Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
c5aad202 by Andreas Tille at 2020-03-05T13:44:27+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,242 +1,243 @@
-Last-Update: Thu, 05 Mar 2020 01:42:03 +0000
+Last-Update: Thu, 05 Mar 2020 13:42:03 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------
dcmtk | 175 | {imaging} |
- orthanc | 97 | {practice,imaging} |
+ orthanc | 95 | {practice,imaging} |
gdcm | 45 | {imaging-dev} |
- orthanc-wsi | 39 | {oncology,laboratory,imaging,his,practice} |
+ orthanc-wsi | 38 | {oncology,laboratory,imaging,his,practice} |
dcm2niix | 37 | {imaging} |
amide | 35 | {imaging} |
- dicomscope | 27 | {imaging} |
- medicalterms | 27 | {tools} |
+ dicomscope | 29 | {imaging} |
dicom3tools | 26 | {imaging} |
- htsjdk | 22 | {bio-dev} |
- gdcm | 17 | {imaging} |
+ medicalterms | 26 | {tools} |
+ htsjdk | 24 | {bio-dev} |
+ gdcm | 18 | {imaging} |
gnumed-server | 17 | {practice} |
- invesalius | 13 | {imaging} |
- pixelmed | 13 | {imaging} |
+ invesalius | 15 | {imaging} |
+ pixelmed | 14 | {imaging} |
+ ngs-sdk | 13 | {bio-dev} |
adun.app | 12 | {bio} |
minc-tools | 12 | {imaging} |
- ngs-sdk | 12 | {bio-dev} |
- gdcm | 9 | {imaging-dev} |
- insighttoolkit4 | 9 | {imaging-dev} |
- jebl2 | 9 | {bio-dev} |
- king | 9 | {imaging,typesetting} |
+ insighttoolkit4 | 11 | {imaging-dev} |
+ king | 11 | {imaging,typesetting} |
+ vtk-dicom | 11 | {imaging} |
+ gdcm | 10 | {imaging-dev} |
+ jebl2 | 10 | {bio-dev} |
mia | 9 | {imaging} |
tree-puzzle | 9 | {bio,bio-phylogeny,cloud} |
- vtk-dicom | 9 | {imaging} |
- biojava-live | 8 | {bio-dev} |
+ biosig4c++ | 8 | {imaging,physics} |
+ librg-utils-perl | 8 | {bio} |
ngs-sdk | 8 | {bio-dev} |
- obitools | 8 | {bio} |
+ openslide | 8 | {imaging} |
plastimatch | 8 | {imaging} |
psychopy | 8 | {psychology} |
- biosig4c++ | 7 | {imaging,physics} |
+ biojava-live | 7 | {bio-dev} |
+ fastlink | 7 | {cloud,bio} |
+ melting | 7 | {bio,cloud} |
ncbi-entrez-direct | 7 | {bio} |
+ obitools | 7 | {bio} |
arden | 6 | {cloud,bio} |
- cgview | 6 | {bio} |
- cluster3 | 6 | {bio} |
- fastlink | 6 | {cloud,bio} |
- librg-utils-perl | 6 | {bio} |
+ dicompyler | 6 | {oncology} |
maqview | 6 | {bio} |
- melting | 6 | {bio,cloud} |
mipe | 6 | {bio,cloud} |
- openslide | 6 | {imaging} |
- orthanc-webviewer | 6 | {imaging} |
- dazzdb | 5 | {bio} |
- dicompyler | 5 | {oncology} |
- embassy-domainatrix | 5 | {cloud,bio} |
+ 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} |
+ jaligner | 5 | {bio} |
+ king-probe | 5 | {bio} |
lagan | 5 | {bio} |
- ncbi-seg | 5 | {bio} |
- norsp | 5 | {bio} |
+ neobio | 5 | {cloud,bio} |
openslide | 5 | {imaging-dev} |
+ orthanc-webviewer | 5 | {imaging} |
+ phyutility | 5 | {bio,cloud} |
+ piler | 5 | {bio} |
pymia | 5 | {imaging-dev} |
radiant | 5 | {bio} |
sibsim4 | 5 | {cloud,bio} |
sigma-align | 5 | {bio-phylogeny,bio,cloud} |
- sortmerna | 5 | {bio} |
+ ampliconnoise | 4 | {cloud,bio} |
anfo | 4 | {cloud,bio} |
biomaj3-cli | 4 | {cloud} |
bio-tradis | 4 | {bio-dev,bio} |
+ dazzdb | 4 | {bio} |
+ ea-utils | 4 | {bio} |
+ ecopcr | 4 | {bio} |
+ edtsurf | 4 | {bio} |
+ embassy-domainatrix | 4 | {cloud,bio} |
embassy-domalign | 4 | {bio,cloud} |
embassy-domsearch | 4 | {bio,cloud} |
- estscan | 4 | {bio} |
- gasic | 4 | {cloud,bio} |
- idba | 4 | {bio,cloud} |
+ fitgcp | 4 | {bio,cloud} |
+ freecontact | 4 | {bio,cloud} |
+ indelible | 4 | {bio} |
ipig | 4 | {bio} |
- jaligner | 4 | {bio} |
- king-probe | 4 | {bio} |
+ jellyfish1 | 4 | {bio} |
libdivsufsort | 4 | {bio-dev} |
mapsembler2 | 4 | {bio,cloud} |
- mrs | 4 | {bio} |
- neobio | 4 | {cloud,bio} |
- orthanc-dicomweb | 4 | {imaging} |
+ mauve-aligner | 4 | {bio} |
paml | 4 | {bio} |
- phyutility | 4 | {bio,cloud} |
- piler | 4 | {bio} |
+ paraclu | 4 | {cloud,bio} |
+ parsnp | 4 | {bio} |
+ perm | 4 | {cloud,bio} |
+ plasmidseeker | 4 | {bio} |
+ predictprotein | 4 | {bio} |
+ proalign | 4 | {bio-phylogeny,bio} |
+ probabel | 4 | {bio,cloud} |
relion | 4 | {bio} |
+ seqtools | 4 | {bio} |
squizz | 4 | {bio,cloud} |
- staden | 4 | {bio} |
tracetuner | 4 | {bio} |
transtermhp | 4 | {bio} |
treeview | 4 | {bio-phylogeny,bio} |
velvetoptimiser | 4 | {bio} |
zalign | 4 | {cloud,bio} |
- abacas | 3 | {bio} |
- ampliconnoise | 3 | {cloud,bio} |
assemblytics | 3 | {bio} |
bandage | 3 | {bio} |
+ beast2-mcmc | 3 | {bio} |
biomaj3-daemon | 3 | {bio} |
bppsuite | 3 | {bio} |
brig | 3 | {bio} |
+ canu | 3 | {bio} |
codonw | 3 | {bio} |
- ea-utils | 3 | {bio} |
- ecopcr | 3 | {bio} |
- edtsurf | 3 | {bio} |
- fitgcp | 3 | {bio,cloud} |
- freecontact | 3 | {bio,cloud} |
+ delly | 3 | {bio} |
+ diamond-aligner | 3 | {bio} |
+ elph | 3 | {bio} |
+ gatb-core | 3 | {bio} |
getdata | 3 | {bio} |
- indelible | 3 | {bio} |
- jellyfish1 | 3 | {bio} |
+ ghmm | 3 | {bio} |
+ harvest-tools | 3 | {bio} |
+ libgff | 3 | {bio-dev} |
libminc | 3 | {imaging-dev} |
+ libncl | 3 | {bio} |
libsbml | 3 | {bio-dev} |
- mauve-aligner | 3 | {bio} |
- nutsqlite | 3 | {tools} |
- paraclu | 3 | {cloud,bio} |
- parsnp | 3 | {bio} |
- perm | 3 | {cloud,bio} |
+ lucy | 3 | {bio} |
+ mhap | 3 | {bio-ngs,bio} |
+ microbegps | 3 | {bio} |
+ mlv-smile | 3 | {cloud,bio} |
+ murasaki | 3 | {bio} |
+ orthanc-dicomweb | 3 | {imaging} |
+ pbdagcon | 3 | {bio} |
phast | 3 | {bio} |
- plasmidseeker | 3 | {bio} |
- predictprotein | 3 | {bio} |
- proalign | 3 | {bio-phylogeny,bio} |
- probabel | 3 | {bio,cloud} |
+ pilon | 3 | {bio} |
+ placnet | 3 | {bio} |
+ 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} |
seqtools | 3 | {bio} |
spread-phy | 3 | {bio-phylogeny,bio} |
- tvc | 3 | {bio} |
+ vsearch | 3 | {bio} |
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} |
- beast2-mcmc | 2 | {bio} |
+ beads | 2 | {bio} |
+ beast-mcmc | 2 | {bio-phylogeny,bio} |
+ bio-rainbow | 2 | {bio} |
biosig4c++ | 2 | {physics,imaging-dev} |
bitseq | 2 | {bio} |
- canu | 2 | {bio} |
+ blasr | 2 | {bio-ngs,bio} |
centrifuge | 2 | {bio} |
clonalorigin | 2 | {bio} |
cufflinks | 2 | {bio,cloud} |
- delly | 2 | {bio} |
- diamond-aligner | 2 | {bio} |
- elph | 2 | {bio} |
- gatb-core | 2 | {bio} |
- ghmm | 2 | {bio} |
- harvest-tools | 2 | {bio} |
- libgff | 2 | {bio-dev} |
- libncl | 2 | {bio} |
+ daligner | 2 | {bio-ngs,bio} |
+ dascrubber | 2 | {bio} |
+ dindel | 2 | {bio} |
+ dwgsim | 2 | {bio} |
+ fastml | 2 | {bio} |
+ fsm-lite | 2 | {bio} |
+ hinge | 2 | {bio} |
+ igor | 2 | {bio} |
+ lamarc | 2 | {bio} |
librdp-taxonomy-tree-java | 2 | {bio-dev} |
- lucy | 2 | {bio} |
- mhap | 2 | {bio-ngs,bio} |
- microbegps | 2 | {bio} |
- mlv-smile | 2 | {cloud,bio} |
- murasaki | 2 | {bio} |
- orthanc-mysql | 2 | {imaging} |
- orthanc-postgresql | 2 | {imaging} |
- pbdagcon | 2 | {bio} |
- pilon | 2 | {bio} |
- placnet | 2 | {bio} |
- prime-phylo | 2 | {cloud,bio} |
- pscan-chip | 2 | {bio} |
+ maffilter | 2 | {bio} |
+ mptp | 2 | {bio} |
+ mrs | 2 | {bio} |
+ nanook | 2 | {bio} |
+ nutsqlite | 2 | {tools} |
+ patman | 2 | {bio} |
+ phipack | 2 | {bio} |
+ phybin | 2 | {bio} |
+ poretools | 2 | {bio} |
qcumber | 2 | {bio} |
- quorum | 2 | {bio} |
rambo-k | 2 | {bio} |
rampler | 2 | {bio} |
rdp-classifier | 2 | {bio} |
relion | 2 | {bio} |
+ repeatmasker-recon | 2 | {bio} |
rtax | 2 | {cloud,bio} |
+ runcircos-gui | 2 | {bio} |
samblaster | 2 | {bio} |
scythe | 2 | {bio} |
- segemehl | 2 | {bio} |
seqtools | 2 | {bio} |
sickle | 2 | {bio} |
+ soapaligner | 2 | {bio} |
soapsnp | 2 | {bio} |
+ sprai | 2 | {bio} |
sumatra | 2 | {bio} |
sweed | 2 | {bio} |
trace2dbest | 2 | {bio} |
transrate-tools | 2 | {bio} |
- vsearch | 2 | {bio} |
- atropos | 1 | {bio} |
- beads | 1 | {bio} |
- beast-mcmc | 1 | {bio-phylogeny,bio} |
- bio-rainbow | 1 | {bio} |
+ tvc | 2 | {bio} |
+ alter-sequence-alignment | 1 | {bio} |
biosig4c++ | 1 | {physics,imaging-dev} |
- blasr | 1 | {bio-ngs,bio} |
blimps | 1 | {bio} |
clonalframeml | 1 | {bio} |
ctn | 1 | {imaging-dev} |
- daligner | 1 | {bio-ngs,bio} |
- dascrubber | 1 | {bio} |
- dindel | 1 | {bio} |
- dwgsim | 1 | {bio} |
edflib | 1 | {imaging-dev} |
elastix | 1 | {imaging} |
embassy-phylip | 1 | {cloud,bio} |
emmax | 1 | {bio} |
fasta3 | 1 | {bio} |
- fastml | 1 | {bio} |
freebayes | 1 | {bio} |
- fsm-lite | 1 | {bio} |
- hinge | 1 | {bio} |
hunspell-en-med | 1 | {tools} |
- igor | 1 | {bio} |
jmodeltest | 1 | {bio-phylogeny,bio} |
kma | 1 | {bio} |
kmerresistance | 1 | {bio} |
- lamarc | 1 | {bio} |
libbio-mage-utils-perl | 1 | {bio-dev} |
libctapimkt | 1 | {practice} |
libhmsbeagle | 1 | {bio-dev} |
libpal-java | 1 | {bio-dev} |
- libsmithwaterman | 1 | {bio-dev} |
libsmithwaterman | 1 | {bio} |
+ libsmithwaterman | 1 | {bio-dev} |
libvistaio | 1 | {imaging-dev} |
logol | 1 | {bio} |
- maffilter | 1 | {bio} |
maxflow | 1 | {imaging-dev} |
medicalterms | 1 | {tools} |
mencal | 1 | {tools} |
- mptp | 1 | {bio} |
- nanook | 1 | {bio} |
+ metaphlan2 | 1 | {bio} |
+ orthanc-mysql | 1 | {imaging} |
+ orthanc-postgresql | 1 | {imaging} |
pal2nal | 1 | {bio} |
- patman | 1 | {bio} |
- phipack | 1 | {bio} |
- phybin | 1 | {bio} |
pilercr | 1 | {bio} |
- poretools | 1 | {bio} |
prottest | 1 | {bio-phylogeny,bio} |
- repeatmasker-recon | 1 | {bio} |
+ python-tinyalign | 1 | {bio-dev,bio} |
roguenarok | 1 | {bio} |
- runcircos-gui | 1 | {bio} |
samtools-legacy | 1 | {bio-dev} |
scrm | 1 | {bio} |
seqan | 1 | {bio-dev} |
seqmagick | 1 | {bio} |
- seqtools | 1 | {bio} |
sga | 1 | {bio} |
sift | 1 | {bio} |
skesa | 1 | {bio} |
snap-aligner | 1 | {bio} |
- soapaligner | 1 | {bio} |
spaced | 1 | {bio} |
- sprai | 1 | {bio} |
srf | 1 | {bio-dev} |
stacks | 1 | {bio} |
stringtie | 1 | {bio} |
@@ -248,6 +249,7 @@ Last-Update: Thu, 05 Mar 2020 01:42:03 +0000
tree-puzzle | 1 | {cloud,bio-phylogeny,bio} |
varscan | 1 | {bio} |
volpack | 1 | {imaging-dev} |
+ atropos | 0 | {bio} |
bambamc | 0 | {bio-dev} |
biobambam2 | 0 | {bio,bio-dev} |
biojava4-live | 0 | {bio-dev} |
@@ -285,7 +287,6 @@ Last-Update: Thu, 05 Mar 2020 01:42:03 +0000
libseqlib | 0 | {bio-dev} |
libstatgen | 0 | {bio-dev} |
libxdf | 0 | {imaging-dev} |
- metaphlan2 | 0 | {bio} |
metastudent-data | 0 | {bio} |
metastudent-data-2 | 0 | {bio} |
mia | 0 | {imaging-dev} |
@@ -305,9 +306,8 @@ Last-Update: Thu, 05 Mar 2020 01:42:03 +0000
python-deeptools | 0 | {bio-dev,bio} |
python-py2bit | 0 | {bio,bio-dev} |
python-pyani | 0 | {bio-dev} |
- python-tinyalign | 0 | {bio-dev,bio} |
- relion | 0 | {bio-dev} |
relion | 0 | {bio} |
+ relion | 0 | {bio-dev} |
sambamba | 0 | {bio} |
sbmltoolbox | 0 | {bio-dev} |
seq-gen | 0 | {bio} |
=====================================
outdated_med-packages.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Thu, 05 Mar 2020 01:42:03 +0000
+Last-Update: Thu, 05 Mar 2020 13:42:03 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+-----------------------------------------------------------------------------+-----------------------+------------------------
@@ -17,6 +17,7 @@ Last-Update: Thu, 05 Mar 2020 01:42:03 +0000
biosig4c++ | 1.9.5 | 2.0.1 | 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
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
elastix | 4.9.0 | 5.0.0 | Gert Wollny,Steve M. Robbins | Andreas Tille | 2019-01-15 11:50:11+00
@@ -91,7 +92,7 @@ Last-Update: Thu, 05 Mar 2020 01:42:03 +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
-(89 rows)
+(90 rows)
source | id | severity | title
@@ -168,7 +169,6 @@ Last-Update: Thu, 05 Mar 2020 01:42:03 +0000
htslib | 922860 | normal | Packages do not contain the upstream README file
idba | 909716 | minor | idba: Please provide autopkgtest
igv | 940606 | normal | new upstream (2.6.3)
- infernal | 953117 | wishlist | infernal: please make the build reproducible
insighttoolkit4 | 724711 | wishlist | insighttoolkit4: Drops architecture support
insighttoolkit4 | 759794 | wishlist | insighttoolkit4: FTBFS on amd64 with ENOSPC
insighttoolkit4 | 780659 | wishlist | insighttoolkit only built on amd64 and i386
@@ -290,5 +290,5 @@ Last-Update: Thu, 05 Mar 2020 01:42:03 +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)
+(193 rows)
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/c5aad202248e674e36fd35e283645e3f094ea23f
--
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/c5aad202248e674e36fd35e283645e3f094ea23f
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