Andreas Tille pushed to branch master at Debian Med / community / helper-scripts
Commits:
c7c9ef3b by Andreas Tille at 2020-02-27T13:45:30+00:00
automatic update
- - - - -
2 changed files:
- debian-med-tests.txt
- outdated_med-packages.txt
Changes:
=====================================
debian-med-tests.txt
=====================================
@@ -1,67 +1,66 @@
-Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
+Last-Update: Thu, 27 Feb 2020 13:42:04 +0000
Source | Vote | Tasks | Tags
-------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------
- dcmtk | 172 | {imaging} |
- orthanc | 91 | {imaging,practice} |
- gdcm | 49 | {imaging-dev} |
- orthanc-wsi | 38 | {his,laboratory,oncology,practice,imaging} |
+ dcmtk | 170 | {imaging} |
+ orthanc | 90 | {imaging,practice} |
+ gdcm | 47 | {imaging-dev} |
+ orthanc-wsi | 37 | {his,imaging,practice,oncology,laboratory} |
cfflib | 35 | {imaging-dev} |
dcm2niix | 33 | {imaging} |
- amide | 31 | {imaging} |
+ amide | 32 | {imaging} |
dicomscope | 25 | {imaging} |
- medicalterms | 25 | {tools} |
- dicom3tools | 22 | {imaging} |
+ medicalterms | 24 | {tools} |
+ dicom3tools | 21 | {imaging} |
htsjdk | 19 | {bio-dev} |
gnumed-server | 17 | {practice} |
gdcm | 16 | {imaging} |
ngs-sdk | 13 | {bio-dev} |
+ adun.app | 12 | {bio} |
pixelmed | 12 | {imaging} |
- adun.app | 11 | {bio} |
- insighttoolkit4 | 11 | {imaging-dev} |
invesalius | 11 | {imaging} |
+ insighttoolkit4 | 10 | {imaging-dev} |
minc-tools | 10 | {imaging} |
jebl2 | 9 | {bio-dev} |
- king | 9 | {imaging,typesetting} |
+ king | 9 | {typesetting,imaging} |
mia | 9 | {imaging} |
- tree-puzzle | 9 | {bio-phylogeny,bio,cloud} |
+ tree-puzzle | 9 | {bio,bio-phylogeny,cloud} |
vtk-dicom | 9 | {imaging} |
gdcm | 8 | {imaging-dev} |
librg-utils-perl | 8 | {bio} |
plastimatch | 8 | {imaging} |
biojava-live | 7 | {bio-dev} |
- fastlink | 7 | {bio,cloud} |
- melting | 7 | {cloud,bio} |
+ fastlink | 7 | {cloud,bio} |
+ melting | 7 | {bio,cloud} |
ncbi-seg | 7 | {bio} |
norsp | 7 | {bio} |
obitools | 7 | {bio} |
psychopy | 7 | {psychology} |
maqview | 6 | {bio} |
+ ncbi-entrez-direct | 6 | {bio} |
openslide | 6 | {imaging} |
- orthanc-webviewer | 6 | {imaging} |
sortmerna | 6 | {bio} |
staden | 6 | {bio} |
- cgview | 5 | {bio} |
dicompyler | 5 | {oncology} |
- embassy-domainatrix | 5 | {bio,cloud} |
+ embassy-domainatrix | 5 | {cloud,bio} |
freecontact | 5 | {cloud,bio} |
ipig | 5 | {bio} |
jaligner | 5 | {bio} |
king-probe | 5 | {bio} |
libdivsufsort | 5 | {bio-dev} |
mapsembler2 | 5 | {cloud,bio} |
- mipe | 5 | {bio,cloud} |
- ncbi-entrez-direct | 5 | {bio} |
- neobio | 5 | {bio,cloud} |
+ mipe | 5 | {cloud,bio} |
+ neobio | 5 | {cloud,bio} |
ngs-sdk | 5 | {bio-dev} |
- openslide | 5 | {imaging-dev} |
+ orthanc-webviewer | 5 | {imaging} |
sibsim4 | 5 | {bio,cloud} |
sigma-align | 5 | {bio,bio-phylogeny,cloud} |
- ampliconnoise | 4 | {bio,cloud} |
+ ampliconnoise | 4 | {cloud,bio} |
anfo | 4 | {cloud,bio} |
arden | 4 | {cloud,bio} |
bandage | 4 | {bio} |
- brig | 4 | {bio} |
+ cgview | 4 | {bio} |
+ cluster3 | 4 | {bio} |
dazzdb | 4 | {bio} |
diamond-aligner | 4 | {bio} |
ea-utils | 4 | {bio} |
@@ -70,22 +69,23 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
estscan | 4 | {bio} |
gatb-core | 4 | {bio} |
ghmm | 4 | {bio} |
- idba | 4 | {cloud,bio} |
+ idba | 4 | {bio,cloud} |
indelible | 4 | {bio} |
jellyfish1 | 4 | {bio} |
lagan | 4 | {bio} |
mlv-smile | 4 | {cloud,bio} |
nutsqlite | 4 | {tools} |
+ openslide | 4 | {imaging-dev} |
orthanc-dicomweb | 4 | {imaging} |
orthanc-mysql | 4 | {imaging} |
paml | 4 | {bio} |
- phyutility | 4 | {cloud,bio} |
+ phyutility | 4 | {bio,cloud} |
piler | 4 | {bio} |
predictprotein | 4 | {bio} |
prime-phylo | 4 | {bio,cloud} |
pymia | 4 | {imaging-dev} |
seqtools | 4 | {bio} |
- squizz | 4 | {bio,cloud} |
+ squizz | 4 | {cloud,bio} |
tracetuner | 4 | {bio} |
transtermhp | 4 | {bio} |
treeview | 4 | {bio-phylogeny,bio} |
@@ -98,12 +98,12 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
bio-tradis | 3 | {bio-dev,bio} |
blasr | 3 | {bio,bio-ngs} |
bppsuite | 3 | {bio} |
+ brig | 3 | {bio} |
canu | 3 | {bio} |
- cluster3 | 3 | {bio} |
delly | 3 | {bio} |
ecopcr | 3 | {bio} |
elph | 3 | {bio} |
- embassy-domsearch | 3 | {bio,cloud} |
+ embassy-domsearch | 3 | {cloud,bio} |
fitgcp | 3 | {cloud,bio} |
gasic | 3 | {cloud,bio} |
getdata | 3 | {bio} |
@@ -112,12 +112,12 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
libsbml | 3 | {bio-dev} |
lucy | 3 | {bio} |
mauve-aligner | 3 | {bio} |
- mhap | 3 | {bio,bio-ngs} |
+ mhap | 3 | {bio-ngs,bio} |
microbegps | 3 | {bio} |
mrs | 3 | {bio} |
- paraclu | 3 | {bio,cloud} |
+ paraclu | 3 | {cloud,bio} |
perm | 3 | {cloud,bio} |
- proalign | 3 | {bio,bio-phylogeny} |
+ proalign | 3 | {bio-phylogeny,bio} |
probabel | 3 | {cloud,bio} |
qrisk2 | 3 | {practice} |
radiant | 3 | {bio} |
@@ -138,15 +138,15 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
baitfisher | 2 | {bio} |
bart-view | 2 | {imaging} |
beads | 2 | {bio} |
- beast-mcmc | 2 | {bio-phylogeny,bio} |
+ beast-mcmc | 2 | {bio,bio-phylogeny} |
bio-rainbow | 2 | {bio} |
bitseq | 2 | {bio} |
centrifuge | 2 | {bio} |
clonalframeml | 2 | {bio} |
clonalorigin | 2 | {bio} |
codonw | 2 | {bio} |
- cufflinks | 2 | {bio,cloud} |
- daligner | 2 | {bio,bio-ngs} |
+ cufflinks | 2 | {cloud,bio} |
+ daligner | 2 | {bio-ngs,bio} |
dascrubber | 2 | {bio} |
dindel | 2 | {bio} |
dwgsim | 2 | {bio} |
@@ -156,7 +156,7 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
harvest-tools | 2 | {bio} |
hinge | 2 | {bio} |
igor | 2 | {bio} |
- jmodeltest | 2 | {bio,bio-phylogeny} |
+ jmodeltest | 2 | {bio-phylogeny,bio} |
lamarc | 2 | {bio} |
libgff | 2 | {bio-dev} |
libpal-java | 2 | {bio-dev} |
@@ -179,7 +179,7 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
rampler | 2 | {bio} |
rdp-classifier | 2 | {bio} |
relion | 2 | {bio} |
- rtax | 2 | {bio,cloud} |
+ rtax | 2 | {cloud,bio} |
runcircos-gui | 2 | {bio} |
samblaster | 2 | {bio} |
scythe | 2 | {bio} |
@@ -197,7 +197,7 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
blimps | 1 | {bio} |
ctn | 1 | {imaging-dev} |
edflib | 1 | {imaging-dev} |
- embassy-phylip | 1 | {bio,cloud} |
+ embassy-phylip | 1 | {cloud,bio} |
emmax | 1 | {bio} |
freebayes | 1 | {bio} |
hunspell-en-med | 1 | {tools} |
@@ -243,7 +243,7 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
sumaclust | 1 | {bio} |
surankco | 1 | {bio} |
tnseq-transit | 1 | {bio} |
- tree-puzzle | 1 | {cloud,bio,bio-phylogeny} |
+ tree-puzzle | 1 | {bio,bio-phylogeny,cloud} |
varscan | 1 | {bio} |
volpack | 1 | {imaging-dev} |
bambamc | 0 | {bio-dev} |
@@ -297,13 +297,14 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
opencfu | 0 | {laboratory} |
opensurgsim | 0 | {imaging-dev} |
orthanc-imagej | 0 | {imaging} |
- oscar | 0 | {tools,data,practice} |
+ oscar | 0 | {tools,practice,data} |
papyrus | 0 | {imaging-dev} |
pbcopper | 0 | {bio-dev} |
pbseqlib | 0 | {bio-dev} |
- python-deeptools | 0 | {bio,bio-dev} |
- python-py2bit | 0 | {bio,bio-dev} |
+ python-deeptools | 0 | {bio-dev,bio} |
+ python-py2bit | 0 | {bio-dev,bio} |
python-pyani | 0 | {bio-dev} |
+ python-tinyalign | 0 | {bio-dev} |
relion | 0 | {bio-dev} |
relion | 0 | {bio} |
sambamba | 0 | {bio} |
@@ -317,5 +318,5 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
trim-galore | 0 | {bio} |
varna | 0 | {bio} |
vtk-dicom | 0 | {imaging-dev} |
-(347 rows)
+(348 rows)
=====================================
outdated_med-packages.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
+Last-Update: Thu, 27 Feb 2020 13:42:04 +0000
source | version | upstream_version | uploaders | Last uploader | Last uploaded
-------------------------------+---------------------------------+---------------------------------+-----------------------------------------------------------------------------+----------------------+------------------------
@@ -49,17 +49,19 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
mothur | 1.42.1 | 1.43.0 | Andreas Tille,Steffen Moeller,Tomasz Buchert | Andreas Tille | 2019-08-01 19:09:05+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 | 13.5.20200221 | Aaron M. Ucko | Aaron M. Ucko | 2020-02-03 03:53:53+00
nibabel | 2.5.1 | 3.0.1 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-01-20 10:35:09+00
pbcopper | 1.3.0 | 1.4.0 | Andreas Tille | Andreas Tille | 2020-01-29 08:51:15+00
pbgenomicconsensus | 2.3.2 | 2.3.3 | Andreas Tille | Liubov Chuprikova | 2019-04-07 15:33:36+00
pbh5tools | 0.8.0+git20170929.58d54ff | 0.8.0+git20181212.9fa8fc4 | Afif Elghraoui | Andreas Tille | 2018-07-13 14:49:05+00
pbseqlib | 5.3.3 | 5.3.4 | Andreas Tille | Andreas Tille | 2020-01-29 15:04:33+00
picard-tools | 2.18.25 | 2.21.9 | Andreas Tille,Charles Plessy,Olivier Sallou,Steffen Moeller,Vincent Danjean | Andreas Tille | 2019-02-04 09:20:37+00
- plink2 | 2.00~a3-200217 | 200222 | Dylan Aïssi | Dylan Aïssi | 2020-02-19 06:19:18+00
+ plink2 | 2.00~a3-200217 | 200225 | Dylan Aïssi | Dylan Aïssi | 2020-02-19 06:19:18+00
prokka | 1.14.5 | 1.14.6 | Andreas Tille,Michael R. Crusoe | Michael R. Crusoe | 2019-12-04 11:00:31+00
pydicom | 1.4.1 | 1.4.2 | Michael Hanke,Yaroslav Halchenko | Andreas Tille | 2020-01-23 12:34:53+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 | 1.4.2 | Yaroslav Halchenko | Yaroslav Halchenko | 2019-08-17 19:00:11+00
+ python-cgecore | 1.5.2 | 1.5.3 | Andreas Tille | Steffen Moeller | 2020-01-06 17:05:53+00
python-cobra | 0.14.2 | 0.17.1 | 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-pbcommand | 1.1.1+git20191122.ec024c3 | 1.1.1+git20200211.116b09f | Andreas Tille | Andreas Tille | 2019-12-19 08:42:03+00
@@ -80,7 +82,7 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
unanimity | 3.3.0 | 4.2.0 | 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
-(78 rows)
+(80 rows)
source | id | severity | title
@@ -274,7 +276,7 @@ Last-Update: Thu, 27 Feb 2020 01:42:03 +0000
sofa-framework | 735099 | normal | sofa-framework: FTBFS on sparc, powerpc (and ia64)
sofa-framework | 875184 | serious | [sofa-framework] Future Qt4 removal from Buster
spades | 853113 | normal | spades: Fails to build with unhelpful error message in a "low" memory machine
- spdlog | 952625 | serious | libspdlog-dev: .pc Requires: fmt which doesn't have a .pc file, breaking pkg-config on spdlog.pc
+ spdlog | 952625 | serious | libspdlog-dev: needs to Depend on libfmt-dev (>= 6.1.2+ds-1) (Requires: fmt)
sprai | 943280 | normal | sprai: Python2 removal in sid/bullseye
sra-sdk | 943231 | normal | sra-sdk: Python2 removal in sid/bullseye
sra-sdk | 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/c7c9ef3bc3870ef5dc69bed89ff640140a48dbd7
--
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/c7c9ef3bc3870ef5dc69bed89ff640140a48dbd7
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