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

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

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

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

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

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 >

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:

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:

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

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

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.

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

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

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 ->

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: > >

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

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

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

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': , > >

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

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

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 >

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

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

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

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

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

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
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/366edd672be428cc553b34b99bc614aa698175d6

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

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.

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,

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

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

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

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

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

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

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. --

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:

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

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

Bug#938795: vmtk does not build any more

2020-12-08 Thread Andreas Tille
Hi, On Tue, Dec 08, 2020 at 04:21:01AM +0800, Drew Parsons wrote: > First thing to try would be building against vtk9, which Anton recently > released for us. Thanks for the hint but switching to vtk9 leads to cmake errors: -- The imported target "vtkgdcmsharpglue" references the file

Bug#938795: vmtk does not build any more

2020-12-07 Thread Andreas Tille
Hi, vmtk is using Python3 in Git[1], but there are build issues with vtk7: ... cd /build/vmtk-1.4.0+dfsg/obj-x86_64-linux-gnu/vtkVmtk/ComputationalGeometry && /usr/bin/c++ -DITK_IO_FACTORY_REGISTER_MANAGER -DvtkvmtkComputationalGeometry_EXPORTS -I/build/vmtk-1.4.0+

Bug#972921: Shasta now fails again for other reasons

2020-12-07 Thread Andreas Tille
Control: tags -1 pending Hi Nilesh, I've finally fixed shasta in 48e257cd5d5ee64fc095214830e284b016cd83fa (admittedly I don't like that manual solution bit at least it works for the default Python3 version now) and that build worked for me until I pulled your change

Bug#976567: libhmsbeagle: FTBFS: GPUInterface.h:221:27: error: there are no arguments to ‘malloc’ that depend on a template parameter, so a declaration of ‘malloc’ must be available [-fpermissive]

2020-12-05 Thread Andreas Tille
Control: tags -1 help Hi, I need to admit that I have no idea why this error occures on arm64. Any hint would be welcome Andreas. On Sat, Dec 05, 2020 at 01:21:43PM +0100, Lucas Nussbaum wrote: > Source: libhmsbeagle > Version: 3.1.2+dfsg-8 > Severity: serious > Justification: FTBFS on

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

2020-12-05 Thread Andreas Tille
Control: tags -1 help Hi, I wonder why static_cast(c) < 256 triggers a "error: comparison is always true due to limited range of data type [-Werror=type-limits]" only on arm64 but not on amd64. Any hint how to fix this bug would be welcome. Kind regards Andreas. On Sat, Dec 05,

Bug#976572: bio-eagle: FTBFS: MemoryUtils.hpp:34:10: fatal error: xmmintrin.h: No such file or directory

2020-12-05 Thread Andreas Tille
Control: tags -1 help Hi Lucas, On Sat, Dec 05, 2020 at 01:15:52PM +0100, Lucas Nussbaum wrote: > During a rebuild of all packages in sid, your package failed to build > on arm64 (I don't know if it also fails on amd64). I admit I have currently no chance to test on arm64 but the package builds

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

2020-12-05 Thread Andreas Tille
12:09, Andreas Tille wrote: > | this issue is something for our advent calendar. Anybody with cblas > | knowledge? > > I am the GNU GSL maintainer, and I at one point also worked a lot with the > Atlas and other LAPACK/BLAS packages. I think Mo may be wrong here: I did the > same app

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

2020-12-05 Thread Andreas Tille
Hi folks, this issue is something for our advent calendar. Anybody with cblas knowledge? Kind regards Andreas. On Mon, Jan 27, 2020 at 10:55:25AM +0100, Andreas Tille wrote: > Hi again, > > with my last mail I wanted to express: H, to stupid to turn > this hint in

Bug#974168: Bug#974168: Bug #974168: bioperl-run: autopkgtest issue fixed, now different build time error

2020-12-04 Thread Andreas Tille
Hi Étienne, On Fri, Dec 04, 2020 at 09:56:20PM +0100, Étienne Mollier wrote: > I think I'm on a trail with bioperl-run, and could fix a couple > of issues already. I'm however unsure it might make it for the > 4th of the advent calendar: fixing the initial issue pulls in > gradually more tests,

Bug#974075: ugene: FTBFS with Qt 5.15

2020-12-04 Thread Andreas Tille
Hi Tony, On Fri, Dec 04, 2020 at 12:52:07PM -0800, tony mancill wrote: > Hi Debian-Med, hi Steffen: > > I grabbed this bug to fix the QPainterPath include and noticed that > packaging of 36.0 is underway on the master branch. I have updated the > debian/patches to apply against this new

Bug#974168: Bug #974168: bioperl-run: autopkgtest issue fixed, now different build time error

2020-12-03 Thread Andreas Tille
Control: tags -1 pending Control: tags -1 help Hi, while the original issue of this bug report is fixed by adding the missing libfile-sort-perl dependency it has a new build time error in t/BEDTools.t. Any help to fix this is welcome Andreas. -- http://fam-tille.de

Bug#973789: src:parsinsert: fails to migrate to testing for too long: FTBFS on armel, armhf, mips64el and ppc64el

2020-12-03 Thread Andreas Tille
Control: reopen -1 Control: tags -1 help Control: tags -1 upstream Control: forwarded -1 David Knox Hi David, as you can see in the Debian bug the Build logs for mips64el[1] and others[2] the build time tests for parsinsert are failing. From my naive perspective its basically a matter of

Bug#974839: Blocked by two ITP bugs

2020-12-03 Thread Andreas Tille
Control: block -1 by 962717 Control: block -1 by 932050

Bug#974733: q2-quality-filter: unsatisfiable build-dependencies

2020-12-03 Thread Andreas Tille
Control: tags -1 help Hi, I upgraded q2-quality-filter to the latest upstream version in Git. The build time tests were disabled as for other QIIME modules that need registering in QIIME which is not possible at build time. However, also the autopkgtest fails with: autopkgtest [13:08:01]:

Bug#954601: q2cli: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 -s custom "--test-args=cd {build_dir}; HOME=/<> QIIMETEST= nosetests3" returned exit co

2020-12-02 Thread Andreas Tille
On Wed, Dec 02, 2020 at 01:50:55PM +0100, Étienne Mollier wrote: > Synchronizing work on q2-* modules update, I think I'm on a good > trail for q2cli. Great! Andreas. -- http://fam-tille.de

Bug#976254: Something for our Advent calendar (Was: Bug#976254: rnahybrid: Does not build from source "multiple definition of")

2020-12-02 Thread Andreas Tille
Control: tags -1 help Hi, no idea why this was not catched in the usual gcc-10 rebuilds. Any volunteer? Kind regards Andreas. On Wed, Dec 02, 2020 at 12:08:32AM +0100, Andreas Tille wrote: > Source: rnahybrid > Severity: serious > Tags: ftbfs > Justification: FTBFS > >

Bug#976254: rnahybrid: Does not build from source "multiple definition of"

2020-12-02 Thread Andreas Tille
Source: rnahybrid Severity: serious Tags: ftbfs Justification: FTBFS Hi, I tried to rebuild the package but the build ends in: ... gcc -g -O2 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2

Bug#973148: [help] Error in hdmf possibly caused by hdf5 issue?

2020-12-01 Thread Andreas Tille
Control: tags -1 help Hi, the build log says: ... > == > FAIL: test_link_h5py_dataset_h5dataio_input > (tests.unit.test_io_hdf5_h5tools.H5IOTest) > -- >

Bug#963927: [ROM] Please remove predictprotein

2020-12-01 Thread Andreas Tille
Control: retitle -1 [ROM] Please remove predictprotein Control: reassign -1 ftp.debian.org Hi ftpmaster, the code is not maintained upstream any more and relies on a feature of Perl that was deprecated several versions ago. The Debian Med team consulted Debian Perl team for help but it has

Bug#957206: dh_testroot: error: Package needs targeted root but builder has not provided a gain-root command via ${DEB_GAIN_ROOT_CMD}

2020-12-01 Thread Andreas Tille
Control: tags -1 pending Hi, upstream of fis-gtm package[1] confirmed that the build needs some root permissions. Thus I've set Rules-Requires-Root: yes When trying to build with pbuilder I get: dh_testroot dh_testroot: error: Package needs targeted root but builder has not provided a

Bug#957206: EXTERNAL: Re: Bug#957206: New upstream version available (Was: Bug#957206: fis-gtm: ftbfs with GCC-10)

2020-11-30 Thread Andreas Tille
t; > Thanks, > Amul > > -Original Message- > From: Andreas Tille > Sent: Monday, November 30, 2020 3:40 PM > To: 957206-mainto...@bugs.debian.org; Shah, Amul > Subject: EXTERNAL: Re: Bug#957206: New upstream version available (Was: > Bug#957206: fis-gtm: f

Bug#957206: New upstream version available (Was: Bug#957206: fis-gtm: ftbfs with GCC-10)

2020-11-30 Thread Andreas Tille
Hi again Amul, I updated Git to the next upstream version. It also does not build successfully. We *really* should fix this *right* now. Otherwise fis-gtm will be not released with the next stable release. Kind regards Andreas. On Thu, Oct 01, 2020 at 03:52:01PM +0200, Andreas Tille

Bug#936503: Falcon builds but autopkgtest fails (and some build time test failures are ignored

2020-11-30 Thread Andreas Tille
Control: tags -1 pending Hi, since some time falcon[1] in Git builds with some cheating - some test errors are simply ignored. Also the autopktest is failing. It would be great if someone would spent time on these two RC bugs in an advent calendar attempt. Kind regards Andreas. [1]

Bug#905206: marked as pending in profnet

2020-11-26 Thread Andreas Tille
Control: tag -1 pending Hello, Bug #905206 in profnet reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at:

Bug#922584: [Help] Re: FTBFS against opencv 4.0.1 (exp)

2020-11-23 Thread Andreas Tille
Control: tags -1 help Hi, the configure step checks for the existence of opencv and only if available builds the executable limereg. I found a (hackish) solution in Git[1] to convince configure that opencv is available. However, the code tries to include cv.h which is not available any more.

Bug#963392: [Help] r-cran-bayestestr: autopkgtest regression

2020-11-19 Thread Andreas Tille
Control: tags 972074 pending Control: block 972074 by 963392 On Thu, Nov 19, 2020 at 07:53:06AM -0600, Dirk Eddelbuettel wrote: > | > | I do not have the slightest idea what this might mean. > > ABI/API slippage in the stack. An interface changed but a package didn't > recompile. It seems it

Bug#972074: [Help] r-cran-bayestestr: autopkgtest regression

2020-11-19 Thread Andreas Tille
Control: tags -1 help Hi, since version 0.7.0 (uploaded by Dylan Aïssi in CC) the autopkgtest of r-cran-bayestestr fails with the error mentioned in the bug log. It has slightly changed with the version I pushed to Git. It is now: > library(bayestestR) > > if

Bug#974637: Bug#974637: biosig4c++_1.9.5-1+b2_mipsel-buildd.changes REJECTED

2020-11-19 Thread Andreas Tille
Control: retitle -1 [ROM] Please remove src:biosig4c++ from unstable since it was replaced by biosig Control: reassign -1 ftp.debian.org On Fri, Nov 13, 2020 at 10:21:54AM +0200, Graham Inggs wrote: > On Fri, 13 Nov 2020 at 09:45, Aurelien Jarno wrote: > > Version check failed: > > Your upload

Bug#964688: cherry-pick patch from upstream - fixes #964688

2020-11-16 Thread Andreas Tille
n 11/14/20 11:08 PM, Adrian Bunk wrote: > > On Sat, Nov 14, 2020 at 09:28:53PM +0100, Andreas Tille wrote: > > > Control: tags -1 pending > > > Control: tags 922571 pending > > > > > > Hi, > > > > > > I have moved sigviewer to Debian Med tea

Bug#964688: cherry-pick patch from upstream - fixes #964688

2020-11-14 Thread Andreas Tille
Control: tags -1 pending Control: tags 922571 pending Hi, I have moved sigviewer to Debian Med team[1], fixed the other bug and tried to build the new upstream version 0.6.4 but failed: ... g++ -c -pipe -g -O2 -fdebug-prefix-map=/build/sigviewer-0.6.4=. -fstack-protector-strong -Wformat

Bug#974570: ismrmrd: missing libpugi-dev runtime dependency

2020-11-12 Thread Andreas Tille
Hi Gianfranco, thanks a lot for the fix (I had some race condition with another way to fix it but your's is fine as well) and specifically to also fix #974570. I'll upload once my local build has finished. Kind regards Andreas. On Thu, Nov 12, 2020 at 01:23:51PM +0100, Gianfranco

<    2   3   4   5   6   7   8   9   10   11   >