Bug#981876: gdpc: flaky autopkgtest on i386

2021-05-20 Thread Andreas Tille
Hi Paul, On Thu, May 20, 2021 at 11:52:55AM +0200, Paul Gevers wrote: > > The only solution I can see is to exclude it also from ppc64el > > architecture. > > The test, or the package? Either works for me. I admit I thought about the package - I need to think about just excluding the test. > Ob

Bug#981876: gdpc: flaky autopkgtest on i386

2021-05-20 Thread Andreas Tille
Hi Paul, On Thu, May 20, 2021 at 10:35:27AM +0200, Paul Gevers wrote: > Control: severity -1 serious > Control: retitle -1 gdpc: flaky autopkgtest on ppc64el > ... > > I'm seeing the same error regularly on ppc64el too. The only solution I can see is to exclude it also from ppc64el architecture.

Bug#988650: logol: broken symlink: /usr/share/logol/lib/xml-apis.jar -> ../../java/xml-apis.jar

2021-05-17 Thread Andreas Tille
Hi, I'd like to forward this to Debian Java list for comments. Kind regards Andreas. On Mon, May 17, 2021 at 01:50:01PM +0200, olivier sallou wrote: > Issue seems to be related to xml-apis.jar not being symlinked itself > > /usr/share/java# ls *xml-api* > xml-apis-1.4.01.jar xml-apis-ex

Bug#949767: arrayfire update fails in configure step

2021-04-30 Thread Andreas Tille
On Thu, Apr 29, 2021 at 04:45:20PM +0200, Gard Spreemann wrote: > The capitalization typo seems to be present also in arrayfire's > use_debian_packaged_libs.patch: I believe line 64 of > > > https://salsa.debian.org/science-team/arrayfire/-/blob/a11a6fef7dadf8ce594920626058990fe0caeb2a/debian/pa

Bug#949767: arrayfire update fails in configure step

2021-04-28 Thread Andreas Tille
Hi Aaron, On Tue, Apr 27, 2021 at 08:14:10PM -0400, Aaron M. Ucko wrote: > Please try adding a build dependency on libclfft-dev and replacing > src/backend/opencl/CMakeLists.txt's inclusion of build_clFFT with a call > to > > find_package(clFFT) > > > Thanks a lot for your initial hint Thanks

Bug#949767: arrayfire update fails in configure step

2021-04-27 Thread Andreas Tille
Hi Aaron, On Mon, Apr 26, 2021 at 08:30:39AM -0400, Aaron M. Ucko wrote: > Andreas Tille writes: > > > /usr/bin/ld: cannot find -lpthreads > > Thanks for posting a link to the full log! AFAICT, the actual errors > appear much earlier, on lines 1573-1593: > > C

Bug#949767: arrayfire update fails in configure step

2021-04-26 Thread Andreas Tille
Hi, I personally have no interest in arrayfire but I realised that the Debian packaged version depends clblas (and is the only remaining package that needs cblas and I would like to see it removed from Debian due to bug #949767) Thus I tried to upgrade arrayfire to the latest upstream version in

Bug#985891: [bastula/dicompyler] Please do not use private module matplotlib._cntr (#137)

2021-04-25 Thread Andreas Tille
On Sat, Apr 10, 2021 at 07:20:03AM +0200, Andreas Tille wrote: > ... which will safe it for the next stable release - otherwise it will be > removed from there which would be a shame. This has happened now. It would be great if you could fix this in a next dicompyler release to re-include

Bug#983533: [vinagre] black screen when launching RDP session

2021-04-16 Thread Andreas Tille
Hi, I realised that on one hand there is a patch for this package but no according upload and on the other hand there is the option that the package can be removed without affecting other packages. Any progress on this? Kind regards Andreas. -- http://fam-tille.de

Bug#986592: closed by Debian FTP Masters (reply to u...@debian.org (Aaron M. Ucko)) (Bug#986592: fixed in kaptive 0.7.3-2)

2021-04-16 Thread Andreas Tille
Hi Aaron, On Sun, Apr 11, 2021 at 08:57:05PM +0200, Paul Gevers wrote: > Control: reopen -1 > > On 10-04-2021 00:21, Debian Bug Tracking System wrote: > > which was filed against the kaptive package: > > > > #986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current > > thread >

Bug#986510: lintian-brush: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.9 returned exit code 13

2021-04-16 Thread Andreas Tille
Hi Jelmer, I've got a testing-removal warning for routine-update due this bug. I know you are usually very prompt in replying to issues thus I'm simply wondering whether you might have missed this bug report. I personally have never dived into lintian-brush but if you give some signal that you a

Bug#985891: [bastula/dicompyler] Please do not use private module matplotlib._cntr (#137)

2021-04-09 Thread Andreas Tille
Hi Aditya, On Fri, Apr 09, 2021 at 08:18:15PM -0700, Aditya Panchal wrote: > Hope you are doing well. It is possible to use the `legacycontour` package > available here: https://github.com/matplotlib/legacycontour and follow the > instructions by Alan listed here: > https://github.com/bastula/d

Bug#986592: [Help] Re: Bug#986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread

2021-04-09 Thread Andreas Tille
On Fri, Apr 09, 2021 at 08:13:52AM -0400, Aaron M. Ucko wrote: > Don't worry, I am still looking into this crash, and had primarily > intended that comment as a public note to myself -- the crash occured > within a (presumably valid) call to ncbi-blast+, and wound up taking > quite a few tries to r

Bug#986592: [Help] Re: Bug#986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread

2021-04-09 Thread Andreas Tille
Hi Aaron, On Fri, Apr 09, 2021 at 12:01:21AM -0400, Aaron M. Ucko wrote: > Never mind, this appears to be a different issue, per a backtrace > obtained with EXCEPTION_STACK_TRACE_LEVEL=Error and a great deal of > patience: > > Error: tblastn encountered an error: > terminate called after throwing

Bug#986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread

2021-04-07 Thread Andreas Tille
Control: tags -1 help Hi Aaron, do you have possibly any hint what might be wrong here? Kind regards Andreas. On Wed, Apr 07, 2021 at 09:35:42PM +0200, Paul Gevers wrote: > Source: kleborate > Version: 2.0.1-1 > Severity: serious > Tags: sid bullseye > X-Debbugs-CC: debian...@lists.debi

Bug#982692: gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2

2021-04-07 Thread Andreas Tille
Hi Lucas, On Wed, Apr 07, 2021 at 08:49:27AM +0200, Lucas Nussbaum wrote: > I confirm that I can still reproduce this failure in a testing chroot. Thank you for your information. I have tried to create a diff between the successful build log of the autobuilders[1] where all architectures have pa

Bug#985281: r-cran-dt: unhandled symlink to directory conversion: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions -> ../../../../../../share/javascript/jquery-datatables-extensions

2021-03-29 Thread Andreas Tille
fun). > > > > Can you take care of that? > > I was to file bugs to notify Debian Javascript Maintainers this > evening, but I see Andreas Tille already uploaded the fix. Both packages are uploaded and according unblock bugs to release.d.o filed. :-) Kind regards Andreas. -- http://fam-tille.de

Bug#985281: [R-pkg-team] [RFS] r-cran-dt 0.17+dfsg-3

2021-03-28 Thread Andreas Tille
og > r-cran-dt-0.17+dfsg/debian/changelog > --- r-cran-dt-0.17+dfsg/debian/changelog 2021-02-12 08:11:25.0 > +0100 > +++ r-cran-dt-0.17+dfsg/debian/changelog 2021-03-28 11:38:02.0 > +0200 > @@ -1,3 +1,20 @@ > +r-cran-dt (0.17+dfsg-3) unstable; u

Bug#985281: r-cran-dt: unhandled symlink to directory conversion: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions -> ../../../../../../share/javascript/jquery-datatables-extensions

2021-03-28 Thread Andreas Tille
Hi Étienne, thanks a lot for working on this. On Sat, Mar 27, 2021 at 10:43:10PM +0100, Étienne Mollier wrote: > Hi, > > I pushed a change on Salsa[1] to make sure that the two > following piuparts upgrade paths are working okay (thanks > Andreas Tille for the permission): &g

Bug#985281: r-cran-dt: unhandled symlink to directory conversion: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions -> ../../../../../../share/javascript/jquery-datatables-extensions

2021-03-19 Thread Andreas Tille
Control: tags -1 - moreinfo OK, I was able to reproduce the issue with > sudo piuparts --fail-on-broken-symlinks --warn-on-leftovers-after-purge > r-cran-dt_0.17+dfsg-2_amd64.changes ... 1m7.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/tmp/tmpc4jzyfzf'] 1m9.2s

Bug#985281: r-cran-dt: unhandled symlink to directory conversion: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions -> ../../../../../../share/javascript/jquery-datatables-extensions

2021-03-19 Thread Andreas Tille
Control: tags -1 moreinfo Hi Andreas. > >From the attached log (scroll to the bottom...): > > 1m34.8s ERROR: FAIL: silently overwrites files via directory symlinks: > /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/AutoFill > (r-cran-dt) != /usr/share/javascript/jquery-datata

Bug#985004: gemma: flaky armhf autopkgtest: regularly times out after 2:47 h

2021-03-11 Thread Andreas Tille
Hi, I recommend to remove armhf from the list of architectures. This kind of software is possibly not used on armhf and upstream (in CC) will probably confirm this. Kind regards Andreas. On Thu, Mar 11, 2021 at 09:08:15PM +0100, Paul Gevers wrote: > Source: gemma > Version: 0.98.3+dfsg-1 > S

Bug#984702: r-cran-effectsize: autopkgtest regression

2021-03-08 Thread Andreas Tille
Hi, it would be great if someone could have a look at this. I can not work on this issue until next week. Kind regards Andreas. On Sun, Mar 07, 2021 at 02:28:17PM +0200, Graham Inggs wrote: > Source: r-cran-effectsize > Version: 0.4.3-1 > Severity: serious > Tags: bullseye sid > X-Debb

Bug#983748: dh-r: pkg-r-autopkgtest breaks autopkgtests

2021-03-04 Thread Andreas Tille
HI Graham, On Thu, Mar 04, 2021 at 05:40:34PM +0200, Graham Inggs wrote: > > No, the tests that britney schedules for migration are run in testing, > and usually only the package to be tested comes from unstable. The > idea is to simulate what would break in testing, if this package from > unsta

Bug#983748: dh-r: pkg-r-autopkgtest breaks autopkgtests

2021-03-04 Thread Andreas Tille
Hi Graham, On Thu, Mar 04, 2021 at 03:27:49PM +0200, Graham Inggs wrote: > > >https://ci.debian.net/packages/r/r-bioc-mutationalpatterns/ > > > > I discussed several times with Paul Gevers about this view. I consider > > it not helpful to print test results of very outdated versions for > >

Bug#983748: dh-r: pkg-r-autopkgtest breaks autopkgtests

2021-03-04 Thread Andreas Tille
nd whether you know a link where I can have a simple access to the most recent test results. Kind regards Andreas. On Wed, Mar 03, 2021 at 12:44:34PM +0200, Graham Inggs wrote: > Hi Andreas > > On Wed, 3 Mar 2021 at 12:12, Andreas Tille wrote: > > My motivation fo

Bug#983748: dh-r: pkg-r-autopkgtest breaks autopkgtests

2021-03-03 Thread Andreas Tille
Hi Graham, On Wed, Mar 03, 2021 at 12:44:34PM +0200, Graham Inggs wrote: > Hi Andreas > > On Wed, 3 Mar 2021 at 12:12, Andreas Tille wrote: > > My motivation for the change was that for > > example in r-bioc-mutationalpatterns (see bug #983027) the > > autopkgtest-pkg

Bug#983748: dh-r: pkg-r-autopkgtest breaks autopkgtests

2021-03-03 Thread Andreas Tille
Hi Graham, sorry for all the mess. My motivation for the change was that for example in r-bioc-mutationalpatterns (see bug #983027) the autopkgtest-pkg-r script failed to install all needed packages to run its test. This was not the only package that was affected. I perfectly agree that this wa

Bug#983605: dicomscope: Files missing from distribution

2021-03-02 Thread Andreas Tille
Control: tags -1 moreinfo Control: severity -1 important Hi John, thanks a lot for your attempt to use Debian packaged dicomscope and your bug report as response to our work. On Sat, Feb 27, 2021 at 08:01:55AM +, John Talbut wrote: > After attempting to install this package it does not work

Bug#982567: openms build-depends on removed package

2021-03-02 Thread Andreas Tille
On Tue, Mar 02, 2021 at 09:16:46AM +0100, Filippo Rusconi wrote: > > The brute force approach works for me: > > 1. install seqan-dev from buster (for step 2) > > 2. cp -a /usr/include/seqan debian/ > > 3. in debian/control remove the seqan-dev build dependency > > 4. in debian/rules pass -DSEQAN_IN

Bug#983723: Additional issues on arm64 and mips64el (Was: Bug#983723: rna-star FTBFS on ppc64el due to -march=native)

2021-03-01 Thread Andreas Tille
Hi, besides this on arm64[1] and mips64el: ... cd opal && \ g++ -c -O3 -std=c++11 -march=native opal.cpp opal.cpp:9:10: fatal error: immintrin.h: No such file or directory 9 | #include // AVX2 and lower | ^ compilation terminated. Since this seems to be somehow r

Bug#983748: dh-r: pkg-r-autopkgtest breaks autopkgtests

2021-03-01 Thread Andreas Tille
Hi Graham, I've uploaded a change that (hopefully!) fixes the issue. On Mon, Mar 01, 2021 at 08:24:09AM +0200, Graham Inggs wrote: > The recent upload of dh-r causes autopkgtests using pkg-r-autopkgtest > to fail. See for example the output of r-bioc-affy [1] below. > Presumably caused by this c

Bug#980809: rmatrix: breaks autopkgtest of r-cran-glmmtmb on s390x

2021-02-23 Thread Andreas Tille
Hi, any update to this bug? If we do not find a timely solution what do you think about excluding s390x temporarily from the list of architectures of this package and set this bug to "important"? I would not be happy about this but the issue creates some autoremoval warnings on other packages wh

Bug#982567: openms build-depends on removed package

2021-02-20 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/OpenMS/OpenMS/issues/5151

Bug#982567: openms build-depends on removed package

2021-02-19 Thread Andreas Tille
Hi Filippo, this is extremely unfortunate. However, I guess the alternative would have been to keep some RC buggy seqan-dev which would not have helped openms as well. I tried the same as Peter and replaced the Build-Depends seqan-dev by libseqan2-dev. I can confirm the observation from Peter a

Bug#982869: datamash FTBFS on !x86 32bit: FAIL: tests/decorate-errors

2021-02-19 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 assafgor...@gmail.com Control: severity -1 important Hi Assaf, as you can read in a recent bug report in Debian[1] datamash fails for some architectures (namely the Debian release architectures armel, armhf and mipsel) its build time test in some pa

Bug#983027: r-bioc-mutationalpatterns: autopkgtest regression in testing: no package called ‘BSgenome.Hsapiens.UCSC.hg19’

2021-02-18 Thread Andreas Tille
Hi folks, I think this is a consequence of running autopkgtest-pkg-r blindly for all bioc packages since we are adding Testsuite: autopkgtest-pkg-r automatically to all packages. The "manual" test is prevented by simply renaming the debian/tests/control file to https://salsa.debian.org/

Bug#971681: r-cran-openmx regression on arm, will not migrate to testing due to failing autopkgtests

2021-02-16 Thread Andreas Tille
Hi Joshua, On Fri, Feb 12, 2021 at 01:03:23PM -0500, Joshua N Pritikin wrote: > > I submitted a new release to CRAN yesterday. It usually takes a few days > > to correct any lingering issues and get it approved. > > CRAN peeps said that v2.19.1 is accepted. I know the package info page > isn't

Bug#978257: pynwb is marked for autoremoval from testing

2021-02-14 Thread Andreas Tille
On Sun, Feb 14, 2021 at 11:38:35PM -0500, Yaroslav Halchenko wrote: > failed to arrive with working minimal patch against that elderly 1.2.1 > > FWIW built current snapshot which seems to be ok. but I am reluctant to > upload that one since it has breaking (we have no rev-depends though in > debi

Bug#982692: gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2

2021-02-14 Thread Andreas Tille
Control: severity -1 important Control: tags -1 moreinfo Control: tags -1 unreproducible On Sat, Feb 13, 2021 at 06:12:12PM +0100, Lucas Nussbaum wrote: > Source: gemma > Version: 0.98.4+dfsg-1 > Severity: serious > Justification: FTBFS on amd64 > Tags: bullseye sid ftbfs > Usertags: ftbfs-202102

Bug#978257: pynwb is marked for autoremoval from testing

2021-02-13 Thread Andreas Tille
Hi Yaroslav, could you please have a look. I'm occupied by many other things and will not care for this one. Kind regards Andreas. - Forwarded message from Debian testing autoremoval watch - Date: Sun, 14 Feb 2021 04:39:04 + From: Debian testing autoremoval watch To: py.

Bug#982483: Bug in r-base and r-cran-rcppparallel

2021-02-10 Thread Andreas Tille
Hi Kevin, On Wed, Feb 10, 2021 at 11:20:38AM -0800, Kevin Ushey wrote: > Perhaps I'm misunderstanding, but there is a Debian patch for RcppParallel > here: > > https://sources.debian.org/patches/r-cran-rcppparallel/5.0.2+dfsg-3/use_debian_packaged_libtbb.patch/ > > and all that does is force Rc

Bug#982483: Bug in r-base and r-cran-rcppparallel

2021-02-10 Thread Andreas Tille
Hi Bastian, On Wed, Feb 10, 2021 at 06:55:57PM +0100, Bastian Blank wrote: > Control: retitle -2 r-cran-rcppparallel: generates broken load path for > libtbb and fails on several architectures Thanks a lot for the bug report including explanation and patch. > - r-cran-rcppparallel trying to wor

Bug#981293: [Help] Re: metastudent-data breaks metastudent autopkgtest: 255

2021-02-10 Thread Andreas Tille
Control: tags -1 help Aaron (or whoever might want to check), do you have any idea? Kind regards Andreas. -- http://fam-tille.de

Bug#978261: swiglpk: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.9 returned exit code 13

2021-02-08 Thread Andreas Tille
On Mon, Feb 08, 2021 at 10:43:00PM +0200, Adrian Bunk wrote: > Control: tags -1 patch fixed-upstream > > ... > Attached are the relevant parts from the upstream fix. Thanks. Uploaded. > After that, it is worth trying whether this fixed python-cobra. Python-cobra builds nicely now. Unfortunate

Bug#982111: [b...@debian.org: Bug#982111: r-cran-rcdk: autopkgtest failure]

2021-02-07 Thread Andreas Tille
Control: tags -1 help Hi Pierre, do you have some idea how to fix this? Kind regards - Forwarded message from Adrian Bunk - Date: Sat, 06 Feb 2021 17:55:20 +0200 From: Adrian Bunk To: Debian Bug Tracking System Subject: Bug#982111: r-cran-rcdk: autopkgtest failure X-Debian-PR-Messag

Bug#981876: gdpc: flaky autopkgtest on i386

2021-02-06 Thread Andreas Tille
On Sat, Feb 06, 2021 at 01:23:26PM +0100, Étienne Mollier wrote: > I would be inclined to vote for a removal on that > architecture. Fully ACK! Just go for it. Thanks a lot for caring Andreas. -- http://fam-tille.de

Bug#981820: r-bioc-purecn: autopkgtest failure

2021-02-05 Thread Andreas Tille
Control: tags -1 help On Thu, Feb 04, 2021 at 12:44:46PM +0200, Adrian Bunk wrote: > ══ Failed tests > > ── Error (test_annotateTargets.R:2:1): (code run outside of `test_that()`) > ─ > Error: there is no package called ‘TxDb.H

Bug#980632: cloud-sptheme: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.9 returned exit code 13

2021-01-29 Thread Andreas Tille
Control: tags -1 help Hi, I have updated Git[1] to the latest upstream version to potentially solve this issue. Unfortunately the build stops with: ... copying cloud_sptheme/ext/static/auto_redirect.html_t -> /build/cloud-sptheme-1.10.1.post20200504175005/.pybuild/cpython3_3.9/build/cloud_spth

Bug#980635: pyglet: FTBFS: E: Build killed with signal TERM after 150 minutes of inactivity

2021-01-29 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/pyglet/pyglet/issues/346 Hi, I have opened an issue on Github about this issue. It persists for the latest upstream version 1.5.14 as well. Kind regards Andreas. -- http://fam-tille.de

Bug#974839: [Help] Test failures in q2-feature-classifier

2021-01-27 Thread Andreas Tille
Hi Étienne, On Wed, Jan 27, 2021 at 07:58:51PM +0100, Étienne Mollier wrote: > > Your guess is right; setting the PYTHONPATH to the build > directory allows most tests to run. There were a couple of > tests which then still failed to execute with the following > symptom though: > > Comman

Bug#980082: ShortRead fails test test_readPrb.R for non-Intel architectures

2021-01-26 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 Bioconductor Package Maintainer Hi, the Debian packaged ShortRead is tested in CI test on different hardware architectures. On the debci page[1] you can see the matrix for success and failure which shows that amd64 and i386 are passing the comple

Bug#978198: r-cran-rstan: FTBFS: Eigen_NumTraits.hpp:200:77: error: wrong number of template arguments (8, should be 9)

2021-01-26 Thread Andreas Tille
Control: tags -1 moreinfo, unreproducible Control: severity -1 important Hi Lucas, I've build r-cran-rstan in a clean chroot and it builds nicely as expected. May be the issue you observed has vanished? Could you please re-check whether I'm missing something? I've set severity to important mea

Bug#978032: python-cobra: autopkgtest regression in testing

2021-01-25 Thread Andreas Tille
On Mon, Jan 25, 2021 at 04:51:18PM +0200, Adrian Bunk wrote: > this bug report is from 24 Dec, so the breakage was not caused by the > libsbml 5.19 upgrade. > > python-cobra seems to have been broken by Python 3.8 -> 3.9 Yes, but it seems cobra 0.20 is broken by libsbml 5.19 which is no real los

Bug#978032: python-cobra: autopkgtest regression in testing

2021-01-25 Thread Andreas Tille
Hi Adrian, On Mon, Jan 25, 2021 at 12:07:27AM +0200, Adrian Bunk wrote: > > __ ERROR at setup of TestManipulation.test_escape_ids > > __ > > > > filename = '/usr/lib/python3/dist-packages/cobra/test/data/textbook.xml.gz' > > number = > > f_replace = {'F_GENE': , > > 'F_G

Bug#974839: [Help] Test failures in q2-feature-classifier

2021-01-22 Thread Andreas Tille
Hi, thanks to Nilesh and ftpmaster finally the needed dependencies for q2-feature-classifier are available. Unfortunately when I tried to build the package there where some test failures in autopkgtest: ... test session starts == platform

Bug#980685: seqan: FTBFS: dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j4 test ARGS\+=-j4 returned exit code 2

2021-01-22 Thread Andreas Tille
Hi Michael, On Fri, Jan 22, 2021 at 10:32:29AM +0100, Michael R. Crusoe wrote: > FYI: Seqan 1 is no longer supported upstream, and the only package in Debian > that uses it is also no longer available/maintained. if there are no rdepends of seqan1 any more feel free to file a ROM bug. Kind regar

Bug#980671: bmtk: FTBFS: Signal: Aborted (6)

2021-01-21 Thread Andreas Tille
Control: severity -1 important On Thu, Jan 21, 2021 at 10:49:20PM +0100, Étienne Mollier wrote: > Control: tag -1 moreinfo > Control: tag -1 unreproducible > ... > Anyone else is able to reproduce the problem ? The package builds nicely in my pbuilder chroot as well. So I'm setting severity from

Bug#980740: r-bioc-geoquery: flaky autopkgtests failing to download test data

2021-01-21 Thread Andreas Tille
Hi Graham, so what is you suggestion? Simply droping the test is possibly not the best solution. Marking it flaky comes to mind. What do you think? Kind regards Andreas. On Thu, Jan 21, 2021 at 10:52:49AM +0200, Graham Inggs wrote: > Source: r-bioc-geoquery > Version: 2.58.0+dfsg-1 > S

Bug#957471: ready for upload: librcsb-core-wrapper: ftbfs with GCC-10

2021-01-15 Thread Andreas Tille
Dear Juhani, On Fri, Jan 15, 2021 at 11:51:05AM +0200, Juhani Numminen wrote: > > > > make[3]: Entering directory '/<>/common' > > libtool --mode=compile -Wdate-time -D_FORTIFY_SOURCE=2 -c > > src/RcsbPlatform.C -o ./obj/RcsbPlatform.

Bug#972246: Anybody tried new version of numba (0.52.0)

2021-01-14 Thread Andreas Tille
Hi, I was just looking into a rdepends of numba which does not build currently. Did anybody yet had a look into version 0.52.0 of numba whether it solves the current issues? Kind regards Andreas. -- http://fam-tille.de

Bug#979727: racon: FTBFS: fatal error: bioparser/bioparser.hpp: No such file or directory

2021-01-13 Thread Andreas Tille
Control: tags -1 help Control: tags -1 - pending Hi, there is a remaining build time test issue which I reported upstream: https://github.com/lbcb-sci/racon/issues/50 I have no idea how to fix this since gdb does not really give a good hint about the SIGSEGV that occures. Kind regards

Bug#933928: macsyfinder: Upstream released Python3 version but "error: 'setuptools' is not supported. Please use 'pip' instead."

2021-01-13 Thread Andreas Tille
Control: tags -1 - upstream Hi, upstream has released a Python3 version of macsyfinder which I pushed to Git[1]. When trying to build I get a strange error: dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root '/build/macsyfinder-2.0~rc1/debi

Bug#969597: libzstd: Please correct version in symbol file

2021-01-11 Thread Andreas Tille
Hi Alex, On Mon, Jan 11, 2021 at 02:48:50PM +0100, Alex Mestiashvili wrote: > > No, I didn't correct this specific issue. Just added the new symbols from > the new release. However a patch or a list of "all" symbols is very welcome. I'd like to repeat my suggestion to move that package to a team

Bug#976929: parsinsert: FTBFS on ppc64el: incorrect result

2021-01-07 Thread Andreas Tille
ere you can see what architectures are running the build time test successfully (and which not): https://buildd.debian.org/status/package.php?p=parsinsert Hope this is answering your question. Kind regards Andreas. > On Thu, Jan 7, 2021 at 9:43 AM Andreas Tille wrote: > > >

Bug#976929: parsinsert: FTBFS on ppc64el: incorrect result

2021-01-07 Thread Andreas Tille
Control: tags -1 upstream Control: tags -1 help Control: forwarded -1 David Knox Hi David, there is a bug[1] report filed against the Debian packaged version of ParsInsert. The full build log for ppc64el can be found here[2]. The problem is also present for other architectures like mips64el[3]

Bug#969597: libzstd: Please correct version in symbol file

2021-01-07 Thread Andreas Tille
Hi Alex, did you possibly by chance forgot to close #969597 in your latest upload of libzstd 1.4.8+dfsg-1 ? Kind regards Andreas. -- http://fam-tille.de

Bug#932197: Isn't that bug done now?

2021-01-04 Thread Andreas Tille
Hi Yaroslav, shouldn't this bug be closed now? Kind regards Andreas. -- http://fam-tille.de

Bug#978316: libbio-db-embl-perl: FTBFS: dh_auto_test: error: make -j4 test TEST_VERBOSE=1 returned exit code 2

2021-01-04 Thread Andreas Tille
Control: severity -1 important The failing test is skiped in the latest upload which not really fixes the bug but enables building and testing the package.

Bug#978316: libbio-db-embl-perl: FTBFS: dh_auto_test: error: make -j4 test TEST_VERBOSE=1 returned exit code 2

2021-01-04 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/bioperl/Bio-DB-EMBL/issues/2

Bug#978257: pynwb: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.9 returned exit code 13

2021-01-04 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/NeurodataWithoutBorders/pynwb/issues/1329

Bug#977473: Re-activate test for gdcm

2020-12-28 Thread Andreas Tille
Control: retitle -1 Reactivate test for gdcm which was excluded due to failure Control: severity -1 important This single test prevented testing migration of this package and all its dependencies. Thus the test was deactivated for the moment to enable building the package. But the issue should b

Bug#976952: [Help] Re: lmfit-py: FTBFS on ppc64el (arch:all-only src pkg): dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13

2020-12-18 Thread Andreas Tille
On Fri, Dec 18, 2020 at 04:44:04PM +0100, John Paul Adrian Glaubitz wrote: > > > > so it does not fit with our policy: do not hide problems ;) Well, we do not need to *hide* the problem. We can exclude the test and *document* the problem - say in a README.Debian on the affected architecture. >

Bug#977308: dpkg-shlibdeps: error: cannot find library (Was: Bug#977308: shasta: hardcoded dependencies on boost 1.71)

2020-12-18 Thread Andreas Tille
On Fri, Dec 18, 2020 at 07:37:12PM +0500, Andrey Rahmatullin wrote: > On Fri, Dec 18, 2020 at 03:32:01PM +0100, Andreas Tille wrote: > > I tried no override_dh_shlibdeps in shasta debian/rules, which has lead > > to: > > > > dpkg-shlibdeps: error: cannot find library

Bug#976952: [Help] Re: lmfit-py: FTBFS on ppc64el (arch:all-only src pkg): dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13

2020-12-18 Thread Andreas Tille
On Fri, Dec 18, 2020 at 03:41:58PM +0100, John Paul Adrian Glaubitz wrote: > On 12/18/20 3:19 PM, Andreas Tille wrote: > > I wonder whether we could get some help from PowerPC team to solve this > > issue. If we can not get that test working I see only two options: > >

Bug#977308: dpkg-shlibdeps: error: cannot find library (Was: Bug#977308: shasta: hardcoded dependencies on boost 1.71)

2020-12-18 Thread Andreas Tille
> > On Fri, 18 Dec 2020 at 15:53, Andreas Tille wrote: > > > Control: tags -1 help > > > > Hi, > > > > I tried to fix the issue by making dh_shlibdeps work. In > > > > > > https://salsa.debian.org/med-team/shasta/-/commit/366edd672be428c

Bug#976952: [Help] Re: lmfit-py: FTBFS on ppc64el (arch:all-only src pkg): dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13

2020-12-18 Thread Andreas Tille
welcome. Kind regards Andreas. - Forwarded message from Matt Newville - Date: Fri, 18 Dec 2020 05:35:01 -0800 From: Matt Newville To: lmfit/lmfit-py Cc: Andreas Tille , Author Subject: Re: [lmfit/lmfit-py] Test failure on ppc64el (#692) This is a duplicate of #686. Personally

Bug#977308: shasta: hardcoded dependencies on boost 1.71

2020-12-18 Thread Andreas Tille
Control: tags -1 help Hi, I tried to fix the issue by making dh_shlibdeps work. In https://salsa.debian.org/med-team/shasta/-/commit/366edd672be428cc553b34b99bc614aa698175d6 I documented what I tried but all failed and I think the key to this bug is just making it work. Any idea? Kind re

Bug#976952: lmfit-py: FTBFS on ppc64el (arch:all-only src pkg): dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13

2020-12-18 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/lmfit/lmfit-py/issues/692

Bug#971681: r-cran-openmx regression on arm, will not migrate to testing due to failing autopkgtests

2020-12-17 Thread Andreas Tille
Hi Joshua, On Thu, Dec 17, 2020 at 08:59:39AM -0500, Joshua N Pritikin wrote: > Yeah, that sounds like a good solution. I don't anticipate a lot of > demand for OpenMx on 32bit arm. I believe we already have 64bit arm > working. We'll try to get a new release out soon. That's very helpful. Ple

Bug#936609: cblas / gsl hint needed (Was: Bug#936609: Ported ghmm to Python3 but issues with clapack)

2020-12-17 Thread Andreas Tille
On Thu, Dec 17, 2020 at 09:45:30AM +, PICCA Frederic-Emmanuel wrote: > I just built ghmm by removing --with-gsl. > > It seems that the gsl implementation of blas conflict with the one provided > in atlas. > so --enable-gsl + --enable-atlas seems wrong... Works, uploaded, thanks a lot, Andre

Bug#971681: r-cran-openmx regression on arm, will not migrate to testing due to failing autopkgtests

2020-12-17 Thread Andreas Tille
Hi Joshua, On Tue, Oct 06, 2020 at 10:59:18AM -0400, Joshua N Pritikin wrote: > On Tue, Oct 06, 2020 at 04:07:59PM +0200, Andreas Tille wrote: > > While I could include this as a patch I wonder whether you plan to do a > > new release featuring this patch in the next couple of da

Bug#962494: [ROM] python3-backports.weakref: Please remove since seems to be useless

2020-12-17 Thread Andreas Tille
Control: reasign -1 ftp.debian.org As the bug reporter stated the package is useless and should be removed from Debian Kind regards Andreas. -- http://fam-tille.de

Bug#888733: [ROM] hyantesite: Please remove hyantesite since Uploader seems not active any more and several attempts to fix FTBFS issues have failed

2020-12-17 Thread Andreas Tille
Control: retitle -1 [ROM] hyantesite: Please remove hyantesite since Uploader seems not active any more and several attempts to fix FTBFS issues have failed Control: reassign -1 ftp.debian.org Hi ftpmasters, as the bug log shows several people who failed to fix FTBFS issues in this package have

Bug#936609: cblas / gsl hint needed (Was: Bug#936609: Ported ghmm to Python3 but issues with clapack)

2020-12-17 Thread Andreas Tille
Hi again, any more hints how we finally can build ghmm? Kind regards Andreas. On Sat, Dec 05, 2020 at 04:52:14PM +0100, Andreas Tille wrote: > Hi Dirk, > > thanks for the hint but simply using gsl as is was done in this package > and now it does not build any more. Howe

Bug#977473: Would you mind updating insighttoolkit4

2020-12-15 Thread Andreas Tille
Hi again, sorry, I intended to respond to bug #977473 as well which really should be dealt with, Kind regards Andreas. On Tue, Dec 15, 2020 at 06:09:08PM +0100, Andreas Tille wrote: > Hi Steve and Gert, > > besides bug #977120 which is tagged patch insighttoolkit4 should be

Bug#972921: reopening 972921 (Was: shasta: binary-all FTBFS)

2020-12-14 Thread Andreas Tille
Control: tags -1 moreinfo Hi Adrian, On Tue, Dec 08, 2020 at 12:12:31PM +, Debian Bug Tracking System wrote: > Please contact me if you need assistance. I think I need assistance. The Auto-Building page[1] shows green for all, amd64 and arm64 and https://buildd.debian.org/status/fetch.

Bug#977308: shasta: hardcoded dependencies on boost 1.71

2020-12-14 Thread Andreas Tille
Hi Shayan, did you had some reasons to add this hardcoded dependency? Kind regards Andreas. On Sun, Dec 13, 2020 at 10:15:44PM +0200, Graham Inggs wrote: > Source: shasta > Version: 0.6.0-4 > Severity: serious > Tags: ftbfs > > Hi Maintainer > > Binary package shasta has a hardcoded depe

Bug#976906: Possible lex issue for ppc64el (Was: Bug#976906: libpll: FTBFS on ppc64el: lex_utree.l:22:10: fatal error: parse_utree.h: No such file or directory)

2020-12-11 Thread Andreas Tille
Hi Frédéric On Fri, Dec 11, 2020 at 09:59:03AM +0100, Frédéric Bonnard wrote: > Here is a patch based on this : > https://www.gnu.org/software/automake/manual/html_node/Yacc-and-Lex.html > > Tested on a power machine (where the build failed) and it seems to work. Thanks a lot Andreas. -

Bug#976906: Possible lex issue for ppc64el (Was: Bug#976906: libpll: FTBFS on ppc64el: lex_utree.l:22:10: fatal error: parse_utree.h: No such file or directory)

2020-12-10 Thread Andreas Tille
Hi Mathieu, On Thu, Dec 10, 2020 at 11:10:17AM +0100, Mathieu Malaterre wrote: > "make -j160" > > that would be my guess :) This sounds pretty likely, thought. Thanks for the hint. > remove parallel from the dh option, and try again (fixes symptoms) To cure the real issue rather than the symp

Bug#954270: [RFS] kmc: arm64 autopkgtest time out

2020-12-10 Thread Andreas Tille
On Thu, Dec 10, 2020 at 11:58:23AM +0100, Paul Gevers wrote: > > In the kmc case I'm seriously wondering whether we should restrict > > the architectures to those that are relevant in practice. It seems > > to be in line with upstream and I'm tempted to follow Étienne's > > suggestion to upgrade t

Bug#954270: [RFS] kmc: arm64 autopkgtest time out

2020-12-10 Thread Andreas Tille
Hi Paul, just a general question: The general overview page like https://ci.debian.net/packages/k/kmc/ does not seem to be updated while the specific architecture pages like https://ci.debian.net/packages/k/kmc/testing/armhf/ shows the issue. I remember I was asking in connection with

Bug#976906: Possible lex issue for ppc64el (Was: Bug#976906: libpll: FTBFS on ppc64el: lex_utree.l:22:10: fatal error: parse_utree.h: No such file or directory)

2020-12-10 Thread Andreas Tille
Control: tags -1 help Hi, I tried to investigate the situation below and my guess is that lex has somehow problems to create the missing header files. I've found the files in upstreams .gitignore file so these need to be created but this does not seem to work on ppc64el (any more - since the pac

Bug#975843: sopt: FTBFS: core.h:270: undefined reference to `fmt::v6::internal::assert_fail(char const*, int, char const*)'

2020-12-09 Thread Andreas Tille
Control: tags -1 confirmed Control: tags -1 help Hi, I can reproduce the issue but unfortunately I have no idea how to solve this. Kind regards Andreas. -- http://fam-tille.de

Bug#959138: Error in build time tests (Was: numpy breaks nipy autopkgtest: No module named 'numpy.testing.decorators')

2020-12-08 Thread Andreas Tille
Control: forwarded -1 https://github.com/nipy/nipy/issues/466

Bug#959138: Error in build time tests (Was: numpy breaks nipy autopkgtest: No module named 'numpy.testing.decorators')

2020-12-08 Thread Andreas Tille
On Tue, Dec 08, 2020 at 11:11:27PM +0500, Andrey Rahmatullin wrote: > https://github.com/nipy/nipy/issues/461 As far as I can see that's included into 0.4.3~rc1. Yaroslav, would you mind commenting on this? It would be great to have some kind of 0.4.3~rc2 to get nipy fixed. Kind regards

Bug#976585: libcereal: FTBFS: writer.h:430:67: error: comparison is always true due to limited range of data type [-Werror=type-limits]

2020-12-08 Thread Andreas Tille
Control: severity -1 important Control: tags -1 confirmed > This package only builds Arch:all binary packages. ... Thus I'm decreasing its severity. I was able to reproduce the issue on my pinebook64 and will try to forward the issue upstream. Kind regards Andreas. -- http://fam-tille.

Bug#959138: Error in build time tests (Was: numpy breaks nipy autopkgtest: No module named 'numpy.testing.decorators')

2020-12-08 Thread Andreas Tille
Control: tags -1 pending Control: tags -1 help Hi, I've updated nipy Git[1] to version 0.4.3~rc1 which solves the originally reported issue. However, there are some remaining failures in the build time test: ... == ERROR: Failu

Bug#976779: Python3.9 issue: '"yield from" can't be applied to "Condition"' (Was: Bug#976779: mypy FTBFS with only python 3.9)

2020-12-08 Thread Andreas Tille
Control: tags -1 pending Control: tags -1 help On Mon, Dec 07, 2020 at 11:24:34PM +0200, Adrian Bunk wrote: > ... > #set -e; for v in 3.9; do > set -e; for v in 3.8; do \ > PATH=$PATH:/<>/debian/mypy/usr/bin/ python$v -m pytest -n > auto \ > -o testpaths=mypy/test -o python_files=test

Bug#973148: hdmf: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.9 3.8" returned exit code 13

2020-12-08 Thread Andreas Tille
Control: tags -1 help Control: tags -1 upstream Control: forwarded https://github.com/hdmf-dev/hdmf/issues/494

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