed | 14 | {imaging} |
- ngs-sdk | 13 | {bio-dev} |
+ king | 14 | {imaging,typesetting} |
+ ngs-sdk | 14 | {bio-dev} |
+ minc-tools | 13 | {imaging} |
adun.app | 12 | {bio} |
- minc-tools | 12 | {imaging} |
insighttoolkit4 | 11 | {imaging-dev} |
- king | 11 | {imaging,typesetting} |
vtk-dicom | 11 | {imaging} |
- gdcm | 10 | {imaging-dev} |
+ biosig4c++ | 10 | {imaging,physics} |
jebl2 | 10 | {bio-dev} |
- mia | 9 | {imaging} |
- tree-puzzle | 9 | {bio,bio-phylogeny,cloud} |
- biosig4c++ | 8 | {imaging,physics} |
+ mia | 10 | {imaging} |
+ openslide | 10 | {imaging} |
+ tree-puzzle | 10 | {bio,bio-phylogeny,cloud} |
+ gdcm | 9 | {imaging-dev} |
+ plastimatch | 9 | {imaging} |
librg-utils-perl | 8 | {bio} |
+ ncbi-entrez-direct | 8 | {bio} |
ngs-sdk | 8 | {bio-dev} |
- openslide | 8 | {imaging} |
- plastimatch | 8 | {imaging} |
- psychopy | 8 | {psychology} |
biojava-live | 7 | {bio-dev} |
+ dicompyler | 7 | {oncology} |
fastlink | 7 | {cloud,bio} |
melting | 7 | {bio,cloud} |
- ncbi-entrez-direct | 7 | {bio} |
obitools | 7 | {bio} |
+ psychopy | 7 | {psychology} |
+ sortmerna | 7 | {bio} |
+ staden | 7 | {bio} |
arden | 6 | {cloud,bio} |
- dicompyler | 6 | {oncology} |
+ cgview | 6 | {bio} |
maqview | 6 | {bio} |
mipe | 6 | {bio,cloud} |
ncbi-seg | 6 | {bio} |
norsp | 6 | {bio} |
- sortmerna | 6 | {bio} |
- staden | 6 | {bio} |
- cgview | 5 | {bio} |
- cluster3 | 5 | {bio} |
estscan | 5 | {bio} |
gasic | 5 | {cloud,bio} |
idba | 5 | {bio,cloud} |
@@ -66,7 +65,9 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
anfo | 4 | {cloud,bio} |
biomaj3-cli | 4 | {cloud} |
bio-tradis | 4 | {bio-dev,bio} |
+ cluster3 | 4 | {bio} |
dazzdb | 4 | {bio} |
+ diamond-aligner | 4 | {bio} |
ea-utils | 4 | {bio} |
ecopcr | 4 | {bio} |
edtsurf | 4 | {bio} |
@@ -79,6 +80,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
ipig | 4 | {bio} |
jellyfish1 | 4 | {bio} |
libdivsufsort | 4 | {bio-dev} |
+ libsbml | 4 | {bio-dev} |
mapsembler2 | 4 | {bio,cloud} |
mauve-aligner | 4 | {bio} |
paml | 4 | {bio} |
@@ -90,6 +92,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
proalign | 4 | {bio-phylogeny,bio} |
probabel | 4 | {bio,cloud} |
relion | 4 | {bio} |
+ salmon | 4 | {bio} |
seqtools | 4 | {bio} |
squizz | 4 | {bio,cloud} |
tracetuner | 4 | {bio} |
@@ -106,7 +109,6 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
canu | 3 | {bio} |
codonw | 3 | {bio} |
delly | 3 | {bio} |
- diamond-aligner | 3 | {bio} |
elph | 3 | {bio} |
gatb-core | 3 | {bio} |
getdata | 3 | {bio} |
@@ -115,7 +117,6 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
libgff | 3 | {bio-dev} |
libminc | 3 | {imaging-dev} |
libncl | 3 | {bio} |
- libsbml | 3 | {bio-dev} |
lucy | 3 | {bio} |
mhap | 3 | {bio-ngs,bio} |
microbegps | 3 | {bio} |
@@ -129,12 +130,10 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
prime-phylo | 3 | {cloud,bio} |
pscan-chip | 3 | {bio} |
pscan-tfbs | 3 | {bio} |
- qrisk2 | 3 | {practice} |
quorum | 3 | {bio} |
rdp-alignment | 3 | {bio} |
rdp-readseq | 3 | {bio} |
saint | 3 | {bio} |
- salmon | 3 | {bio} |
seer | 3 | {bio} |
segemehl | 3 | {bio} |
seqsero | 3 | {bio} |
@@ -144,6 +143,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
yaha | 3 | {bio} |
abacas | 2 | {bio} |
acedb | 2 | {bio,cloud} |
+ alter-sequence-alignment | 2 | {bio} |
andi | 2 | {bio} |
baitfisher | 2 | {bio} |
bart-view | 2 | {imaging} |
@@ -155,6 +155,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
blasr | 2 | {bio-ngs,bio} |
centrifuge | 2 | {bio} |
clonalorigin | 2 | {bio} |
+ ctn | 2 | {imaging-dev} |
cufflinks | 2 | {bio,cloud} |
daligner | 2 | {bio-ngs,bio} |
dascrubber | 2 | {bio} |
@@ -165,6 +166,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
hinge | 2 | {bio} |
igor | 2 | {bio} |
lamarc | 2 | {bio} |
+ libpal-java | 2 | {bio-dev} |
librdp-taxonomy-tree-java | 2 | {bio-dev} |
maffilter | 2 | {bio} |
mptp | 2 | {bio} |
@@ -175,7 +177,9 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
phipack | 2 | {bio} |
phybin | 2 | {bio} |
poretools | 2 | {bio} |
+ prottest | 2 | {bio-phylogeny,bio} |
qcumber | 2 | {bio} |
+ qrisk2 | 2 | {practice} |
rambo-k | 2 | {bio} |
rampler | 2 | {bio} |
rdp-classifier | 2 | {bio} |
@@ -195,11 +199,9 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
trace2dbest | 2 | {bio} |
transrate-tools | 2 | {bio} |
tvc | 2 | {bio} |
- alter-sequence-alignment | 1 | {bio} |
biosig4c++ | 1 | {physics,imaging-dev} |
blimps | 1 | {bio} |
clonalframeml | 1 | {bio} |
- ctn | 1 | {imaging-dev} |
edflib | 1 | {imaging-dev} |
elastix | 1 | {imaging} |
embassy-phylip | 1 | {cloud,bio} |
@@ -213,20 +215,20 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
libbio-mage-utils-perl | 1 | {bio-dev} |
libctapimkt | 1 | {practice} |
libhmsbeagle | 1 | {bio-dev} |
- libpal-java | 1 | {bio-dev} |
- libsmithwaterman | 1 | {bio} |
libsmithwaterman | 1 | {bio-dev} |
+ libsmithwaterman | 1 | {bio} |
libvistaio | 1 | {imaging-dev} |
logol | 1 | {bio} |
maxflow | 1 | {imaging-dev} |
medicalterms | 1 | {tools} |
mencal | 1 | {tools} |
metaphlan2 | 1 | {bio} |
+ opencfu | 1 | {laboratory} |
orthanc-mysql | 1 | {imaging} |
orthanc-postgresql | 1 | {imaging} |
pal2nal | 1 | {bio} |
+ papyrus | 1 | {imaging-dev} |
pilercr | 1 | {bio} |
- prottest | 1 | {bio-phylogeny,bio} |
python-tinyalign | 1 | {bio-dev,bio} |
roguenarok | 1 | {bio} |
samtools-legacy | 1 | {bio-dev} |
@@ -249,6 +251,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
tree-puzzle | 1 | {cloud,bio-phylogeny,bio} |
varscan | 1 | {bio} |
volpack | 1 | {imaging-dev} |
+ vtk-dicom | 1 | {imaging-dev} |
atropos | 0 | {bio} |
bambamc | 0 | {bio-dev} |
biobambam2 | 0 | {bio,bio-dev} |
@@ -296,11 +299,9 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
murasaki | 0 | {bio} |
ncbi-vdb | 0 | {bio-dev} |
ngs-sdk | 0 | {bio-dev} |
- opencfu | 0 | {laboratory} |
opensurgsim | 0 | {imaging-dev} |
orthanc-imagej | 0 | {imaging} |
oscar | 0 | {tools,data,practice} |
- papyrus | 0 | {imaging-dev} |
pbcopper | 0 | {bio-dev} |
pbseqlib | 0 | {bio-dev} |
python-deeptools | 0 | {bio-dev,bio} |
@@ -318,6 +319,5 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
spaln | 0 | {bio} |
trim-galore | 0 | {bio} |
varna | 0 | {bio} |
- vtk-dicom | 0 | {imaging-dev} |
(347 rows)
=====================================
outdated_med-packages.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
+Last-Update: Fri, 06 Mar 2020 13:42:03 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+-----------------------------------------------------------------------------+-----------------------+------------------------
@@ -14,7 +14,7 @@ Last-Update: Fri, 06 Mar 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
- biosig4c++ | 1.9.5 | 2.0.1 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-03-02 08:38:37+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 | 2.0.20200303141624 | Michael R. Crusoe | Michael R. Crusoe | 2020-02-26 12:07:54+00
@@ -26,7 +26,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
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
gdcm | 3.0.4 | 3.0.5 | Gert Wollny,Sébastien Jodogne,Steve M. Robbins | Gert Wollny | 2019-11-07 11:49:02+00
- hdmf | 1.5.4 | 1.6.0 | Yaroslav Halchenko | Yaroslav Halchenko | 2020-02-03 03:01:25+00
+ hdmf | 1.5.4 | 1.6.1 | Yaroslav Halchenko | Yaroslav Halchenko | 2020-02-03 03:01:25+00
htsjdk | 2.18.2 | 2.21.2 | Andreas Tille,Charles Plessy,Olivier Sallou,Vincent Danjean | Andreas Tille | 2019-03-01 22:19:40+00
hyphy | 2.5.1 | 2.5.5 | Andreas Tille | Andreas Tille | 2020-01-07 21:19:50+00
igdiscover | 0.11 | 0.12.2 | Steffen Moeller | Andreas Tille | 2019-09-06 07:04:02+00
@@ -50,6 +50,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
mothur | 1.42.1 | 1.43.0 | Andreas Tille,Steffen Moeller,Tomasz Buchert | Andreas Tille | 2019-08-01 19:09:05+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 | 13.5.20200304 | 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
pbcopper | 1.3.0 | 1.4.0 | Andreas Tille | Andreas Tille | 2020-01-29 08:51:15+00
@@ -67,6 +68,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
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+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-schema-salad | 5.0.20200220195218 | 5.0.20200302192450 | Michael R. Crusoe | Michael R. Crusoe | 2020-02-27 19:19:53+00
python-treetime | 0.7.1 | 0.7.4 | Andreas Tille | Steffen Moeller | 2020-01-18 20:52:48+00
q2cli | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2019-12-16 10:20:08+00
q2-cutadapt | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2020-01-26 07:34:32+00
@@ -85,13 +87,14 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
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
+ spoa | 3.0.1 | 3.0.2 | Andreas Tille | Andreas Tille | 2019-09-16 11:53:05+00
sra-sdk | 2.9.3 | 2.10.4 | Andreas Tille,Charles Plessy | Steffen Moeller | 2018-10-23 20:40:02+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
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
-(89 rows)
+(92 rows)
source | id | severity | title
@@ -237,6 +240,7 @@ Last-Update: Fri, 06 Mar 2020 01:42:04 +0000
prokka | 924128 | normal | prokka: creates world writable directory tree /var/lib/prokka/*
psychopy | 730810 | normal | psychopy: Movie support suboptimal
psychopy | 829424 | normal | psychopy: ioHub uses inappropriate PID file location
+ psychopy | 937330 | normal | psychopy: Python2 removal in sid/bullseye
psychopy | 953052 | important | psychopy: python2 dependencies
psychopy | 953053 | important | psychopy: missing python3 dependencies
pynast | 937488 | normal | pynast: Python2 removal in sid/bullseye
@@ -290,5 +294,5 @@ Last-Update: Fri, 06 Mar 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
-(194 rows)
+(195 rows)
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/f0bb75b897d46feb37b50d8d9a718a27af38f546
--
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