debian-med Dec 2021 by author

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Étienne Mollier

• [Advent bug squashing] Bug#996409: marked as done (libstatgen breaks minimac4 autopkgtest: Segmentation fault) Dec 07
• Re: Any help to get pydicom build welcome Dec 10
• Re: Any help to get pydicom build welcome Dec 07
• Re: Bug#984063: itk libtiff test issues (Was: Bug#984063) Dec 11
• [Advent bug squashing] Bug#1000475: marked as done (minimac4: autopkgtest regression: *** stack smashing detected ***: terminated) Dec 09
• [Advent bug squashing] Bug#1002365: marked as done (pynn: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.10 3.9" returned exit code 13) Dec 22
• [Advent bug squashing] (Thanks: Andreas) Bug#993773: marked as done (nipype: uses invalid profile "needsrebuildorfix") Dec 11
• [Advent bug squashing] Bug#997884: marked as done (libgclib breaks cdbfasta autopkgtest: ABI breakage?) Dec 02
• Re: [Debian-med-packaging] insighttoolkit5_5.2.1-1_amd64.changes ACCEPTED into unstable, unstable Dec 05
• [Advent bug squashing] Bug#981688: marked as done (graphlan: Wrong homepage) Dec 12
• [Advent bug squashing] Bug#841073: marked as done (python-ruffus: Needs 18 GB of RAM to build) Dec 06
• [Advent bug squashing] Bug#985580: marked as done (odin: please consider autopkgtest) Dec 05
• [Advent bug squashing] Bug#974764: marked as done (python-dipy-doc: suggests removed package python-dipy) Dec 12
• Re: Bug#984063: itk libtiff test issues (Was: Bug#984063) Dec 11
• [Advent bug squashing] src:prime-phylo: no autopkgtest available yet Dec 05
• [Advent bug squashing] Bug#988852: marked as done (transdecoder: broken symlink: /usr/lib/transdecoder/util/__pwm_tests/pasa_assemblies.fasta.gz -> ../../sample_data/pasa_example/pasa_assemblies.fasta.gz) Dec 13

Fabian Klötzl

• Re: RFS: andi and phylonium Dec 30
• RFS: andi and phylonium Dec 30

Steffen Möller

• Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with Dec 10
• RFS: r-cran-sparql - dependency for a more typical Med package Dec 21
• r-bioc-txdb.hsapiens.ucsc.hg19.knowngene on salsa Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with Dec 13
• Re: Moving python-bioblend to med-team? Dec 21
• please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with Dec 09
• Re: RF peer review: r-other-ibi-disgenet2r freshly injected into salsa Dec 22
• RF peer review: r-other-ibi-disgenet2r freshly injected into salsa Dec 22

Aaron M. Ucko

• Re: Help with possibly broken ar archive Dec 22

Adrian Bunk

• Re: Bug#984063: [Debian-med-packaging] Bug#984063: Please lets coordinate itk4/itk5 issues (Was: Bug#984063) Dec 09

Andreas Tille

• [Advent bug squashing]: Bug#985071: marked as done (smalt: native FTBFS with DEB_BUILD_OPTIONS=nocheck) Dec 13
• [Advent bug squashing] Bug#1001282: marked as done (samtools: libhts-dev build dependency must be bumped to >= 1.14) Dec 08
• [Advent bug squashing] Bug#1001020: marked as done (python-anndata: FTBFS with sklearn 1.0.1-1: ModuleNotFoundError: No module named 'sklearn.utils.testing') Dec 10
• [Advent bug squashing] Bug#995781: marked as done (python-sqlsoup autopkgtest fails with SQLAlchemy 1.4.23+ds1-2)] Dec 06
• Somehow some dh_auto_test of Python3 packages insist to install wheel via pip Dec 23
• [Advent bug squashing] (Honor belongs to Nilesh Patra): Bug#965361: marked as done (python-cooler: please make the build reproducible) Dec 09
• Re: RF peer review: r-other-ibi-disgenet2r freshly injected into salsa Dec 22
• Re: RFS: andi and phylonium Dec 30
• [Advent bug squashing] Bug#979625: marked as done (autopkgtest: ModuleNotFoundError (ipytree) and AssertionError) Dec 09
• Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with Dec 10
• Re: [Bug 1956094] Re: deborphan guess-work removes too many files Dec 31
• [Advent bug squashing] Re: FTBFS: error: package org.testng does not exist Dec 23
• Re: Scala error when trying to build latest version of pilon Dec 18
• [Advent bug squashing] Thanks to Olivier Sallou: Bug#982036: marked as done (emboss: FTBFS with OpenJDK 17 due to com.sun.net.ssl removal)] Dec 23
• [Advent bug squashing] bcftools: FTBFS: any-i386 - floating point idiosyncracies - solved in recent versions Dec 07
• [Advent bug squashing] Bug#909280: marked as done (elastix: New upstream available) Dec 06
• [Advent bug squashing] Thanks to Julien Lamy: Bug#1002134: odil: FTBFS: Value.cpp:269:69: error: wrong number of template arguments (4, should be at least 5) Dec 22
• [Advent bug squashing] Bug#977033: marked as done (parallel: Multiple threads on multiple hosts with same home directory fails) Dec 17
• Re: How to do 32-bit build in AMD64 chroot -- problem with SSE instructions? Dec 12
• [Advent bug squashing] Bug#981753: marked as done (COPY cannot find "/usr/share/nodejs/axios/dist/axios.min.js") Dec 05
• Re: Debian Med video conference tomorrow, Friday 2021-12-17 18:00 UTC Dec 16
• [Advent bug squashing] Bug#963866: marked as done (libbio-cluster-perl: circular dependency hell) Dec 02
• Re: [lucas@debian.org: Bug#1002203: mrtrix3: FTBFS: ./core/types.h:326:49: error: ‘using Vector3 = class Eigen::Matrix<double, 3, 1>’ redeclared as different kind of entity] Dec 22
• Re: [Advent bug squashing] Bug#979625: marked as done (autopkgtest: ModuleNotFoundError (ipytree) and AssertionError) Dec 09
• Re: [Advent bug squashing] Pierre Gruet fixed: Bug#1002155: marked as done (libgoby-java: FTBFS: [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist)] Dec 23
• [Advent bug squashing]: Bug#986555: marked as done (mark one more symbol as optional) Dec 11
• Re: libgoby-java: FTBFS: [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist Dec 22
• [Advent bug squashing] Bug#995409: marked as done (ball: Please build depend on qtwebengine5-dev also on mips64el) Dec 13
• Re: Packaging TechneNotes [Was: Re: Project proposal for the Debian Med group] Dec 08
• Help with possibly broken ar archive (Was: Bug#1002253: libatomic-queue: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below) Dec 21
• Re: bart: version 0.7.00 Dec 30
• [Advent bug squashing] Bug#1000224: marked as done (plastimatch: DCMTK was configured to use C++14 features, but your compiler does not or was not configured to provide them.)] Dec 19
• Re: Any help to get pydicom build welcome Dec 08
• Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with Dec 10
• [Advent bug squashing] Bug#997325: marked as done (python-sqlsoup: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.9 returned exit code 13) Dec 06
• Debian Med video conference tomorrow, Thursday 2021-12-02 18:00 UTC Dec 01
• [Advent bug squashing] Bug#995831: marked as done (find_package(charls 2.2.0 REQUIRED) not working) Dec 21
• [Advent bug squashing] Bug#982365: marked as done (ball: reduce Build-Depends) Dec 12
• [Advent bug squashing] 982383 Done: Confusing patch description Dec 20
• [Advent bug squashing] Bug#962675: marked as done (can cdbfasta be marked Multi-Arch: foreign?) Dec 03
• Re: [Advent bug squashing] Bug#988852: marked as done (transdecoder: broken symlink: /usr/lib/transdecoder/util/__pwm_tests/pasa_assemblies.fasta.gz -> ../../sample_data/pasa_example/pasa_assemblies.fasta.gz) Dec 13
• [Advent bug squashing] Thanks to Nilesh Patra: Bug#1002355: marked as done (hdmf: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" returned exit code 13)] Dec 22
• Re: [Help needed] Racon Dec 30
• [Advent bug squashing] Close bugs that were not closed in changelogs Dec 12
• [Advent bug squashing] Bug#987287: marked as done (python-bz2file: no longer useful since Python 3.3) Dec 16
• [Advent bug squashing] Pierre Gruet fixed: Bug#1002155: marked as done (libgoby-java: FTBFS: [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist)] Dec 23
• [Advent bug squashing] ftpmaster has closed "#875184: [sofa-framework] Future Qt4 removal from Buster" for us Dec 02
• [Advent bug squashing] By Lance Lin: Bug#986201: marked as done (fsm-lite: Please provide autopkgtest) Dec 21
• [Advent bug squashing] Bug#1001520: marked as done (fastp: FTBFS on riscv64, linked with -lpthread instead of -pthread) Dec 11
• Re: Any help to get pydicom build welcome Dec 10
• [Advent bug squashing] r-bioc-dropletutils: autopkgtest failures ... fixed with new version thus closing the bug Dec 07
• [Advent bug squashing] Bug#994286: marked as done (r-bioc-destiny: Orphaned upstream, marked for removal in next BioConductor release) Dec 20
• Re: [Advent bug squashing] Bug#979625: marked as done (autopkgtest: ModuleNotFoundError (ipytree) and AssertionError) Dec 09
• [Advent bug squashing] Bug#989014: marked as done (vcflib: executables in scripts/* are not packaged) Dec 24
• Re: [Advent bug squashing] r-bioc-dropletutils: autopkgtest failures ... fixed with new version thus closing the bug Dec 07
• [Advent bug squashing] #1000814 python-cooler: 10 test failures with pandas 1.3: TypeError: 'IOHandles' object is not subscriptable Dec 09
• Re: r-bioc-txdb.hsapiens.ucsc.hg19.knowngene on salsa Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with Dec 13
• Re: emboss: FTBFS with OpenJDK 17 due to com.sun.net.ssl removal Dec 13
• Re: Help with possibly broken ar archive Dec 22
• [Advent bug squashing] Bug#999525: marked as done (bmtk: FTBFS with numpy 1.21 (in experimental): dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13)] Dec 04
• Re: Acquiring Dental RVG on Linux Dec 21
• [Advent bug squashing] Bug#1001657: marked as done (ball: binary-any FTBFS) Dec 18
• [Advent bug squashing] Bug#1001614: marked as done (odil: FTBFS on armhf: 91 - MoveSCU_Move (Failed)) Dec 16
• Re: Please upload htcondor to take over maintenance of Debian HPC Team (Was: Moving htcondor to Debian Med and trying to upgrade) Dec 31
• [Advent bug squashing] Thanks again to Julien Lamy: Bug#1002203: marked as done (mrtrix3: FTBFS: ./core/types.h:326:49: error: ‘using Vector3 = class Eigen::Matrix<double, 3, 1>’ redeclared as different kind of entity)] Dec 22
• [Advent bug squashing] Bug#1002217: marked as done (gatb-core: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below)] Dec 22
• [Advent bug squashing] Bug is fixed due to upload of recent numpy Dec 04
• [Advent bug squashing] Bug#935340: marked as done (obitools: Port to Python3 needed) Dec 14
• Re: RFS: r-cran-sparql - dependency for a more typical Med package Dec 21
• Re: [Advent bug squashing] Bug#997884: marked as done (libgclib breaks cdbfasta autopkgtest: ABI breakage?) Dec 02
• [Advent bug squashing] Bug#1001349: marked as done (python-anndata: autopkgtest fail with pandas 1.3: missing openpyxl) Dec 10
• [Advent bug squashing] Closing 7 year old bug of ancient version with no response from reporter Dec 04
• [Advent bug squashing] #1000856, #1000857 Please join our advent bug squashing party Dec 01
• [Advent bug squashing] Bug#1002236: marked as done (conda-package-handling: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13)] Dec 22
• Re: emboss: FTBFS with OpenJDK 17 due to com.sun.net.ssl removal Dec 13
• Please upload htcondor to take over maintenance of Debian HPC Team (Was: Moving htcondor to Debian Med and trying to upgrade) Dec 28
• [Advent bug squashing] Bug#1002253: marked as done Dec 22
• [Advent bug squashing] Bug#919052: marked as done (python-pbcore: some docs for pbcore are not found) Dec 24
• [lucas@debian.org: Bug#1002203: mrtrix3: FTBFS: ./core/types.h:326:49: error: ‘using Vector3 = class Eigen::Matrix<double, 3, 1>’ redeclared as different kind of entity] Dec 22
• Re: jblas update to 1.2.5? Dec 10
• [Advent bug squashing] Bug#1001284: marked as done (python-pysam: libhts-dev build dependency must be bumped to >= 1.14) Dec 08
• Re: [Help needed] Racon Dec 19
• Re: python-pbcore: some docs for pbcore are not found Dec 23
• [Advent bug squashing] Bug#1001305: marked as done (orthanc ftbfs with glibc 2.34) Dec 08
• Re: Somehow some dh_auto_test of Python3 packages insist to install wheel via pip Dec 23
• Any help to get pydicom build welcome Dec 07
• Re: Moving python-bioblend to med-team? Dec 19
• [Advent bug squashing] Bug#1002230: marked as done (Ocaml build error: expression was expected of type) Dec 22
• [Advent bug squashing] Bug#929700: marked as done (pymol: Deprecation warning during startup) Dec 15
• New versions of htslib, samtools, bcftools and python-pysam in experimental - at least one package jellyfish does not work with these Dec 07

Andrius Merkys

• Re: Packaging TechneNotes [Was: Re: Project proposal for the Debian Med group] Dec 09
• Re: emboss: FTBFS with OpenJDK 17 due to com.sun.net.ssl removal Dec 13
• Re: Project proposal for the Debian Med group Dec 05
• Packaging TechneNotes [Was: Re: Project proposal for the Debian Med group] Dec 08
• Re: Somehow some dh_auto_test of Python3 packages insist to install wheel via pip Dec 23
• Re: Somehow some dh_auto_test of Python3 packages insist to install wheel via pip Dec 23

Julien Lamy

• Re: [lucas@debian.org: Bug#1002203: mrtrix3: FTBFS: ./core/types.h:326:49: error: ‘using Vector3 = class Eigen::Matrix<double, 3, 1>’ redeclared as different kind of entity] Dec 22

Karsten Hilbert

• [Karsten.Hilbert@gmx.net: Re: Acquiring Dental RVG on Linux] Dec 24
• Aw: Re: [Karsten.Hilbert@gmx.net: Re: Acquiring Dental RVG on Linux] Dec 26
• Re: Acquiring Dental RVG on Linux Dec 27
• Aw: Re: [Karsten.Hilbert@gmx.net: Re: Acquiring Dental RVG on Linux] Dec 26
• Aw: Re: [Karsten.Hilbert@gmx.net: Re: Acquiring Dental RVG on Linux] Dec 26

Lance Lin

• autopkgtest requiring large data sets (pique, hinge) Dec 21
• Re: Re: autopkgtest requiring large data sets (pique, hinge) Dec 22

Martin Uecker

• Re: [Fwd: Bug#1001916: src:bart-view: fails to migrate to testing for too long: FTBFS on armel and s390x] Dec 29
• Re: [Fwd: Bug#1001916: src:bart-view: fails to migrate to testing for too long: FTBFS on armel and s390x] Dec 29
• [Fwd: Bug#1001916: src:bart-view: fails to migrate to testing for too long: FTBFS on armel and s390x] Dec 28
• Re: [Fwd: Bug#1001916: src:bart-view: fails to migrate to testing for too long: FTBFS on armel and s390x] Dec 29

Mathieu Malaterre

• Re: Any help to get pydicom build welcome Dec 10
• Re: Any help to get pydicom build welcome Dec 08
• Re: Any help to get pydicom build welcome Dec 10

Mayuresh

• Acquiring Dental RVG on Linux Dec 21
• Re: Acquiring Dental RVG on Linux Dec 21
• Re: [Karsten.Hilbert@gmx.net: Re: Acquiring Dental RVG on Linux] Dec 26

Nilesh Patra

• bart-cuda fails its autopkgtest (Was: Re: bart: version 0.7.00) Dec 31
• Re: [Help needed] Racon Dec 30
• Re: [Advent bug squashing] Bug#989014: marked as done (vcflib: executables in scripts/* are not packaged) Dec 24
• [RFH] Bug#1000812: pyrle: import fails on Python 3.10 Dec 04
• Re: please kindly review: r-bioc-fishpond -- Fishpond: differential transcript and gene expression with Dec 09
• Re: [Advent bug squashing] Bug#979625: marked as done (autopkgtest: ModuleNotFoundError (ipytree) and AssertionError) Dec 09
• [Advent bug squashing] Bug#1001535: marked as done (busco: (autopkgtest) needs update for python3.10) Dec 12
• Re: [Help needed] Racon Dec 21
• Re: bart-cuda fails its autopkgtest (Was: Re: bart: version 0.7.00) Dec 31
• Re: bart-cuda fails its autopkgtest (Was: Re: bart: version 0.7.00) Dec 31
• [Advent bug squashing] Bug#1001932: marked as done (smart-open: FTBFS with dpkg-buildpackage -nc/--no-pre-clean) Dec 19
• Re: [Fwd: Bug#1001916: src:bart-view: fails to migrate to testing for too long: FTBFS on armel and s390x] Dec 29
• Re: bart: version 0.7.00 Dec 30
• Re: [Advent bug squashing] Bug#979625: marked as done (autopkgtest: ModuleNotFoundError (ipytree) and AssertionError) Dec 09
• Re: src:prime-phylo: no autopkgtest available yet Dec 04
• Re: autopkgtest requiring large data sets (pique, hinge) Dec 21
• Re: RFS: andi and phylonium Dec 30
• Re: [Help needed] Racon Dec 19
• [Advent bug squashing] Bug#995258: marked as done (python-pairix: please make the build reproducible) Dec 04
• Re: [RFH] Bug#1000812: pyrle: import fails on Python 3.10 Dec 04
• [Help needed] Racon Dec 19
• Re: [lucas@debian.org: Bug#1002203: mrtrix3: FTBFS: ./core/types.h:326:49: error: ‘using Vector3 = class Eigen::Matrix<double, 3, 1>’ redeclared as different kind of entity] Dec 22
• Re: [Debian-med-packaging] insighttoolkit5_5.2.1-1_amd64.changes ACCEPTED into unstable, unstable Dec 05
• Re: Re: autopkgtest requiring large data sets (pique, hinge) Dec 22
• [Advent bug squashing]: Bug#999632: marked as done (r-bioc-isoformswitchanalyzer FTBFS: ERROR: dependencies ‘DRIMSeq’, ‘tximeta’ are not available) Dec 11
• [Advent bug squashing] Bug#1001410: marked as done (python-csb: (autopkgtest) needs update for python3.10: TypeError: multiple bases have instance lay-out conflict) Dec 09
• [Advent bug squashing] Bug#1000812: marked as done (pyrle: import fails on Python 3.10) Dec 04
• Re: [Fwd: Bug#1001916: src:bart-view: fails to migrate to testing for too long: FTBFS on armel and s390x] Dec 28
• Re: [Advent bug squashing] Bug#982365: marked as done (ball: reduce Build-Depends) Dec 12
• Moving python-bioblend to med-team? Dec 19
• Re: damapper update - elf issue Dec 30
• Re: Somehow some dh_auto_test of Python3 packages insist to install wheel via pip Dec 23
• [Advent bug squashing] Bug#950914 python3-biomaj3: Depends on python-influxdb Dec 04
• Re: bart: version 0.7.00 Dec 30
• Re: python-pbcore: some docs for pbcore are not found Dec 23
• Re: [Advent bug squashing] r-bioc-dropletutils: autopkgtest failures ... fixed with new version thus closing the bug Dec 07

olivier sallou

• Re: emboss: FTBFS with OpenJDK 17 due to com.sun.net.ssl removal Dec 13
• Re: emboss: FTBFS with OpenJDK 17 due to com.sun.net.ssl removal Dec 13

Peter Rice

• Re: emboss: FTBFS with OpenJDK 17 due to com.sun.net.ssl removal Dec 13

Pierre Gruet

• Re: Scala error when trying to build latest version of pilon Dec 17
• Re: [Advent bug squashing] Pierre Gruet fixed: Bug#1002155: marked as done (libgoby-java: FTBFS: [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist)] Dec 23
• [Advent bug squashing] Bugs #989328 and #989961 : newest picard-tools in unstable Dec 02
• Re: autopkgtest requiring large data sets (pique, hinge) Dec 21
• [Advent bug squashing] Fwd: Bug#1001681: marked as done (sight: FTBFS in unstable) Dec 16
• Re: [Advent bug squashing] Pierre Gruet fixed: Bug#1002155: marked as done (libgoby-java: FTBFS: [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist)] Dec 24
• Re: Scala error when trying to build latest version of pilon Dec 18
• Re: libgoby-java: FTBFS: [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist Dec 22

rhkramer

• Re: Identity Theft Dec 27
• Re: [Karsten.Hilbert@gmx.net: Re: Acquiring Dental RVG on Linux] Dec 26

Shayan Doust

• damapper update - elf issue Dec 30

Stefano Rivera

• Re: [RFH] Bug#1000812: pyrle: import fails on Python 3.10 Dec 04

Steven Robbins

• How to do 32-bit build in AMD64 chroot -- problem with SSE instructions? Dec 11
• Re: autopkgtest requiring large data sets (pique, hinge) Dec 21
• Re: Bug#984063: itk libtiff test issues (Was: Bug#984063) Dec 11

tony mancill

• Re: [Help needed] Racon Dec 19
• jblas update to 1.2.5? Dec 09
• Re: [Help needed] Racon Dec 30
• Re: [Help needed] Racon Dec 29
• Re: [Help needed] Racon Dec 24

Tony Travis

• Re: [Bug 1956094] Re: deborphan guess-work removes too many files Dec 31
• Re: autopkgtest requiring large data sets (pique, hinge) Dec 21
• Re: autopkgtest requiring large data sets (pique, hinge) Dec 21

Uecker, Martin

• Re: bart: version 0.7.00 Dec 30
• Re: bart: version 0.7.00 Dec 30
• Re: bart-cuda fails its autopkgtest (Was: Re: bart: version 0.7.00) Dec 31

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