Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
05a645c4 by Andreas Tille at 2020-04-10T13:44:44+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,42 +1,42 @@
-Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
+Last-Update: Fri, 10 Apr 2020 13:42:03 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk | 170 | {imaging,covid-19} |
- orthanc | 95 | {imaging,covid-19,practice} |
- gdcm | 43 | {imaging-dev} |
- orthanc-wsi | 41 | {imaging,laboratory,covid-19,practice,oncology,his} |
+ dcmtk | 177 | {imaging,covid-19} |
+ orthanc | 97 | {covid-19,practice,imaging} |
+ gdcm | 44 | {imaging-dev} |
+ orthanc-wsi | 41 | {practice,laboratory,imaging,oncology,his,covid-19} |
amide | 30 | {imaging} |
- htsjdk | 29 | {bio-dev} |
- dcm2niix | 26 | {imaging} |
+ htsjdk | 30 | {bio-dev} |
+ dcm2niix | 25 | {imaging} |
dicom3tools | 24 | {imaging} |
- dicomscope | 24 | {imaging} |
- gdcm | 22 | {covid-19,imaging} |
+ dicomscope | 23 | {imaging} |
+ gdcm | 22 | {imaging,covid-19} |
gnumed-server | 19 | {covid-19,practice} |
- ngs-sdk | 17 | {bio-dev} |
+ ngs-sdk | 19 | {bio-dev} |
minc-tools | 14 | {imaging} |
ncbi-entrez-direct | 14 | {bio} |
- adun.app | 12 | {bio} |
+ adun.app | 13 | {bio} |
+ hunspell-en-med | 13 | {tools} |
invesalius | 12 | {imaging} |
- king | 12 | {typesetting,imaging} |
+ king | 12 | {imaging,typesetting} |
vtk-dicom | 12 | {imaging} |
- hunspell-en-med | 11 | {tools} |
pixelmed | 11 | {imaging} |
cgview | 10 | {bio} |
ea-utils | 10 | {bio} |
+ gasic | 10 | {cloud,bio} |
insighttoolkit4 | 10 | {imaging-dev} |
mia | 10 | {imaging} |
+ ngs-sdk | 10 | {bio-dev} |
openslide | 10 | {imaging} |
- psychopy | 10 | {psychology} |
staden | 10 | {bio} |
- gasic | 9 | {bio,cloud} |
+ biosig4c++ | 9 | {physics,imaging} |
gdcm | 9 | {imaging-dev} |
jebl2 | 9 | {bio-dev} |
king-probe | 9 | {bio} |
- ngs-sdk | 9 | {bio-dev} |
obitools | 9 | {bio} |
+ psychopy | 9 | {psychology} |
biojava-live | 8 | {bio-dev} |
- biosig4c++ | 8 | {physics,imaging} |
dazzdb | 8 | {bio} |
librg-utils-perl | 8 | {bio} |
mipe | 8 | {bio,cloud} |
@@ -46,7 +46,7 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
arden | 7 | {cloud,bio} |
biomaj3-cli | 7 | {cloud} |
bppsuite | 7 | {bio} |
- diamond-aligner | 7 | {covid-19,bio} |
+ diamond-aligner | 7 | {bio,covid-19} |
fitgcp | 7 | {cloud,bio} |
lagan | 7 | {bio} |
phast | 7 | {bio} |
@@ -54,19 +54,18 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
salmon | 7 | {bio} |
tree-puzzle | 7 | {bio,cloud,bio-phylogeny} |
abacas | 6 | {bio} |
- anfo | 6 | {cloud,bio} |
+ anfo | 6 | {bio,cloud} |
biomaj3-daemon | 6 | {bio} |
- cluster3 | 6 | {bio} |
ecopcr | 6 | {bio} |
embassy-domainatrix | 6 | {bio,cloud} |
fastlink | 6 | {cloud,bio} |
- freecontact | 6 | {cloud,bio} |
+ freecontact | 6 | {bio,cloud} |
ncbi-seg | 6 | {bio} |
neobio | 6 | {bio,cloud} |
norsp | 6 | {bio} |
orthanc-webviewer | 6 | {imaging} |
piler | 6 | {bio} |
- prime-phylo | 6 | {bio,cloud} |
+ prime-phylo | 6 | {cloud,bio} |
pscan-tfbs | 6 | {bio} |
pymia | 6 | {imaging-dev} |
seqsero | 6 | {bio} |
@@ -78,6 +77,7 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
bio-rainbow | 5 | {bio} |
bitseq | 5 | {bio} |
clonalorigin | 5 | {bio} |
+ cluster3 | 5 | {bio} |
codonw | 5 | {bio} |
daligner | 5 | {bio-ngs,bio} |
edtsurf | 5 | {bio} |
@@ -92,8 +92,10 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
indelible | 5 | {bio} |
jaligner | 5 | {bio} |
jellyfish1 | 5 | {bio} |
+ libncl | 5 | {bio} |
maqview | 5 | {bio} |
melting | 5 | {cloud,bio} |
+ mrs | 5 | {bio} |
phyutility | 5 | {bio,cloud} |
placnet | 5 | {bio} |
predictprotein | 5 | {bio} |
@@ -101,20 +103,20 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
rambo-k | 5 | {bio} |
seer | 5 | {bio} |
seqtools | 5 | {bio} |
- sibsim4 | 5 | {bio,cloud} |
+ sibsim4 | 5 | {cloud,bio} |
sigma-align | 5 | {cloud,bio,bio-phylogeny} |
sumatra | 5 | {bio} |
vsearch | 5 | {bio} |
baitfisher | 4 | {bio} |
bart-view | 4 | {imaging} |
beads | 4 | {bio} |
- beast-mcmc | 4 | {bio,bio-phylogeny} |
+ beast-mcmc | 4 | {bio-phylogeny,bio} |
bio-tradis | 4 | {bio,bio-dev} |
brig | 4 | {bio} |
centrifuge | 4 | {bio} |
clonalframeml | 4 | {covid-19,bio} |
dascrubber | 4 | {bio} |
- delly | 4 | {bio,covid-19} |
+ delly | 4 | {covid-19,bio} |
dindel | 4 | {bio} |
dwgsim | 4 | {bio} |
elph | 4 | {bio} |
@@ -123,19 +125,17 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
ipig | 4 | {bio} |
lamarc | 4 | {bio} |
libdivsufsort | 4 | {bio-dev} |
- libncl | 4 | {bio} |
mapsembler2 | 4 | {bio,cloud} |
mencal | 4 | {tools} |
microbegps | 4 | {bio} |
mlv-smile | 4 | {bio,cloud} |
- mrs | 4 | {bio} |
murasaki | 4 | {bio} |
openslide | 4 | {imaging-dev} |
paraclu | 4 | {cloud,bio} |
perm | 4 | {bio,cloud} |
poretools | 4 | {bio} |
- proalign | 4 | {bio-phylogeny,bio} |
- probabel | 4 | {cloud,bio} |
+ proalign | 4 | {bio,bio-phylogeny} |
+ probabel | 4 | {bio,cloud} |
quorum | 4 | {bio} |
rdp-alignment | 4 | {bio} |
rdp-readseq | 4 | {bio} |
@@ -149,8 +149,9 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
treeview | 4 | {bio-phylogeny,bio} |
assemblytics | 3 | {bio} |
beast2-mcmc | 3 | {bio} |
- blasr | 3 | {bio-ngs,bio} |
+ blasr | 3 | {bio,bio-ngs} |
canu | 3 | {bio} |
+ cufflinks | 3 | {bio,cloud} |
dicompyler | 3 | {oncology} |
jmodeltest | 3 | {bio-phylogeny,bio} |
libgff | 3 | {bio-dev} |
@@ -165,13 +166,13 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
metaphlan2 | 3 | {bio} |
mptp | 3 | {bio} |
nutsqlite | 3 | {tools} |
- orthanc-dicomweb | 3 | {imaging,covid-19} |
+ orthanc-dicomweb | 3 | {covid-19,imaging} |
orthanc-mysql | 3 | {imaging} |
patman | 3 | {bio} |
pbdagcon | 3 | {bio} |
prottest | 3 | {bio-phylogeny,bio} |
rdp-classifier | 3 | {bio} |
- samblaster | 3 | {covid-19,bio} |
+ samblaster | 3 | {bio,covid-19} |
scythe | 3 | {bio} |
segemehl | 3 | {bio} |
sga | 3 | {bio} |
@@ -180,12 +181,11 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
stacks | 3 | {bio} |
transrate-tools | 3 | {bio} |
biosig4c++ | 2 | {imaging-dev,physics} |
- cufflinks | 2 | {bio,cloud} |
elastix | 2 | {imaging} |
getdata | 2 | {bio} |
igor | 2 | {bio} |
libsmithwaterman | 2 | {bio} |
- mhap | 2 | {bio,bio-ngs} |
+ mhap | 2 | {bio-ngs,bio} |
ngs-sdk | 2 | {bio-dev} |
pal2nal | 2 | {bio} |
phipack | 2 | {bio} |
@@ -208,17 +208,17 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
suitename | 2 | {bio} |
surankco | 2 | {bio} |
sweed | 2 | {bio} |
- thesias | 2 | {bio,covid-19} |
- tnseq-transit | 2 | {covid-19,bio} |
+ thesias | 2 | {covid-19,bio} |
+ tnseq-transit | 2 | {bio,covid-19} |
tvc | 2 | {bio} |
varscan | 2 | {bio} |
yaha | 2 | {bio} |
- zalign | 2 | {bio,cloud} |
+ zalign | 2 | {cloud,bio} |
atropos | 1 | {bio} |
- biosig4c++ | 1 | {imaging-dev,physics} |
+ biosig4c++ | 1 | {physics,imaging-dev} |
blimps | 1 | {bio} |
ctn | 1 | {imaging-dev} |
- embassy-phylip | 1 | {cloud,bio} |
+ embassy-phylip | 1 | {bio,cloud} |
kma | 1 | {bio} |
kmerresistance | 1 | {bio} |
libchado-perl | 1 | {bio-dev} |
@@ -234,7 +234,7 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
samtools-legacy | 1 | {bio-dev} |
sift | 1 | {bio} |
skesa | 1 | {bio} |
- stringtie | 1 | {covid-19,bio} |
+ stringtie | 1 | {bio,covid-19} |
trace2dbest | 1 | {bio} |
tree-puzzle | 1 | {bio-phylogeny,bio,cloud} |
velvetoptimiser | 1 | {bio} |
@@ -254,7 +254,7 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +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} |
libbio-mage-utils-perl | 0 | {bio-dev} |
@@ -270,9 +270,9 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
libgenome | 0 | {bio-dev} |
libgkarrays | 0 | {bio-dev} |
libhmsbeagle | 0 | {bio-dev} |
- libics | 0 | {covid-19,imaging-dev} |
+ libics | 0 | {imaging-dev,covid-19} |
libjloda-java | 0 | {bio-dev} |
- libmaus2 | 0 | {covid-19,bio-dev} |
+ libmaus2 | 0 | {bio-dev,covid-19} |
libmems | 0 | {bio-dev} |
libmialm | 0 | {imaging-dev} |
libmuscle | 0 | {bio-dev} |
@@ -296,10 +296,10 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
ncbi-vdb | 0 | {bio-dev} |
opencfu | 0 | {laboratory} |
orthanc-imagej | 0 | {imaging} |
- oscar | 0 | {practice,data,tools} |
+ oscar | 0 | {data,tools,practice} |
pbcopper | 0 | {bio-dev} |
pbseqlib | 0 | {bio-dev} |
- python-py2bit | 0 | {bio-dev,bio} |
+ python-py2bit | 0 | {bio,bio-dev} |
relion | 0 | {bio} |
relion | 0 | {bio-dev} |
sambamba | 0 | {bio} |
@@ -310,12 +310,12 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
skewer | 0 | {bio} |
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} |
+ wtdbg2 | 0 | {covid-19} |
bustools | -1 | {bio} |
relion | -1 | {bio} |
- wtdbg2 | -1 | {covid-19} |
(345 rows)
=====================================
outdated_med-packages.txt
=====================================
@@ -1,9 +1,8 @@
-Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
+Last-Update: Fri, 10 Apr 2020 13:42:04 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+-------------------------------------------------------------------------+----------------------+------------------------
artemis | 17.0.1 | 18.1.0 | Andreas Tille | Andreas Tille | 2019-02-08 11:19:24+00
- atropos | 1.1.24 | 2.0.0-alpha.4 | Andreas Tille | Steffen Moeller | 2019-11-30 12:19:31+00
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 | 38.80 | Andreas Tille | Andreas Tille | 2020-02-27 11:08:04+00
biobambam2 | 2.0.160 | 2.0.162+ds | Andreas Tille | Andreas Tille | 2020-03-27 10:34:45+00
@@ -37,19 +36,21 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
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
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
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
plink2 | 2.00~a3-200217 | 200328 | 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
python-avro | 1.9.1 | 1.9.2 | Afif Elghraoui | Andreas Tille | 2019-12-18 08:41:55+00
python-bids-validator | 1.2.4 | 1.5.1 | Yaroslav Halchenko | Yaroslav Halchenko | 2019-08-17 19:00:11+00
python-cgecore | 1.5.3 | 1.5.4 | Andreas Tille | Steffen Moeller | 2020-03-17 12:49:52+00
python-colormap | 1.0.2 | 1.0.3 | Andreas Tille | Andreas Tille | 2019-12-06 16:51:43+00
- python-pbcore | 1.7.1+git20200313.41ba394 | 1.7.1+git20200326.ea0808a | Andreas Tille | Steffen Moeller | 2020-03-21 19:39:08+00
+ python-pbcore | 1.7.1+git20200313.41ba394 | 1.7.1+git20200408.0579ac1 | Andreas Tille | Steffen Moeller | 2020-03-21 19:39:08+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-xopen | 0.8.4 | 0.9.0 | Andreas Tille | Steffen Moeller | 2019-11-05 15:34:45+00
- q2-types | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2019-12-23 20:39:42+00
+ q2cli | 2019.10.0 | 2020.2.0 | Liubov Chuprikova | Liubov Chuprikova | 2019-12-16 10:20:08+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+git20200408.0322c0d | Andreas Tille | Andreas Tille | 2019-11-16 23:00:12+00
seaview | 4.7 | 5.0.2 | Andreas Tille,Charles Plessy | Andreas Tille | 2018-05-09 13:43:40+00
@@ -64,7 +65,7 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
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 | 4.2.0-1 | Afif Elghraoui,Andreas Tille | Adrian Bunk | 2019-02-06 07:34:42+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
@@ -210,6 +211,7 @@ Last-Update: Fri, 10 Apr 2020 01:42:04 +0000
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
+ python-biopython | 956324 | serious | python-biopython: FTBFS on mipsel
python-cobra | 955656 | serious | python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'
python-cogent | 950474 | important | python-cogent FTBFS on armel and i386: test failures
python-intervaltree-bio | 920545 | serious | python-intervaltree breaks python-intervaltree-bio autopkgtest
@@ -262,5 +264,5 @@ Last-Update: Fri, 10 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
-(193 rows)
+(194 rows)
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/05a645c49c230ce3a4fedebfb0ab0bb2eee3268e
--
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/05a645c49c230ce3a4fedebfb0ab0bb2eee3268e
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