Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
2b508b65 by Andreas Tille at 2020-04-06T13:44:39+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,75 +1,75 @@
-Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
+Last-Update: Mon, 06 Apr 2020 13:42:03 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk | 163 | {imaging,covid-19} |
- orthanc | 93 | {practice,imaging,covid-19} |
- gdcm | 52 | {imaging-dev} |
- orthanc-wsi | 38 | {practice,his,laboratory,imaging,oncology,covid-19} |
+ dcmtk | 165 | {imaging,covid-19} |
+ orthanc | 94 | {practice,imaging,covid-19} |
+ gdcm | 47 | {imaging-dev} |
+ orthanc-wsi | 39 | {practice,his,laboratory,imaging,oncology,covid-19} |
htsjdk | 30 | {bio-dev} |
- amide | 28 | {imaging} |
+ amide | 29 | {imaging} |
dcm2niix | 26 | {imaging} |
dicomscope | 24 | {imaging} |
dicom3tools | 22 | {imaging} |
gdcm | 21 | {covid-19,imaging} |
- gnumed-server | 17 | {covid-19,practice} |
+ gnumed-server | 18 | {covid-19,practice} |
ngs-sdk | 17 | {bio-dev} |
invesalius | 14 | {imaging} |
king | 14 | {typesetting,imaging} |
minc-tools | 14 | {imaging} |
- insighttoolkit4 | 13 | {imaging-dev} |
ncbi-entrez-direct | 13 | {bio} |
pixelmed | 13 | {imaging} |
- cgview | 12 | {bio} |
+ insighttoolkit4 | 12 | {imaging-dev} |
vtk-dicom | 12 | {imaging} |
adun.app | 11 | {bio} |
biojava-live | 11 | {bio-dev} |
+ cgview | 11 | {bio} |
openslide | 11 | {imaging} |
+ psychopy | 11 | {psychology} |
jebl2 | 10 | {bio-dev} |
mia | 10 | {imaging} |
- seqsero | 10 | {bio} |
+ obitools | 10 | {bio} |
staden | 10 | {bio} |
ea-utils | 9 | {bio} |
- gasic | 9 | {cloud,bio} |
+ hunspell-en-med | 9 | {tools} |
king-probe | 9 | {bio} |
ngs-sdk | 9 | {bio-dev} |
- obitools | 9 | {bio} |
- plastimatch | 9 | {imaging} |
- psychopy | 9 | {psychology} |
biosig4c++ | 8 | {imaging,physics} |
dazzdb | 8 | {bio} |
+ gasic | 8 | {cloud,bio} |
gdcm | 8 | {imaging-dev} |
mipe | 8 | {bio,cloud} |
+ plastimatch | 8 | {imaging} |
radiant | 8 | {bio} |
+ seqsero | 8 | {bio} |
tree-puzzle | 8 | {cloud,bio,bio-phylogeny} |
abacas | 7 | {bio} |
alter-sequence-alignment | 7 | {bio} |
bppsuite | 7 | {bio} |
diamond-aligner | 7 | {bio,covid-19} |
fastlink | 7 | {bio,cloud} |
- fitgcp | 7 | {cloud,bio} |
- hunspell-en-med | 7 | {tools} |
librg-utils-perl | 7 | {bio} |
ncbi-seg | 7 | {bio} |
+ neobio | 7 | {cloud,bio} |
norsp | 7 | {bio} |
+ paml | 7 | {bio} |
parsnp | 7 | {bio} |
phast | 7 | {bio} |
anfo | 6 | {cloud,bio} |
arden | 6 | {bio,cloud} |
biomaj3-cli | 6 | {cloud} |
- brig | 6 | {bio} |
+ cluster3 | 6 | {bio} |
daligner | 6 | {bio-ngs,bio} |
ecopcr | 6 | {bio} |
embassy-domainatrix | 6 | {bio,cloud} |
embassy-domsearch | 6 | {bio,cloud} |
+ fitgcp | 6 | {cloud,bio} |
freecontact | 6 | {bio,cloud} |
jaligner | 6 | {bio} |
lagan | 6 | {bio} |
maqview | 6 | {bio} |
melting | 6 | {cloud,bio} |
- neobio | 6 | {cloud,bio} |
orthanc-webviewer | 6 | {imaging} |
- paml | 6 | {bio} |
phyutility | 6 | {bio,cloud} |
piler | 6 | {bio} |
placnet | 6 | {bio} |
@@ -77,7 +77,6 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
prime-phylo | 6 | {bio,cloud} |
pscan-tfbs | 6 | {bio} |
pymia | 6 | {imaging-dev} |
- rambo-k | 6 | {bio} |
rdp-readseq | 6 | {bio} |
salmon | 6 | {bio} |
seqtools | 6 | {bio} |
@@ -92,8 +91,8 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
biomaj3-daemon | 5 | {bio} |
bio-rainbow | 5 | {bio} |
bitseq | 5 | {bio} |
+ brig | 5 | {bio} |
canu | 5 | {bio} |
- cluster3 | 5 | {bio} |
codonw | 5 | {bio} |
edtsurf | 5 | {bio} |
embassy-domalign | 5 | {cloud,bio} |
@@ -119,6 +118,7 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
probabel | 5 | {cloud,bio} |
pscan-chip | 5 | {bio} |
quorum | 5 | {bio} |
+ rambo-k | 5 | {bio} |
rdp-alignment | 5 | {bio} |
saint | 5 | {bio} |
seqtools | 5 | {bio} |
@@ -143,7 +143,6 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
harvest-tools | 4 | {bio} |
hinge | 4 | {bio} |
jmodeltest | 4 | {bio,bio-phylogeny} |
- libminc | 4 | {imaging-dev} |
libpal-java | 4 | {bio-dev} |
librdp-taxonomy-tree-java | 4 | {bio-dev} |
logol | 4 | {bio} |
@@ -163,15 +162,17 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
blasr | 3 | {bio,bio-ngs} |
delly | 3 | {bio,covid-19} |
dindel | 3 | {bio} |
- elastix | 3 | {imaging} |
fsm-lite | 3 | {bio} |
+ libminc | 3 | {imaging-dev} |
libncl | 3 | {bio} |
libsbml | 3 | {bio-dev} |
maffilter | 3 | {bio} |
+ mencal | 3 | {tools} |
metaphlan2 | 3 | {bio} |
mptp | 3 | {bio} |
mrs | 3 | {bio} |
murasaki | 3 | {bio} |
+ ngs-sdk | 3 | {bio-dev} |
nutsqlite | 3 | {tools} |
orthanc-dicomweb | 3 | {covid-19,imaging} |
orthanc-mysql | 3 | {imaging} |
@@ -200,15 +201,15 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
biosig4c++ | 2 | {physics,imaging-dev} |
cufflinks | 2 | {bio,cloud} |
dicompyler | 2 | {oncology} |
+ elastix | 2 | {imaging} |
getdata | 2 | {bio} |
igor | 2 | {bio} |
kma | 2 | {bio} |
kmerresistance | 2 | {bio} |
libgff | 2 | {bio-dev} |
libsmithwaterman | 2 | {bio} |
- mencal | 2 | {tools} |
- ngs-sdk | 2 | {bio-dev} |
qcumber | 2 | {bio} |
+ qrisk2 | 2 | {practice} |
scrm | 2 | {bio} |
segemehl | 2 | {bio} |
skesa | 2 | {bio} |
@@ -233,7 +234,7 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
pal2nal | 1 | {bio} |
papyrus | 1 | {imaging-dev} |
pilercr | 1 | {bio} |
- qrisk2 | 1 | {practice} |
+ python-questplus | 1 | {covid-19} |
samtools-legacy | 1 | {bio-dev} |
sift | 1 | {bio} |
stringtie | 1 | {bio,covid-19} |
@@ -298,12 +299,10 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
oscar | 0 | {tools,data,practice} |
pbcopper | 0 | {bio-dev} |
pbseqlib | 0 | {bio-dev} |
- python-etelemetry | 0 | {covid-19} |
python-py2bit | 0 | {bio-dev,bio} |
- python-questplus | 0 | {covid-19} |
python-scitrack | 0 | {covid-19} |
- relion | 0 | {bio} |
relion | 0 | {bio-dev} |
+ relion | 0 | {bio} |
sambamba | 0 | {bio} |
sbmltoolbox | 0 | {bio-dev} |
seqan | 0 | {bio-dev} |
@@ -317,5 +316,6 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
varna | 0 | {bio} |
vtk-dicom | 0 | {imaging-dev} |
bustools | -1 | {bio} |
+ wtdbg2 | -1 | {covid-19} |
(345 rows)
=====================================
outdated_med-packages.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
+Last-Update: Mon, 06 Apr 2020 13:42:04 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+-----------------------------------------------------------------------------+----------------------+------------------------
@@ -26,6 +26,7 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
kineticstools | 0.6.1+git20180425.27a1878 | 0.6.1+git20200325.3558942 | Andreas Tille | Andreas Tille | 2019-02-14 13:26:09+00
king-probe | 2.16.160404+git20180613.a09b012 | 2.16.160404+git20200121.9b198c1 | Andreas Tille,Malihe Asemani,Michael Prisant | Andreas Tille | 2018-07-16 07:34:48+00
kma | 1.2.21 | 1.2.22 | Andreas Tille | Steffen Moeller | 2020-01-17 22:54:10+00
+ libgclib | 0.11.4 | 0.11.7 | Andreas Tille,Michael R. Crusoe,Steffen Moeller | Michael R. Crusoe | 2020-02-14 13:04:26+00
libjloda-java | 0.0+git20180523.cbaf6d1 | 0.0+git20200330.cb91494 | Andreas Tille | Andreas Tille | 2018-05-25 21:49:43+00
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
@@ -50,18 +51,21 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
q2-demux | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2020-01-26 07:34:40+00
q2-feature-classifier | 2019.4.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2019-11-11 10:00:33+00
q2-metadata | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Andreas Tille | 2020-02-03 08:42:28+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
salmon | 0.12.0 | 1.1.0 | 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
+ 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
sra-sdk | 2.9.3 | 2.10.5 | Andreas Tille,Charles Plessy | Steffen Moeller | 2018-10-23 20:40:02+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
+ toil | 3.24.0 | 4.0.0 | Michael R. Crusoe,Steffen Moeller | Michael R. Crusoe | 2020-02-14 13:05:40+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
-(59 rows)
+(63 rows)
source | id | severity | title
@@ -129,7 +133,7 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
gdcm | 826048 | wishlist | Faulty CMake file impairs compiling against GDCM
gemma | 952190 | serious | gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2
gentle | 732691 | normal | Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button
- ghmm | 936609 | normal | ghmm: Python2 removal in sid/bullseye
+ ghmm | 936609 | serious | ghmm: Python2 removal in sid/bullseye
harvest-tools | 943055 | normal | harvest-tools: Python2 removal in sid/bullseye
htsjdk | 877590 | normal | FTBFS: error: package org.testng does not exist
htsjdk | 920588 | normal | htsjdk: Autopkgtest for htsjdk
@@ -147,9 +151,9 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
khmer | 851830 | minor | arm64 has flaky tests
khmer | 955566 | serious | khmer: autopkgtest regression: undefined references
kineticstools | 936797 | serious | kineticstools: Python2 removal in sid/bullseye
- kissplice | 936798 | normal | kissplice: Python2 removal in sid/bullseye
+ kissplice | 936798 | serious | kissplice: Python2 removal in sid/bullseye
kmc | 954270 | important | kmc: arm64 autopkgtest time out
- kmer | 936802 | normal | kmer: Python2 removal in sid/bullseye
+ kmer | 936802 | serious | kmer: Python2 removal in sid/bullseye
libgtextutils | 925745 | serious | libgtextutils: ftbfs with GCC-9
libhmsbeagle | 950367 | normal | confuses DEB_HOST_MULTIARCH and DEB_HOST_GNU_TYPE
libjung-free-java | 884379 | minor | libjung-free-java: New version available
@@ -165,7 +169,7 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
macs | 949204 | serious | macs FTBFS on most architectures. test failures
macs | 953323 | serious | src:macs: fails to migrate to testing for too long
macsyfinder | 933928 | normal | macsyfinder: Port to Python3 needed
- macsyfinder | 936977 | normal | macsyfinder: Python2 removal in sid/bullseye
+ macsyfinder | 936977 | serious | macsyfinder: Python2 removal in sid/bullseye
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
@@ -188,7 +192,7 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
orthanc-postgresql | 829383 | wishlist | orthanc-postgresql: please provide backup script
orthanc-webviewer | 828949 | minor | orthanc-webviewer: "better" suggestion for cache location
paleomix | 933750 | normal | paleomix: Port to Python3 needed
- paleomix | 937232 | normal | paleomix: Python2 removal in sid/bullseye
+ paleomix | 937232 | serious | paleomix: Python2 removal in sid/bullseye
pbbam | 829741 | important | pbbam: FTBFS (32-bit): pbmerge assertion failure
pbgenomicconsensus | 937255 | serious | pbgenomicconsensus: Python2 removal in sid/bullseye
phast | 911983 | important | phast FTBFS on architectures where char is unsigned
@@ -200,7 +204,6 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
pixelmed | 728569 | normal | Add PixelMed SCP
praat | 919490 | normal | praat FTCBFS: many reasons
praat | 955576 | serious | src:praat: fails to migrate to testing for too long: ftbfs mips64el
- praat | 955659 | serious | praat: FTBFS: failed tests
profnet | 905206 | serious | profnet: autopkgtest regression
profphd | 897605 | normal | profphd failure in stretch
profphd | 942064 | grave | profphd: autopkgtest failure
@@ -209,7 +212,7 @@ Last-Update: Mon, 06 Apr 2020 01:42:04 +0000
psychopy | 829424 | normal | psychopy: ioHub uses inappropriate PID file location
psychopy | 953052 | important | psychopy: python2 dependencies
psychopy | 953053 | important | psychopy: missing python3 dependencies
- pynast | 937488 | normal | pynast: Python2 removal in sid/bullseye
+ pynast | 937488 | serious | pynast: Python2 removal in sid/bullseye
pynast | 948081 | serious | pynast build depends on and recommends the removed blast2 transitional package
python-biom-format | 820060 | normal | python-biom-format: broken on big-endian architectures
python-biom-format | 950929 | normal | python-biom-format: FTBFS with pandas 1.0: test failures
@@ -267,5 +270,5 @@ Last-Update: Mon, 06 Apr 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
-(201 rows)
+(200 rows)
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/2b508b65c27b189b82d9908fc22e3ff52bcd26fd
--
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