Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
92e61b27 by Andreas Tille at 2020-03-29T13:44:39+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,51 +1,51 @@
-Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
+Last-Update: Sun, 29 Mar 2020 13:42:04 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk | 167 | {imaging,covid-19} |
- orthanc | 97 | {imaging,practice,covid-19} |
+ 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 | 35 | {imaging} |
+ amide | 34 | {imaging} |
htsjdk | 34 | {bio-dev} |
- dcm2niix | 31 | {imaging} |
- dicomscope | 28 | {imaging} |
- dicom3tools | 26 | {imaging} |
- gdcm | 21 | {covid-19,imaging} |
+ dcm2niix | 30 | {imaging} |
+ dicomscope | 27 | {imaging} |
+ dicom3tools | 25 | {imaging} |
+ gdcm | 20 | {covid-19,imaging} |
minc-tools | 19 | {imaging} |
- pixelmed | 19 | {imaging} |
gnumed-server | 18 | {covid-19,practice} |
+ pixelmed | 18 | {imaging} |
ngs-sdk | 17 | {bio-dev} |
- openslide | 16 | {imaging} |
invesalius | 15 | {imaging} |
+ ncbi-entrez-direct | 15 | {bio} |
+ openslide | 15 | {imaging} |
vtk-dicom | 15 | {imaging} |
biojava-live | 14 | {bio-dev} |
+ insighttoolkit4 | 14 | {imaging-dev} |
king | 14 | {imaging,typesetting} |
- ncbi-entrez-direct | 14 | {bio} |
- adun.app | 13 | {bio} |
- insighttoolkit4 | 13 | {imaging-dev} |
cgview | 12 | {bio} |
mia | 12 | {imaging} |
psychopy | 12 | {psychology} |
+ adun.app | 11 | {bio} |
ea-utils | 11 | {bio} |
jebl2 | 11 | {bio-dev} |
+ plastimatch | 11 | {imaging} |
radiant | 11 | {bio} |
- biosig4c++ | 10 | {physics,imaging} |
+ 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} |
- plastimatch | 10 | {imaging} |
- staden | 10 | {bio} |
tree-puzzle | 10 | {bio,cloud,bio-phylogeny} |
+ biosig4c++ | 9 | {physics,imaging} |
bppsuite | 9 | {bio} |
fastlink | 9 | {bio,cloud} |
gdcm | 9 | {imaging-dev} |
mipe | 9 | {bio,cloud} |
ncbi-seg | 9 | {bio} |
- ngs-sdk | 9 | {bio-dev} |
phast | 9 | {bio} |
prime-phylo | 9 | {bio,cloud} |
abacas | 8 | {bio} |
@@ -83,6 +83,7 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
lucy | 7 | {bio} |
mauve-aligner | 7 | {bio} |
microbegps | 7 | {bio} |
+ mlv-smile | 7 | {cloud,bio} |
paraclu | 7 | {cloud,bio} |
perm | 7 | {cloud,bio} |
placnet | 7 | {bio} |
@@ -108,18 +109,19 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
dascrubber | 6 | {bio} |
elph | 6 | {bio} |
gatb-core | 6 | {bio} |
+ ghmm | 6 | {bio} |
harvest-tools | 6 | {bio} |
indelible | 6 | {bio} |
ipig | 6 | {bio} |
jellyfish1 | 6 | {bio} |
logol | 6 | {bio} |
mapsembler2 | 6 | {bio,cloud} |
- mlv-smile | 6 | {cloud,bio} |
murasaki | 6 | {bio} |
orthanc-webviewer | 6 | {imaging} |
parsnp | 6 | {bio} |
proalign | 6 | {bio-phylogeny,bio} |
pscan-chip | 6 | {bio} |
+ pymia | 6 | {imaging-dev} |
quorum | 6 | {bio} |
rambo-k | 6 | {bio} |
rdp-readseq | 6 | {bio} |
@@ -141,7 +143,6 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
cluster3 | 5 | {bio} |
dwgsim | 5 | {bio} |
fastml | 5 | {bio} |
- ghmm | 5 | {bio} |
hinge | 5 | {bio} |
jmodeltest | 5 | {bio,bio-phylogeny} |
libminc | 5 | {imaging-dev} |
@@ -154,8 +155,8 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
openslide | 5 | {imaging-dev} |
patman | 5 | {bio} |
phipack | 5 | {bio} |
- pymia | 5 | {imaging-dev} |
rdp-classifier | 5 | {bio} |
+ salmon | 5 | {bio} |
sumatra | 5 | {bio} |
tvc | 5 | {bio} |
blasr | 4 | {bio-ngs,bio} |
@@ -177,7 +178,6 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
relion | 4 | {bio} |
roguenarok | 4 | {bio} |
runcircos-gui | 4 | {bio} |
- salmon | 4 | {bio} |
samblaster | 4 | {bio,covid-19} |
sga | 4 | {bio} |
soapsnp | 4 | {bio} |
@@ -210,6 +210,7 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
libsmithwaterman | 2 | {bio} |
mencal | 2 | {tools} |
nanook | 2 | {bio} |
+ ngs-sdk | 2 | {bio-dev} |
qcumber | 2 | {bio} |
qrisk2 | 2 | {practice} |
samtools-legacy | 2 | {bio-dev} |
@@ -221,9 +222,8 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
tree-puzzle | 2 | {cloud,bio,bio-phylogeny} |
volpack | 2 | {imaging-dev} |
atropos | 1 | {bio} |
- biosig4c++ | 1 | {physics,imaging-dev} |
biosig4c++ | 1 | {imaging-dev,physics} |
- blimps | 1 | {bio} |
+ biosig4c++ | 1 | {physics,imaging-dev} |
ctn | 1 | {imaging-dev} |
edflib | 1 | {imaging-dev} |
embassy-phylip | 1 | {cloud,bio} |
@@ -233,7 +233,6 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
libsmithwaterman | 1 | {bio-dev} |
libvistaio | 1 | {imaging-dev} |
maxflow | 1 | {imaging-dev} |
- ngs-sdk | 1 | {bio-dev} |
nutsqlite | 1 | {tools} |
opencfu | 1 | {laboratory} |
opensurgsim | 1 | {imaging-dev} |
@@ -242,7 +241,6 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
papyrus | 1 | {imaging-dev} |
pilercr | 1 | {bio} |
ragout | 1 | {bio,covid-19} |
- sift | 1 | {bio} |
stringtie | 1 | {bio,covid-19} |
trace2dbest | 1 | {bio} |
acedb | 0 | {bio,cloud} |
@@ -253,6 +251,7 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
biojava4-live | 0 | {bio-dev} |
biosig4c++ | 0 | {physics} |
biosyntax | 0 | {bio} |
+ blimps | 0 | {bio} |
camp | 0 | {imaging-dev} |
emboss-explorer | 0 | {bio} |
emmax | 0 | {bio} |
@@ -261,6 +260,7 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
freecontact | 0 | {bio-dev} |
gatb-core | 0 | {bio-dev} |
htscodecs | 0 | {bio-dev,covid-19} |
+ libbigwig | 0 | {bio-dev} |
libbiod | 0 | {bio-dev} |
libbioparser-dev | 0 | {bio-dev} |
libbpp-core | 0 | {bio-dev} |
@@ -309,6 +309,7 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
sbmltoolbox | 0 | {bio-dev} |
seqan | 0 | {bio-dev} |
seq-gen | 0 | {bio} |
+ sift | 0 | {bio} |
simpleitk | 0 | {imaging-dev} |
skewer | 0 | {bio} |
smrtanalysis | 0 | {bio,covid-19} |
@@ -317,5 +318,5 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
trim-galore | 0 | {bio} |
varna | 0 | {bio} |
vtk-dicom | 0 | {imaging-dev} |
-(345 rows)
+(346 rows)
=====================================
outdated_med-packages.txt
=====================================
@@ -1,8 +1,8 @@
-Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
+Last-Update: Sun, 29 Mar 2020 13:42:04 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+---------------------------------------------------------------------------+----------------------+------------------------
- atropos | 1.1.24 | 2.0.0-alpha.4 | Andreas Tille | Steffen Moeller | 2019-11-30 12:19:31+00
+ augur | 6.4.2 | 6.4.3 | Andreas Tille | Andreas Tille | 2020-03-25 07:34:13+00
baitfisher | 1.2.7+git20180107.e92dbf2 | 1.2.7+git20190123.241d060 | Olivier Sallou | Andreas Tille | 2018-09-24 13:04:18+00
beast2-mcmc | 2.6.0 | 2.6.2 | Andreas Tille,Olivier Sallou | Andreas Tille | 2019-07-31 13:08:02+00
biobambam2 | 2.0.160 | 2.0.160+ds | Andreas Tille | Andreas Tille | 2020-03-27 10:34:45+00
@@ -36,7 +36,7 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
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
- pbseqlib | 5.3.3 | 5.3.4 | Andreas Tille | Andreas Tille | 2020-01-29 15:04:33+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
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
@@ -45,6 +45,7 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
python-cobra | 0.14.2 | 0.18.0 | Afif Elghraoui | Liubov Chuprikova | 2019-03-02 06:49:44+00
python-colormap | 1.0.2 | 1.0.3 | Andreas Tille | Andreas Tille | 2019-12-06 16:51:43+00
python-cutadapt | 2.8 | 2.9 | Andreas Tille,Kevin Murray,Olivier Sallou,Steffen Moeller | Steffen Moeller | 2020-02-03 10:50:38+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-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-skbio | 0.5.5 | 0.5.6 | Andreas Tille,Kevin Murray,Tim Booth | Michael R. Crusoe | 2020-02-28 14:48:20+00
@@ -57,12 +58,13 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
scrm | 1.7.3 | 1.7.4 | Kevin Murray | Andreas Tille | 2018-12-17 13:05:34+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
spoa | 3.0.1 | 3.0.2 | Andreas Tille | Andreas Tille | 2019-09-16 11:53:05+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
xmedcon | 0.16.1 | 0.16.2 | Andreas Tille,Roland Marcus Rutschmann | Andreas Tille | 2019-01-25 18:23:59+00
-(60 rows)
+(62 rows)
source | id | severity | title
@@ -124,7 +126,6 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
falcon | 936503 | serious | falcon: Python2 removal in sid/bullseye
fastlink | 909713 | minor | fastlink: Please provide autopkgtest
fastqc | 950311 | normal | fastqc: FAIL strings in output - what does this mean?
- fermi-lite | 954127 | grave | fermi-lite broken on armhf
garli | 907905 | normal | garli: FTBFS randomly (failing tests)
gatb-core | 929564 | normal | gatb-core-testdata: broken symlink: /usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit
gdcm | 731435 | normal | warning: iteration 55823u invokes undefined behavior [-Waggressive-loop-optimizations]
@@ -237,7 +238,6 @@ Last-Update: Sun, 29 Mar 2020 01:42:04 +0000
qiime | 950842 | serious | autopkg tests fail with Python 3.8
qrisk2 | 912118 | normal | qrisk2: 2017 upstream release
qrisk2 | 912119 | normal | qrisk2: please provide qrisk3
- ragout | 953904 | serious | ragout: autopkgtest failure: "sibelia" is not installed.
rapmap | 909766 | important | Use Debian packaged spdlog instead of code copy of old version
relion | 952003 | serious | relion: FTBFS: src/mpi.cpp:56:23: error: call to ‘MPI_Errhandler_set’ declared with attribute error: MPI_Errhandler_set was removed in MPI-3.0. Use MPI_Comm_set_errhandler instead.
salmon | 952102 | serious | salmon: FTBFS: SalmonAlevin.cpp:780:6: error: ‘class rapmap::utils::MappingConfig’ has no member named ‘maxSlack’
@@ -273,5 +273,5 @@ Last-Update: Sun, 29 Mar 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
-(206 rows)
+(204 rows)
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/92e61b2752c01facde9b2583384b9f1bd9b1d578
--
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/92e61b2752c01facde9b2583384b9f1bd9b1d578
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