Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
a353a47b by Andreas Tille at 2020-03-30T13:44:17+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,19 +1,19 @@
-Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
+Last-Update: Mon, 30 Mar 2020 13:42:04 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk | 168 | {imaging,covid-19} |
- orthanc | 95 | {imaging,practice,covid-19} |
- gdcm | 49 | {imaging-dev} |
- orthanc-wsi | 42 | {his,imaging,laboratory,covid-19,practice,oncology} |
- amide | 34 | {imaging} |
+ dcmtk | 166 | {covid-19,imaging} |
+ orthanc | 94 | {imaging,practice,covid-19} |
+ gdcm | 47 | {imaging-dev} |
+ orthanc-wsi | 41 | {oncology,his,imaging,practice,covid-19,laboratory} |
htsjdk | 34 | {bio-dev} |
- dcm2niix | 30 | {imaging} |
+ amide | 33 | {imaging} |
+ dcm2niix | 29 | {imaging} |
dicomscope | 27 | {imaging} |
- dicom3tools | 25 | {imaging} |
- gdcm | 20 | {covid-19,imaging} |
- minc-tools | 19 | {imaging} |
- gnumed-server | 18 | {covid-19,practice} |
+ dicom3tools | 24 | {imaging} |
+ gdcm | 20 | {imaging,covid-19} |
+ gnumed-server | 19 | {covid-19,practice} |
+ minc-tools | 18 | {imaging} |
pixelmed | 18 | {imaging} |
ngs-sdk | 17 | {bio-dev} |
invesalius | 15 | {imaging} |
@@ -21,36 +21,37 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
openslide | 15 | {imaging} |
vtk-dicom | 15 | {imaging} |
biojava-live | 14 | {bio-dev} |
- insighttoolkit4 | 14 | {imaging-dev} |
- king | 14 | {imaging,typesetting} |
+ king | 14 | {typesetting,imaging} |
+ insighttoolkit4 | 13 | {imaging-dev} |
cgview | 12 | {bio} |
+ ea-utils | 12 | {bio} |
mia | 12 | {imaging} |
- psychopy | 12 | {psychology} |
adun.app | 11 | {bio} |
- ea-utils | 11 | {bio} |
+ diamond-aligner | 11 | {covid-19,bio} |
jebl2 | 11 | {bio-dev} |
- plastimatch | 11 | {imaging} |
+ king-probe | 11 | {bio} |
+ psychopy | 11 | {psychology} |
radiant | 11 | {bio} |
staden | 11 | {bio} |
dazzdb | 10 | {bio} |
- diamond-aligner | 10 | {covid-19,bio} |
- king-probe | 10 | {bio} |
librg-utils-perl | 10 | {bio} |
- ngs-sdk | 10 | {bio-dev} |
norsp | 10 | {bio} |
obitools | 10 | {bio} |
- tree-puzzle | 10 | {bio,cloud,bio-phylogeny} |
+ plastimatch | 10 | {imaging} |
+ tree-puzzle | 10 | {bio,bio-phylogeny,cloud} |
biosig4c++ | 9 | {physics,imaging} |
bppsuite | 9 | {bio} |
fastlink | 9 | {bio,cloud} |
gdcm | 9 | {imaging-dev} |
- mipe | 9 | {bio,cloud} |
+ mipe | 9 | {cloud,bio} |
ncbi-seg | 9 | {bio} |
+ ngs-sdk | 9 | {bio-dev} |
phast | 9 | {bio} |
- prime-phylo | 9 | {bio,cloud} |
+ prime-phylo | 9 | {cloud,bio} |
+ pscan-tfbs | 9 | {bio} |
abacas | 8 | {bio} |
- ampliconnoise | 8 | {cloud,bio} |
- anfo | 8 | {bio,cloud} |
+ ampliconnoise | 8 | {bio,cloud} |
+ anfo | 8 | {cloud,bio} |
arden | 8 | {bio,cloud} |
biomaj3-cli | 8 | {cloud} |
daligner | 8 | {bio-ngs,bio} |
@@ -60,43 +61,43 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
hunspell-en-med | 8 | {tools} |
jaligner | 8 | {bio} |
maqview | 8 | {bio} |
- melting | 8 | {cloud,bio} |
+ melting | 8 | {bio,cloud} |
neobio | 8 | {bio,cloud} |
paml | 8 | {bio} |
- phyutility | 8 | {bio,cloud} |
+ phyutility | 8 | {cloud,bio} |
piler | 8 | {bio} |
- pscan-tfbs | 8 | {bio} |
seqsero | 8 | {bio} |
- sigma-align | 8 | {bio,cloud,bio-phylogeny} |
- bio-tradis | 7 | {bio-dev,bio} |
+ sigma-align | 8 | {cloud,bio-phylogeny,bio} |
+ bio-tradis | 7 | {bio,bio-dev} |
bitseq | 7 | {bio} |
codonw | 7 | {bio} |
edtsurf | 7 | {bio} |
embassy-domalign | 7 | {cloud,bio} |
embassy-domsearch | 7 | {bio,cloud} |
estscan | 7 | {bio} |
- fitgcp | 7 | {bio,cloud} |
+ fitgcp | 7 | {cloud,bio} |
freebayes | 7 | {bio} |
- gasic | 7 | {cloud,bio} |
+ gasic | 7 | {bio,cloud} |
lagan | 7 | {bio} |
lamarc | 7 | {bio} |
lucy | 7 | {bio} |
mauve-aligner | 7 | {bio} |
microbegps | 7 | {bio} |
- mlv-smile | 7 | {cloud,bio} |
- paraclu | 7 | {cloud,bio} |
- perm | 7 | {cloud,bio} |
+ mlv-smile | 7 | {bio,cloud} |
+ paraclu | 7 | {bio,cloud} |
+ perm | 7 | {bio,cloud} |
placnet | 7 | {bio} |
poretools | 7 | {bio} |
predictprotein | 7 | {bio} |
- probabel | 7 | {cloud,bio} |
+ probabel | 7 | {bio,cloud} |
saint | 7 | {bio} |
seqtools | 7 | {bio} |
- sibsim4 | 7 | {cloud,bio} |
+ sibsim4 | 7 | {bio,cloud} |
tracetuner | 7 | {bio} |
alter-sequence-alignment | 6 | {bio} |
andi | 6 | {bio} |
baitfisher | 6 | {bio} |
+ bandage | 6 | {bio} |
beads | 6 | {bio} |
beast2-mcmc | 6 | {bio} |
biomaj3-daemon | 6 | {bio} |
@@ -104,7 +105,7 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
brig | 6 | {bio} |
canu | 6 | {bio} |
centrifuge | 6 | {bio} |
- clonalframeml | 6 | {bio,covid-19} |
+ clonalframeml | 6 | {covid-19,bio} |
clonalorigin | 6 | {bio} |
dascrubber | 6 | {bio} |
elph | 6 | {bio} |
@@ -115,11 +116,11 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
ipig | 6 | {bio} |
jellyfish1 | 6 | {bio} |
logol | 6 | {bio} |
- mapsembler2 | 6 | {bio,cloud} |
+ mapsembler2 | 6 | {cloud,bio} |
murasaki | 6 | {bio} |
orthanc-webviewer | 6 | {imaging} |
parsnp | 6 | {bio} |
- proalign | 6 | {bio-phylogeny,bio} |
+ proalign | 6 | {bio,bio-phylogeny} |
pscan-chip | 6 | {bio} |
pymia | 6 | {imaging-dev} |
quorum | 6 | {bio} |
@@ -134,17 +135,17 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
spread-phy | 6 | {bio,bio-phylogeny} |
squizz | 6 | {cloud,bio} |
transtermhp | 6 | {bio} |
- treeview | 6 | {bio-phylogeny,bio} |
+ treeview | 6 | {bio,bio-phylogeny} |
vsearch | 6 | {bio} |
zalign | 6 | {cloud,bio} |
assemblytics | 5 | {bio} |
- bandage | 5 | {bio} |
- beast-mcmc | 5 | {bio-phylogeny,bio} |
+ beast-mcmc | 5 | {bio,bio-phylogeny} |
cluster3 | 5 | {bio} |
dwgsim | 5 | {bio} |
fastml | 5 | {bio} |
hinge | 5 | {bio} |
- jmodeltest | 5 | {bio,bio-phylogeny} |
+ jmodeltest | 5 | {bio-phylogeny,bio} |
+ libdivsufsort | 5 | {bio-dev} |
libminc | 5 | {imaging-dev} |
libncl | 5 | {bio} |
libpal-java | 5 | {bio-dev} |
@@ -165,14 +166,13 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
dindel | 4 | {bio} |
elastix | 4 | {imaging} |
fsm-lite | 4 | {bio} |
- libdivsufsort | 4 | {bio-dev} |
libsbml | 4 | {bio-dev} |
metaphlan2 | 4 | {bio} |
pbdagcon | 4 | {bio} |
phybin | 4 | {bio} |
pilon | 4 | {bio} |
plasmidseeker | 4 | {bio} |
- prottest | 4 | {bio,bio-phylogeny} |
+ prottest | 4 | {bio-phylogeny,bio} |
rampler | 4 | {bio} |
rdp-alignment | 4 | {bio} |
relion | 4 | {bio} |
@@ -191,7 +191,7 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
orthanc-dicomweb | 3 | {imaging,covid-19} |
orthanc-mysql | 3 | {imaging} |
relion | 3 | {bio} |
- rtax | 3 | {bio,cloud} |
+ rtax | 3 | {cloud,bio} |
segemehl | 3 | {bio} |
seqmagick | 3 | {bio,covid-19} |
snap-aligner | 3 | {bio} |
@@ -202,7 +202,8 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
surankco | 3 | {bio} |
tnseq-transit | 3 | {bio,covid-19} |
varscan | 3 | {bio} |
- cufflinks | 2 | {cloud,bio} |
+ biosig4c++ | 2 | {imaging-dev,physics} |
+ cufflinks | 2 | {bio,cloud} |
getdata | 2 | {bio} |
kma | 2 | {bio} |
kmerresistance | 2 | {bio} |
@@ -211,43 +212,40 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
mencal | 2 | {tools} |
nanook | 2 | {bio} |
ngs-sdk | 2 | {bio-dev} |
+ nutsqlite | 2 | {tools} |
qcumber | 2 | {bio} |
- qrisk2 | 2 | {practice} |
samtools-legacy | 2 | {bio-dev} |
scrm | 2 | {bio} |
skesa | 2 | {bio} |
spaced | 2 | {bio} |
srf | 2 | {bio-dev} |
- thesias | 2 | {bio,covid-19} |
- tree-puzzle | 2 | {cloud,bio,bio-phylogeny} |
+ thesias | 2 | {covid-19,bio} |
+ tree-puzzle | 2 | {bio,bio-phylogeny,cloud} |
volpack | 2 | {imaging-dev} |
atropos | 1 | {bio} |
- biosig4c++ | 1 | {imaging-dev,physics} |
biosig4c++ | 1 | {physics,imaging-dev} |
ctn | 1 | {imaging-dev} |
- edflib | 1 | {imaging-dev} |
- embassy-phylip | 1 | {cloud,bio} |
+ embassy-phylip | 1 | {bio,cloud} |
libbio-mage-utils-perl | 1 | {bio-dev} |
libchado-perl | 1 | {bio-dev} |
libctapimkt | 1 | {practice} |
libsmithwaterman | 1 | {bio-dev} |
libvistaio | 1 | {imaging-dev} |
maxflow | 1 | {imaging-dev} |
- nutsqlite | 1 | {tools} |
opencfu | 1 | {laboratory} |
opensurgsim | 1 | {imaging-dev} |
orthanc-postgresql | 1 | {imaging} |
pal2nal | 1 | {bio} |
papyrus | 1 | {imaging-dev} |
pilercr | 1 | {bio} |
- ragout | 1 | {bio,covid-19} |
- stringtie | 1 | {bio,covid-19} |
+ qrisk2 | 1 | {practice} |
+ stringtie | 1 | {covid-19,bio} |
trace2dbest | 1 | {bio} |
- acedb | 0 | {bio,cloud} |
- augur | 0 | {bio,covid-19} |
+ acedb | 0 | {cloud,bio} |
+ augur | 0 | {covid-19,bio} |
bambamc | 0 | {bio-dev} |
bbmap | 0 | {covid-19} |
- biobambam2 | 0 | {covid-19,bio-dev,bio} |
+ biobambam2 | 0 | {covid-19,bio,bio-dev} |
biojava4-live | 0 | {bio-dev} |
biosig4c++ | 0 | {physics} |
biosyntax | 0 | {bio} |
@@ -259,7 +257,7 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
fis-gtm | 0 | {his} |
freecontact | 0 | {bio-dev} |
gatb-core | 0 | {bio-dev} |
- htscodecs | 0 | {bio-dev,covid-19} |
+ htscodecs | 0 | {covid-19,bio-dev} |
libbigwig | 0 | {bio-dev} |
libbiod | 0 | {bio-dev} |
libbioparser-dev | 0 | {bio-dev} |
@@ -274,7 +272,7 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
libgenome | 0 | {bio-dev} |
libgkarrays | 0 | {bio-dev} |
libhmsbeagle | 0 | {bio-dev} |
- libics | 0 | {imaging-dev,covid-19} |
+ libics | 0 | {covid-19,imaging-dev} |
libjloda-java | 0 | {bio-dev} |
libmaus2 | 0 | {covid-19,bio-dev} |
libmems | 0 | {bio-dev} |
@@ -296,15 +294,15 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
murasaki | 0 | {bio} |
ncbi-vdb | 0 | {bio-dev} |
orthanc-imagej | 0 | {imaging} |
- oscar | 0 | {practice,tools,data} |
+ oscar | 0 | {data,practice,tools} |
pbcopper | 0 | {bio-dev} |
pbseqlib | 0 | {bio-dev} |
python-etelemetry | 0 | {covid-19} |
python-py2bit | 0 | {bio,bio-dev} |
python-questplus | 0 | {covid-19} |
python-scitrack | 0 | {covid-19} |
- relion | 0 | {bio-dev} |
relion | 0 | {bio} |
+ relion | 0 | {bio-dev} |
sambamba | 0 | {bio} |
sbmltoolbox | 0 | {bio-dev} |
seqan | 0 | {bio-dev} |
@@ -312,11 +310,11 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
sift | 0 | {bio} |
simpleitk | 0 | {imaging-dev} |
skewer | 0 | {bio} |
- smrtanalysis | 0 | {bio,covid-19} |
+ smrtanalysis | 0 | {covid-19,bio} |
solvate | 0 | {bio} |
- spaln | 0 | {bio,covid-19} |
+ spaln | 0 | {covid-19,bio} |
trim-galore | 0 | {bio} |
varna | 0 | {bio} |
vtk-dicom | 0 | {imaging-dev} |
-(346 rows)
+(344 rows)
=====================================
outdated_med-packages.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
+Last-Update: Mon, 30 Mar 2020 13:42:04 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+---------------------------------------------------------------------------+----------------------+------------------------
@@ -35,9 +35,9 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
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
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 | 13.5.20200306 | Aaron M. Ucko | Aaron M. Ucko | 2020-02-03 03:53:53+00
+ ncbi-entrez-direct | 12.0.20190816 | 13.5.20200326 | Aaron M. Ucko | Aaron M. Ucko | 2020-02-03 03:53:53+00
pbcopper | 1.3.0 | 1.4.0 | Andreas Tille | Andreas Tille | 2020-01-29 08:51:15+00
- plink2 | 2.00~a3-200217 | 200321 | Dylan Aïssi | Dylan Aïssi | 2020-02-19 06:19:18+00
+ plink2 | 2.00~a3-200217 | 200328 | Dylan Aïssi | Dylan Aïssi | 2020-02-19 06:19:18+00
pydicom | 1.4.1 | 1.4.2 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-01-23 12:34:53+00
pynn | 0.7.5 | 0.9.5 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-03-20 11:00:12+00
python-avro | 1.9.1 | 1.9.2 | Afif Elghraoui | Andreas Tille | 2019-12-18 08:41:55+00
@@ -51,7 +51,7 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
python-skbio | 0.5.5 | 0.5.6 | Andreas Tille,Kevin Murray,Tim Booth | Michael R. Crusoe | 2020-02-28 14:48:20+00
python-treetime | 0.7.1 | 0.7.4 | Andreas Tille | Steffen Moeller | 2020-01-18 20:52:48+00
q2-cutadapt | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2020-01-26 07:34:32+00
- q2-demux | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2020-01-26 07:34:40+00
+ q2templates | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2019-11-14 22:00:17+00
relion | 1.4 | 3.0.8 | Andreas Tille,Goswin von Brederlow,Navid Fehrenbacher,Roland Fehrenbacher | Andreas Tille | 2018-06-14 12:49:40+00
resfinder-db | 0.0+git20191001.149209d | 0.0+git20200318.d6f36d3 | 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
@@ -59,12 +59,13 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
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
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
+ stacks | 2.52 | 2.53 | Andreas Tille,Tim Booth | Steffen Moeller | 2020-03-26 02:50:13+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
ugene | 33.0 | 34.0 | Andreas Tille,Olivier Sallou,Steffen Moeller | Andreas Tille | 2020-01-12 16:25:44+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
-(62 rows)
+(63 rows)
source | id | severity | title
@@ -212,7 +213,6 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
psychopy | 829424 | normal | psychopy: ioHub uses inappropriate PID file location
psychopy | 953052 | important | psychopy: python2 dependencies
psychopy | 953053 | important | psychopy: missing python3 dependencies
- pybel | 954253 | serious | python3-pybel: Missing dependency on unpackaged bel_resources
pynast | 937488 | normal | pynast: Python2 removal in sid/bullseye
pynast | 948081 | serious | pynast build depends on and recommends the removed blast2 transitional package
pynn | 813821 | serious | pynn: FTBFS: TypeError: 'float' object cannot be interpreted as an index
@@ -228,6 +228,7 @@ Last-Update: Mon, 30 Mar 2020 01:42:03 +0000
python-pysam | 938092 | normal | python-pysam: Python2 removal in sid/bullseye
python-ruffus | 841073 | wishlist | python-ruffus: Needs 18 GB of RAM to build
python-tinyalign | 952603 | normal | python-tinyalign: license of buildwheels.sh is CC0
+ python-wordcloud | 955336 | normal | python-wordcloud: d/copyright: wordcloud/_version.py has a different license
q2cli | 954601 | serious | q2cli: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 -s custom "--test-args=cd {build_dir}; HOME=/<<PKGBUILDDIR>> QIIMETEST= nosetests3" returned exit code 13
q2-demux | 950933 | normal | q2-demux: FTBFS with pandas 1.0: test failures
q2templates | 950931 | normal | q2templates: FTBFS with pandas 1.0: test failures
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/a353a47be4f719e8b0230eed9345f438c6cbd63d
--
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/a353a47be4f719e8b0230eed9345f438c6cbd63d
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200330/c1712258/attachment-0001.html>