Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
703e993c by Andreas Tille at 2020-04-13T13:46:03+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,171 +1,159 @@
-Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
+Last-Update: Mon, 13 Apr 2020 13:42:03 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk | 175 | {covid-19,imaging} |
- orthanc | 95 | {imaging,covid-19,practice} |
- gdcm | 45 | {imaging-dev} |
- orthanc-wsi | 39 | {laboratory,imaging,his,practice,covid-19,oncology} |
- htsjdk | 30 | {bio-dev} |
- amide | 29 | {imaging} |
- dcm2niix | 25 | {imaging} |
+ dcmtk | 173 | {covid-19,imaging} |
+ orthanc | 94 | {imaging,covid-19,practice} |
+ gdcm | 42 | {imaging-dev} |
+ orthanc-wsi | 38 | {laboratory,imaging,his,practice,covid-19,oncology} |
+ amide | 28 | {imaging} |
+ htsjdk | 28 | {bio-dev} |
+ dcm2niix | 26 | {imaging} |
+ dicomscope | 25 | {imaging} |
dicom3tools | 24 | {imaging} |
- dicomscope | 24 | {imaging} |
- gdcm | 21 | {imaging,covid-19} |
+ gdcm | 22 | {imaging,covid-19} |
gnumed-server | 21 | {covid-19,practice} |
- ngs-sdk | 19 | {bio-dev} |
+ ngs-sdk | 17 | {bio-dev} |
hunspell-en-med | 14 | {tools} |
minc-tools | 14 | {imaging} |
adun.app | 13 | {bio} |
+ vtk-dicom | 13 | {imaging} |
invesalius | 12 | {imaging} |
king | 12 | {imaging,typesetting} |
ncbi-entrez-direct | 12 | {bio} |
- vtk-dicom | 12 | {imaging} |
- insighttoolkit4 | 11 | {imaging-dev} |
pixelmed | 11 | {imaging} |
ea-utils | 10 | {bio} |
- gasic | 10 | {cloud,bio} |
- mia | 10 | {imaging} |
+ insighttoolkit4 | 10 | {imaging-dev} |
ngs-sdk | 10 | {bio-dev} |
- openslide | 10 | {imaging} |
- staden | 10 | {bio} |
biosig4c++ | 9 | {imaging,physics} |
cgview | 9 | {bio} |
+ gasic | 9 | {cloud,bio} |
gdcm | 9 | {imaging-dev} |
jebl2 | 9 | {bio-dev} |
- king-probe | 9 | {bio} |
- plastimatch | 9 | {imaging} |
+ mia | 9 | {imaging} |
+ openslide | 9 | {imaging} |
psychopy | 9 | {psychology} |
- biojava-live | 8 | {bio-dev} |
+ staden | 9 | {bio} |
+ king-probe | 8 | {bio} |
librg-utils-perl | 8 | {bio} |
- mipe | 8 | {cloud,bio} |
- paml | 8 | {bio} |
- parsnp | 8 | {bio} |
+ plastimatch | 8 | {imaging} |
tree-puzzle | 8 | {cloud,bio,bio-phylogeny} |
- dazzdb | 7 | {bio} |
- diamond-aligner | 7 | {bio,covid-19} |
- fitgcp | 7 | {cloud,bio} |
- lagan | 7 | {bio} |
- obitools | 7 | {bio} |
+ mipe | 7 | {cloud,bio} |
+ paml | 7 | {bio} |
+ parsnp | 7 | {bio} |
salmon | 7 | {bio} |
anfo | 6 | {bio,cloud} |
arden | 6 | {cloud,bio} |
- biomaj3-cli | 6 | {cloud} |
+ biojava-live | 6 | {bio-dev} |
bppsuite | 6 | {bio} |
+ dazzdb | 6 | {bio} |
+ diamond-aligner | 6 | {bio,covid-19} |
ecopcr | 6 | {bio} |
- fastlink | 6 | {bio,cloud} |
+ fitgcp | 6 | {cloud,bio} |
+ lagan | 6 | {bio} |
ncbi-seg | 6 | {bio} |
neobio | 6 | {bio,cloud} |
norsp | 6 | {bio} |
+ obitools | 6 | {bio} |
orthanc-webviewer | 6 | {imaging} |
phast | 6 | {bio} |
- piler | 6 | {bio} |
- pscan-tfbs | 6 | {bio} |
pymia | 6 | {imaging-dev} |
- radiant | 6 | {bio} |
- seqsero | 6 | {bio} |
abacas | 5 | {bio} |
- alter-sequence-alignment | 5 | {bio} |
ampliconnoise | 5 | {cloud,bio} |
- bandage | 5 | {bio} |
- biomaj3-daemon | 5 | {bio} |
- bio-rainbow | 5 | {bio} |
clonalorigin | 5 | {bio} |
codonw | 5 | {bio} |
- daligner | 5 | {bio,bio-ngs} |
- edtsurf | 5 | {bio} |
embassy-domainatrix | 5 | {cloud,bio} |
embassy-domalign | 5 | {cloud,bio} |
embassy-domsearch | 5 | {bio,cloud} |
- estscan | 5 | {bio} |
- fastml | 5 | {bio} |
- freebayes | 5 | {bio} |
- freecontact | 5 | {cloud,bio} |
- gatb-core | 5 | {bio} |
- ghmm | 5 | {bio} |
- harvest-tools | 5 | {bio} |
- indelible | 5 | {bio} |
+ fastlink | 5 | {bio,cloud} |
jaligner | 5 | {bio} |
- jellyfish1 | 5 | {bio} |
- libncl | 5 | {bio} |
- maqview | 5 | {bio} |
melting | 5 | {bio,cloud} |
mencal | 5 | {tools} |
mrs | 5 | {bio} |
- phyutility | 5 | {bio,cloud} |
- placnet | 5 | {bio} |
+ openslide | 5 | {imaging-dev} |
+ piler | 5 | {bio} |
predictprotein | 5 | {bio} |
prime-phylo | 5 | {cloud,bio} |
- pscan-chip | 5 | {bio} |
+ pscan-tfbs | 5 | {bio} |
+ radiant | 5 | {bio} |
rambo-k | 5 | {bio} |
seer | 5 | {bio} |
- seqtools | 5 | {bio} |
+ seqsero | 5 | {bio} |
sibsim4 | 5 | {bio,cloud} |
sigma-align | 5 | {bio-phylogeny,bio,cloud} |
sumatra | 5 | {bio} |
tracetuner | 5 | {bio} |
- vsearch | 5 | {bio} |
- baitfisher | 4 | {bio} |
+ alter-sequence-alignment | 4 | {bio} |
+ bandage | 4 | {bio} |
bart-view | 4 | {imaging} |
beads | 4 | {bio} |
beast-mcmc | 4 | {bio,bio-phylogeny} |
+ biomaj3-cli | 4 | {cloud} |
+ biomaj3-daemon | 4 | {bio} |
+ bio-rainbow | 4 | {bio} |
bio-tradis | 4 | {bio,bio-dev} |
bitseq | 4 | {bio} |
- brig | 4 | {bio} |
- centrifuge | 4 | {bio} |
- clonalframeml | 4 | {bio,covid-19} |
cluster3 | 4 | {bio} |
+ daligner | 4 | {bio,bio-ngs} |
dascrubber | 4 | {bio} |
- delly | 4 | {covid-19,bio} |
- dindel | 4 | {bio} |
- dwgsim | 4 | {bio} |
- elph | 4 | {bio} |
- fsm-lite | 4 | {bio} |
- hinge | 4 | {bio} |
- ipig | 4 | {bio} |
- lamarc | 4 | {bio} |
+ edtsurf | 4 | {bio} |
+ estscan | 4 | {bio} |
+ fastml | 4 | {bio} |
+ freebayes | 4 | {bio} |
+ freecontact | 4 | {cloud,bio} |
+ gatb-core | 4 | {bio} |
+ ghmm | 4 | {bio} |
+ harvest-tools | 4 | {bio} |
+ indelible | 4 | {bio} |
+ jellyfish1 | 4 | {bio} |
libdivsufsort | 4 | {bio-dev} |
libminc | 4 | {imaging-dev} |
+ libncl | 4 | {bio} |
libsbml | 4 | {bio-dev} |
- mapsembler2 | 4 | {cloud,bio} |
- microbegps | 4 | {bio} |
- mlv-smile | 4 | {bio,cloud} |
+ maqview | 4 | {bio} |
murasaki | 4 | {bio} |
- openslide | 4 | {imaging-dev} |
- paraclu | 4 | {cloud,bio} |
- perm | 4 | {bio,cloud} |
- poretools | 4 | {bio} |
- proalign | 4 | {bio,bio-phylogeny} |
- probabel | 4 | {bio,cloud} |
+ phyutility | 4 | {bio,cloud} |
+ placnet | 4 | {bio} |
+ pscan-chip | 4 | {bio} |
rdp-alignment | 4 | {bio} |
rdp-readseq | 4 | {bio} |
relion | 4 | {bio} |
repeatmasker-recon | 4 | {bio} |
+ seqtools | 4 | {bio} |
sprai | 4 | {bio} |
spread-phy | 4 | {bio-phylogeny,bio} |
squizz | 4 | {bio,cloud} |
transtermhp | 4 | {bio} |
treeview | 4 | {bio,bio-phylogeny} |
+ vsearch | 4 | {bio} |
assemblytics | 3 | {bio} |
+ baitfisher | 3 | {bio} |
beast2-mcmc | 3 | {bio} |
- canu | 3 | {bio} |
+ brig | 3 | {bio} |
+ centrifuge | 3 | {bio} |
+ clonalframeml | 3 | {bio,covid-19} |
+ delly | 3 | {covid-19,bio} |
dicompyler | 3 | {oncology} |
- jmodeltest | 3 | {bio,bio-phylogeny} |
+ dindel | 3 | {bio} |
+ dwgsim | 3 | {bio} |
+ elph | 3 | {bio} |
+ fsm-lite | 3 | {bio} |
+ hinge | 3 | {bio} |
+ ipig | 3 | {bio} |
libgff | 3 | {bio-dev} |
- libpal-java | 3 | {bio-dev} |
librdp-taxonomy-tree-java | 3 | {bio-dev} |
- logol | 3 | {bio} |
- lucy | 3 | {bio} |
- maffilter | 3 | {bio} |
+ mapsembler2 | 3 | {cloud,bio} |
mauve-aligner | 3 | {bio} |
- metaphlan2 | 3 | {bio} |
- mptp | 3 | {bio} |
+ microbegps | 3 | {bio} |
+ mlv-smile | 3 | {bio,cloud} |
nutsqlite | 3 | {tools} |
orthanc-dicomweb | 3 | {covid-19,imaging} |
orthanc-mysql | 3 | {imaging} |
- patman | 3 | {bio} |
- pbdagcon | 3 | {bio} |
- prottest | 3 | {bio,bio-phylogeny} |
+ paraclu | 3 | {cloud,bio} |
+ perm | 3 | {bio,cloud} |
+ poretools | 3 | {bio} |
+ proalign | 3 | {bio,bio-phylogeny} |
+ probabel | 3 | {bio,cloud} |
quorum | 3 | {bio} |
rdp-classifier | 3 | {bio} |
saint | 3 | {bio} |
@@ -177,19 +165,27 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
stacks | 3 | {bio} |
transrate-tools | 3 | {bio} |
biosig4c++ | 2 | {imaging-dev,physics} |
- blasr | 2 | {bio-ngs,bio} |
+ canu | 2 | {bio} |
cufflinks | 2 | {bio,cloud} |
elastix | 2 | {imaging} |
getdata | 2 | {bio} |
- igor | 2 | {bio} |
+ jmodeltest | 2 | {bio,bio-phylogeny} |
+ lamarc | 2 | {bio} |
+ libpal-java | 2 | {bio-dev} |
libsmithwaterman | 2 | {bio} |
+ logol | 2 | {bio} |
+ lucy | 2 | {bio} |
+ maffilter | 2 | {bio} |
+ metaphlan2 | 2 | {bio} |
mhap | 2 | {bio-ngs,bio} |
- ngs-sdk | 2 | {bio-dev} |
+ mptp | 2 | {bio} |
pal2nal | 2 | {bio} |
+ patman | 2 | {bio} |
+ pbdagcon | 2 | {bio} |
phipack | 2 | {bio} |
phybin | 2 | {bio} |
pilon | 2 | {bio} |
- plasmidseeker | 2 | {bio} |
+ prottest | 2 | {bio,bio-phylogeny} |
qcumber | 2 | {bio} |
qrisk2 | 2 | {practice} |
rampler | 2 | {bio} |
@@ -215,12 +211,13 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
zalign | 2 | {cloud,bio} |
atropos | 1 | {bio} |
biosig4c++ | 1 | {physics,imaging-dev} |
+ blasr | 1 | {bio-ngs,bio} |
blimps | 1 | {bio} |
ctn | 1 | {imaging-dev} |
embassy-phylip | 1 | {cloud,bio} |
+ igor | 1 | {bio} |
kma | 1 | {bio} |
kmerresistance | 1 | {bio} |
- libchado-perl | 1 | {bio-dev} |
libctapimkt | 1 | {practice} |
libsmithwaterman | 1 | {bio-dev} |
libvistaio | 1 | {imaging-dev} |
@@ -230,6 +227,7 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
orthanc-postgresql | 1 | {imaging} |
papyrus | 1 | {imaging-dev} |
pilercr | 1 | {bio} |
+ plasmidseeker | 1 | {bio} |
python-scitrack | 1 | {covid-19} |
relion | 1 | {bio} |
seqan | 1 | {bio-dev} |
@@ -266,6 +264,7 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
libbpp-raa | 0 | {bio-dev} |
libbpp-seq | 0 | {bio-dev} |
libbpp-seq-omics | 0 | {bio-dev} |
+ libchado-perl | 0 | {bio-dev} |
libdisorder | 0 | {bio-dev} |
libgenome | 0 | {bio-dev} |
libgkarrays | 0 | {bio-dev} |
@@ -292,6 +291,7 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
multiqc | 0 | {bio} |
murasaki | 0 | {bio} |
ncbi-vdb | 0 | {bio-dev} |
+ ngs-sdk | 0 | {bio-dev} |
opencfu | 0 | {laboratory} |
orthanc-imagej | 0 | {imaging} |
oscar | 0 | {practice,data,tools} |
=====================================
outdated_med-packages.txt
=====================================
@@ -1,9 +1,10 @@
-Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
+Last-Update: Mon, 13 Apr 2020 13:42:04 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+---------------------------------------------------------------------------+----------------------+------------------------
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 | 38.81 | Andreas Tille | Andreas Tille | 2020-02-27 11:08:04+00
+ bcbio | 1.2.0 | 1.2.3 | Steffen Moeller | Andreas Tille | 2020-03-11 20:50:02+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 | 3.0.23 | 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
@@ -14,10 +15,11 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
discosnp | 2.4.3 | 4.4.4 | Andreas Tille,Olivier Sallou | Andreas Tille | 2020-01-27 15:19:13+00
elastix | 4.9.0 | 5.0.0 | Gert Wollny,Steve M. Robbins | Andreas Tille | 2019-01-15 11:50:11+00
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+git20200330.e99c5d7 | Andreas Tille,Nadiya Sitdykova | Michael R. Crusoe | 2020-02-17 14:52:30+00
+ gatb-core | 1.4.1+git20191209.9398f28 | 1.4.1+git20200412.99f573a | Andreas Tille,Nadiya Sitdykova | Michael R. Crusoe | 2020-02-17 14:52:30+00
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
hyphy | 2.5.1 | 2.5.8 | Andreas Tille | Andreas Tille | 2020-01-07 21:19:50+00
+ igdiscover | 0.11 | 0.12.3 | Steffen Moeller | Andreas Tille | 2019-09-06 07:04:02+00
igor | 1.3.0 | 1.4.0 | Steffen Moeller | Andreas Tille | 2019-01-26 17:51:04+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
@@ -32,12 +34,14 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
libmaus2 | 2.0.713 | 2.0.715 | Andreas Tille,Steffen Moeller | Andreas Tille | 2020-03-27 09:34:39+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
libthread-pool | 2.0.1 | 2.0.2 | Andreas Tille | Andreas Tille | 2019-11-19 21:21:23+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
minia | 3.2.1+git20191130.5b131b9 | 3.2.1+git20200409.489e374 | Andreas Tille,Olivier Sallou | Andreas Tille | 2019-12-16 09:04:06+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 | 13.5.20200326 | Aaron M. Ucko | Aaron M. Ucko | 2020-02-03 03:53:53+00
nibabel | 3.0.1 | 3.0.2 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-03-03 14:58:34+00
+ pbgenomicconsensus | 2.3.2 | 2.3.3 | Andreas Tille | Liubov Chuprikova | 2019-04-07 15:33:36+00
plink2 | 2.00~a3-200217 | 200409 | Dylan Aïssi | Dylan Aïssi | 2020-02-19 06:19:18+00
pybel | 0.14.5 | 0.14.6 | Steffen Moeller | Andreas Tille | 2020-03-29 18:48:55+00
pynn | 0.7.5 | 0.9.5 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-04-03 16:34:56+00
@@ -58,7 +62,7 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
resfinder-db | 0.0+git20191001.149209d | 0.0+git20200408.0322c0d | Andreas Tille | Andreas Tille | 2019-11-16 23:00:12+00
salmon | 0.12.0 | 1.2.0 | Kevin Murray,Michael R. Crusoe | Andreas Tille | 2018-12-13 19:05:56+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
+ simde | 0.0.0.git.20200402 | 0.0.0.git.20200410 | Michael R. Crusoe | Michael R. Crusoe | 2020-04-12 16:00:10+00
simpleitk | 1.0.1 | 1.2.0 | Ghislain Antony Vaillant | Andreas Tille | 2019-01-30 10:06:08+00
snakemake | 5.10.0 | 5.14.0 | Kevin Murray | Andreas Tille | 2020-04-09 09:34:37+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
@@ -68,7 +72,7 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
unanimity | 3.3.0 | 4.2.0-1 | 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
-(66 rows)
+(70 rows)
source | id | severity | title
@@ -171,9 +175,9 @@ Last-Update: Mon, 13 Apr 2020 01:42:03 +0000
medicalterms | 602423 | important | hunspell-de-med: german dictionary unusable
mencal | 607008 | normal | mencal: with l10n, calendar header formatting not aligned with column content
metaphlan2-data | 839925 | important | metaphlan2-data: postinst deletes shipped file: /var/lib/metaphlan2-data/markers.fasta
+ minimap2 | 956136 | serious | "-flto flag breaks nanopolish"
mipe | 890788 | minor | mipe: Please provide autopkgtest
mriconvert | 617342 | normal | 32-bit multiframe image conversion ignores frames
- nanopolish | 956136 | serious | nanopolish: FTBFS (undefined references)
ncbi-blast+ | 891197 | normal | Please switch to pcre2
ncbi-tools6 | 225651 | wishlist | ncbi-tools-x11: want Cn3D++
ncbi-vdb | 952623 | serious | sra-sdk: FTBFS: ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_entropy_init'
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/703e993c33a452ca4b4525453b1c71e0ebecd0ea
--
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