Bug#1014797: FTBFS: test failures with new libgd3

2022-09-29 Thread Andreas Tille
Control: tags -1 help Hi Aaron and Olivier, do you have some idea how to fix this bug? Kind regards Andreas. -- http://fam-tille.de

Bug#1012893: [Help] anfo: ftbfs with GCC-12

2022-09-29 Thread Andreas Tille
Hi Étienne, Am Thu, Sep 29, 2022 at 03:38:23PM +0200 schrieb Étienne Mollier: > I believe in the case of anfo, that warnings about auto_ptr / > unique_ptr are red herrings. If I search for "error:"s, then I > get some errors about no match for operator<: > > In file included from /usr/include/c+

Bug#1012893: [Help] anfo: ftbfs with GCC-12

2022-09-29 Thread Andreas Tille
Hi Aaron, Am Wed, Sep 28, 2022 at 04:06:23PM -0400 schrieb Aaron M. Ucko: > > Per GCC's hint, please try formally substituting unique_ptr for > auto_ptr. I haven't tested that approach for this package, but it's > typically a safe drop-in replacement, and generally yields compilation > errors in

Bug#1017752: Do you see any chance to fix the "virtual memory exhausted" for nheko on mipsel VM

2022-09-28 Thread Andreas Tille
Hi mips porters, in bug #1017752 a FTBFS on mipsel: virtual memory exhausted: Cannot allocate memory is reported. This remains for the new upstream version I've just uploaded to experimental[1]. Do you see any chance to fix the memory constraint for the autobuilder VM? If not I'll remove m

Bug#1012893: [Help] anfo: ftbfs with GCC-12

2022-09-28 Thread Andreas Tille
Control: tags -1 help Could anybody have a look at this gcc failure? Thanks in advance Andreas. -- http://fam-tille.de

Bug#1017752: nheko: FTBFS on mipsel: virtual memory exhausted: Cannot allocate memory

2022-09-28 Thread Andreas Tille
Control: tags -1 moreinfo Hi, I wonder whether this should really tagged RC. If the virtual memory on some mipsel machine is exhaustet shouldn't be someone investigate into that specific machine? Kind regards Andreas. -- http://fam-tille.de

Bug#1017195: Possibly false positive: schedule: FTBFS: AssertionError: ScheduleValueError not raised by until

2022-09-28 Thread Andreas Tille
Control: tags -1 moreinfo Control: severity -1 normal Hi, I've checked the build in my local pbuilder environment which was running successfully and also enabled Salsa CI to have another public instance for the build. This builds successfully as well.[1] So I guess this bug was either a false p

Bug#1019695: r-cran-qpdf: FTBFS with qpdf 11.0.0

2022-09-27 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/ropensci/qpdf/issues/20

Bug#1020035: seqan3: FTBFS: char_traits.h:431:56: error: ‘void* __builtin_memcpy(void*, const void*, long unsigned int) ’ accessing 9223372036854775810 or more bytes at offsets 4 and 3 may overlap up

2022-09-27 Thread Andreas Tille
Control: tags -1 upstream, help Control: forwarded -1 https://github.com/seqan/seqan3/issues/3054

Bug#1020049: [notificati...@github.com: Re: [hhoeflin/hdf5r] datatype_export.c:1903:19: error: storage size of ‘myenum’ isn’t known (Issue #192)]

2022-09-22 Thread Andreas Tille
Control: tags -1 help - Weitergeleitete Nachricht von Holger Hoefling - Date: Wed, 21 Sep 2022 23:17:30 -0700 From: Holger Hoefling To: hhoeflin/hdf5r Cc: Andreas Tille , Author Subject: Re: [hhoeflin/hdf5r] datatype_export.c:1903:19: error: storage size of ‘myenum’ isn’t known

Bug#1020049: r-cran-hdf5r: FTBFS: datatype_export.c:1903:19: error: storage size of ‘myenum’ isn’t known

2022-09-21 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/hhoeflin/hdf5r/issues/192 Am Sun, Sep 18, 2022 at 08:21:55AM +0200 schrieb Lucas Nussbaum: > > gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/hdf5/serial > > -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 > > -ffile-prefix-map

Bug#1003165: Set severity to important

2022-08-22 Thread Andreas Tille
Control: severity -1 important Hi, as discussed on Debian Science the affected test suite errors are ignored for the moment so the package does not FTBFS any more and thus the bug is not serious any more. Since issues are remaining the bugs are not closed yet. Kind regards Andreas. -- ht

Bug#1017402: Reduce severity from serious to important

2022-08-15 Thread Andreas Tille
Control: severity -1 important Hi, as discussed on Debian Science the affected test suite errors are ignored for the moment so the package does not FTBFS any more and thus the bug is not serious any more. Since issues are remaining the bugs are not closed yet. Kind regards Andreas. -- htt

Bug#1003165: scikit-learn testing migration

2022-08-13 Thread Andreas Tille
Hi again, Am Thu, Aug 04, 2022 at 01:25:42PM +0200 schrieb Andreas Tille: > Am Fri, Jul 29, 2022 at 06:09:26AM +0200 schrieb Andreas Tille: > Before we fall into another "do nothing" period: I will upload > scikit-learn restricted to those architectures only which have all

Bug#1012219: Please adjust StanHeaders to new version of (one)tbb

2022-08-12 Thread Andreas Tille
Ping? Is there any place where I can open an issue about this? I've found https://github.com/cran/StanHeaders but this is readonly and has no option to report issues. Kind regards Andreas. Am Mon, Jul 18, 2022 at 10:45:14AM +0200 schrieb Andreas Tille: > Control: tags -1

Bug#1015978: ROM: Please remove falcon (Was: Bug#1015978: Should falcon be removed?)

2022-08-05 Thread Andreas Tille
Control: reassign -1 ftpmaster.debian.org See below, please remove falcon since it is unmaintainable. Thanks for working as ftpmaster Andreas. Am Fri, Aug 05, 2022 at 09:57:26AM +0200 schrieb Moritz Mühlenhoff: > Am Fri, Aug 05, 2022 at 09:36:00AM +0200 schrieb Andreas Tille: > >

Bug#1015978: Should falcon be removed?

2022-08-05 Thread Andreas Tille
Hi Moritz, Am Fri, Jul 29, 2022 at 04:42:00PM +0200 schrieb Moritz Mühlenhoff: > Am Sun, Jul 24, 2022 at 10:06:03PM +0200 schrieb Andreas Tille: > > Unfortunately the package does not build[1] which is probably a gcc > > issue. If someone would volunteer to fix this issue we m

Bug#1016346: [Help] LaTeX error due to encoding issues (Was: Bug#1016346: pycorrfit: FTBFS: make[1]: *** [debian/rules:46: override_dh_auto_build] Error 1)

2022-08-04 Thread Andreas Tille
Control: tags -1 help Hi, Am Fri, Jul 29, 2022 at 08:41:23PM +0200 schrieb Lucas Nussbaum: > > (/usr/share/texlive/texmf-dist/tex/latex/ucs/data/uni-0.def) > > No file PyCorrFit_doc.toc. > > ! Argument of ? has an extra }. > > > > \par > > l.144 \newpage I was able to reproduc

Bug#1003165: scikit-learn testing migration

2022-08-04 Thread Andreas Tille
Hi again, Am Fri, Jul 29, 2022 at 06:09:26AM +0200 schrieb Andreas Tille: > I just like to repeat my point: If the package is to slow on release > architectures, that we will not manage to fix it, it is in the interest > of our users to not support the problematic architectures in

Bug#1015742: libspdlog1: ABI breakage without SONAME bump

2022-08-01 Thread Andreas Tille
Hi, Am Tue, Aug 02, 2022 at 01:38:58AM +0800 schrieb Shengjing Zhu: > To fix the ABI breakage in spdlog/1.10, I request the fmt/9 transition > afterwards. > Since with fmt/9 translation, spdlog ABI will bump to > libspdlog1-fmt9(from libspdlog1-fmt8) anyway. A, OK, I missed that point. Feel

Bug#1015742: Reverted droping symbols

2022-07-31 Thread Andreas Tille
Hi Boyuan Yang, I admit symbols files are a maintenance burden for C++ libraries. However, it helps to spot ABI changes for new upstream versions. To reduce the maintenance burden while keeping that ABI change detection functionality I frequently maintain amd64 symbols only. Motivated by this bu

Bug#1008220: flexbar 3.5.0-4 FTBFS against libtbb-dev 2021.5.0-7

2022-07-29 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/seqan/flexbar/issues/38

Bug#1003165: scikit-learn testing migration

2022-07-28 Thread Andreas Tille
Am Thu, Jul 28, 2022 at 08:15:45PM -0700 schrieb M. Zhou: > I have a long-term power 9 VM (not QEMU) as testbed. > I'm trying to investigate the issues for release architectures, > but this package is too slow to build with QEMU (multiple hours). > (abel.debian.org is also extremely slow for scikit

Bug#1015062: node-shiny-server: FTBFS: ModuleNotFoundError: No module named 'six'

2022-07-28 Thread Andreas Tille
Control: tags -1 moreinfo Control: tags -1 unreproducible Control: severity -1 important Hi Lucas, I can't reproduce the issue at my side. It somehow smells like an issue of some Build-Depends which might have been solved meanwhile. Kind regards Andreas. Am Sat, Jul 16, 2022 at 03:31:35PM

Bug#1015861: bamtools: FTBFS with upcoming doxygen 1.9.4

2022-07-28 Thread Andreas Tille
Control: tags -1 pending This is fixed in Git. Unfortunately the new version is in NEW since 4 months and I do not want to fiddle around with this package. A fix will be uploaded with source-only upload once the package is finally accepted. Kind regards Andreas. -- http://fam-tille.de

Bug#1003165: scikit-learn testing migration

2022-07-28 Thread Andreas Tille
Hi Graham, Am Thu, Jul 28, 2022 at 09:15:06AM +0200 schrieb Graham Inggs: > Hi > > On Wed, 27 Jul 2022 at 17:57, M. Zhou wrote: > > The previous segfault on armel becomes Bus Error on armel and armhf. > > I can build it on Power9, but it seems that the test fails on power8 (our > > buildd). >

Bug#1013940: New version of nfft breaks its autopkgtest (Was: nfft breaks pynfft autopkgtest on i386: Segmentation fault

2022-07-27 Thread Andreas Tille
Hi, I was tempted to upload the patch suggested by Bernhard which I applied to the commit of Ileana with the new upstream version. Unfortunately the new upstream version fails the autopkgtest[1] (which was the same when I tried version 3.5.2 which prevented me from uploading). Does anybody have

Bug#1008369: scikit-learn testing migration

2022-07-27 Thread Andreas Tille
09:23:28PM +0200 schrieb Andreas Tille: > Hi Nilesh, > > Am Wed, Jul 20, 2022 at 06:21:19PM +0530 schrieb Nilesh Patra: > > On 7/20/22 4:50 PM, Andreas Tille wrote: > > > Before we stop progress in Debian for many other architectures since we > > > cant't sol

Bug#1012143: Blocked by bug of r-cran-rstan

2022-07-25 Thread Andreas Tille
Control: block -1 by 1012219 The error Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib/R/site-library/rstan/libs/rstan.so': /usr/lib/R/site-library/rstan/libs/rstan.so: undefined symbol: _ZN3tbb8internal26task_scheduler_observer_v37observeEb Calls:

Bug#994212: ROM: r-cran-gprofiler: Obsolete package, replaced with r-cran-gprofiler2

2022-07-25 Thread Andreas Tille
Control: reassign -1 ftpmaster.debian.org Control: retitle -1 ROM: r-cran-gprofiler: Obsolete package, replaced with r-cran-gprofiler2 Hi, as per bug title this package should be removed from Debian since it is obsolete and unmaintained. Kind regards Andreas. -- http://fam-tille.de

Bug#1015978: Should falcon be removed?

2022-07-24 Thread Andreas Tille
Hi Moritz, thanks for bringing this up. I agree that falcon your point is perfectly valid. On the other hand we have a new upstream version in Git which now depends from Python3 and is a promising candidate to fix the Python3 bug. Unfortunately the package does not build[1] which is probably a

Bug#1004793: vtk7: FTBFS with ffmpeg 5.0

2022-07-22 Thread Andreas Tille
Hi Peter, Am Fri, Jul 22, 2022 at 04:36:13AM +0100 schrieb Peter Green: > vtk7 is one of the (possiblly the) last blockers for the ffmpeg transition > that is in testing and is not marked for autoremoval. > The last 7.x upstream release was over 5 years ago. The last vtk7 upload > by someone liste

Bug#1007984: netpbm-free_10.98.00-1_amd64.changes REJECTED

2022-07-21 Thread Andreas Tille
Hi Thorsten, Am Sat, May 28, 2022 at 07:00:08PM + schrieb Thorsten Alteholz: > > please also mention Todd W. Fuqua and Michael John Muuss in your > debian/copyright. Added these two to d/copyright in a fresh upload. > I stop processing when something is wrong/missing. Please make sure th

Bug#1003165: scikit-learn testing migration

2022-07-20 Thread Andreas Tille
Hi Nilesh, Am Wed, Jul 20, 2022 at 06:21:19PM +0530 schrieb Nilesh Patra: > On 7/20/22 4:50 PM, Andreas Tille wrote: > > Before we stop progress in Debian for many other architectures since we > > cant't solve this on our own or otherwise are burning patience of > >

Bug#1003165: scikit-learn testing migration

2022-07-20 Thread Andreas Tille
Hi, Am Sat, Jul 16, 2022 at 05:58:33PM +0200 schrieb julien.pu...@gmail.com: > > [1]: > > https://buildd.debian.org/status/fetch.php?pkg=scikit-learn&arch=armel&ver=1.1.1-1&stamp=1653343638&raw=0 > > I would open a bug report to upstream pointing to that log, and if the > log isn't enough to pinp

Bug#1012219: Please adjust StanHeaders to new version of (one)tbb

2022-07-18 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 Ben Goodrich Hi Ben, Debian is migrating from old tbb to onetbb (currently version 2021.5.0). When trying to build rstan version 2.21.5 which includes StanHeaders we get the error you can find here in our CI: https://salsa.debian.org/r-pkg-tea

Bug#1011218: Blocked by bug of r-cran-rstan

2022-07-17 Thread Andreas Tille
Control: block -1 by 1012219 The error unable to load shared object '/usr/lib/R/site-library/rstan/libs/rstan.so': /usr/lib/R/site-library/rstan/libs/rstan.so: undefined symbol: _ZN3tbb8internal26task_scheduler_observer_v37observeEb feeds the assumption that once r-cran-rstan is successfull

Bug#1014797: FTBFS: test failures with new libgd3

2022-07-12 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/GMOD/GBrowse/issues/64

Bug#1014104: mothur: autopkgtest regression: did not complete cluster.

2022-06-30 Thread Andreas Tille
Hi Tomasz, could you please have a look? Kind regards Andreas. Am Thu, Jun 30, 2022 at 11:42:46AM +0200 schrieb Paul Gevers: > Source: mothur > Version: 1.48.0-1 > Severity: serious > User: debian...@lists.debian.org > Usertags: regression > > Dear maintainer(s), > > With a recent upload

Bug#1014100: We should do an update of all qiime2 modules as soon as possible (Was: Bug#1014100: qiime: autopkgtest needs update for new version of python-decorator)

2022-06-30 Thread Andreas Tille
Hi, I'd like to point out to this serious bug. Steffen, would you mind koordinating (not doing alone) an upgrade of the qiime infrastructure to make sure everything will go smoothly? Kind regards Andreas. Am Thu, Jun 30, 2022 at 11:30:21AM +0200 schrieb Paul Gevers: > Source: qiime > Vers

Bug#1013451: openssh-client: double free or corruption

2022-06-24 Thread Andreas Tille
Hi, I confirm the very same issue here. I've found another "solution" (if exchanging your ssh-keys is an option for you): Just create new keys with ssh-keygen and push them with ssh-copy-id to your target hosts. This works for me (but is for sure a nuisance when you have lots of hosts to feed th

Bug#1013364: dicomnifti: autopkgtest failure: number of repetitions is less than two

2022-06-23 Thread Andreas Tille
Hi Valerio, Am Wed, Jun 22, 2022 at 05:33:20PM -0400 schrieb Valerio Luccio: > Puzzling, this package has not changed since November 2017. This might meen that the package does not cope well with recent toolset (which is not unusual for packages that do not change for 5 years or longer.) That's

Bug#1013258: autoreconf: error: /usr/bin/autoconf failed with exit status: 1

2022-06-20 Thread Andreas Tille
Am Mon, Jun 20, 2022 at 10:38:12AM +0200 schrieb Mathieu Malaterre: > Source: openslide > Severity: important > Tags: ftbfs > > Dear Maintainer, > > It seems openslide does not build anymore. See for instance: > > * https://salsa.debian.org/med-team/openslide/-/jobs/2899560 I wonder why you ass

Bug#1011446: q2-demux, q2-taxa: replace node-uglifyjs-webpack-plugin with node-terser-webpack-plugin

2022-05-24 Thread Andreas Tille
Am Tue, May 24, 2022 at 12:55:50PM +0530 schrieb Pirate Praveen: > On Tue, 24 May 2022 00:04:21 +0530 Pirate Praveen > wrote: > > No worries. You can refer to > > https://salsa.debian.org/js-team/node-clipboard/-/blob/master/debian/patches/switch-to-terser-webpack-plugin.patch > > I have also sen

Bug#1011446: q2-demux, q2-taxa: replace node-uglifyjs-webpack-plugin with node-terser-webpack-plugin

2022-05-23 Thread Andreas Tille
Dear Pirate, Am Mon, May 23, 2022 at 11:25:54PM +0530 schrieb Pirate Praveen: > >Hmmm, I tried to push a fix quickly but the new package does not seem to > >be a plugin replacment as you can see in Salsa CI: > > > > https://salsa.debian.org/med-team/q2-demux/-/jobs/2798791 > > > >Any idea how thi

Bug#1011446: q2-demux, q2-taxa: replace node-uglifyjs-webpack-plugin with node-terser-webpack-plugin

2022-05-23 Thread Andreas Tille
Hi, Am Mon, May 23, 2022 at 10:12:23AM +0530 schrieb Pirate Praveen: > Package: q2-demux,q2-taxa > severity: serious > Control: block 977311 by -1 > > node-uglifyjs-webpack-plugin is dead upstream and we want to remove it from > debian, please switch to using node-terser-webpack-plugin. Hmmm, I

Bug#1011412: r-bioc-scater: autopkgtest regression in testing

2022-05-22 Thread Andreas Tille
Control: tags -1 pending Control: block -1 by 1011064 The issue is fixed in Git but the new version can not be uploaded since it needs r-cran-rcppml from new. Kind regards Andreas.

Bug#1009467: [Bioconductor/Biostrings] S.h seems to be deprecated (Issue #66)

2022-05-16 Thread Andreas Tille
Hi again Hervé, > @tillea And most importantly, it seems that Debian is building the wrong > version of Bioconductor. The `S.h` file was removed from R 4.2 and they are > reporting a bug for **Biostrings** 2.62.0, which belongs to Bioconductor 3.14 > (the current release). BioC 3.14 should only

Bug#1010536: libdcmimage.so.16: cannot open shared object file: No such file or directory

2022-05-08 Thread Andreas Tille
Hi Johannes, Am Sun, May 08, 2022 at 11:34:15AM +0200 schrieb Johannes Schauer Marin Rodrigues: > > I think I'll go that route then (but probably tomorrow). BTW, I had (again) > > a look into ants and think the new upstream version can help to fix the > > open RC bugs. I once worked on this but

Bug#1010536: libdcmimage.so.16: cannot open shared object file: No such file or directory

2022-05-04 Thread Andreas Tille
Hi Johannes, Am Wed, May 04, 2022 at 04:12:49PM +0200 schrieb Johannes Schauer Marin Rodrigues: > Quoting Andreas Tille (2022-05-04 16:07:27) > > I'm an3as in IRC but I do not lurk in IRC usually. > > Ah, nice word play in the nick. :) I invented it at DebConf Argentina

Bug#872741: ants: frequent test failures on amd64

2022-05-04 Thread Andreas Tille
Control: block -1 by 909833 -- http://fam-tille.de

Bug#905417: ants: broken symlink: /usr/bin/jointfusion -> ../lib/ants/jointfusion

2022-05-04 Thread Andreas Tille
Control: block -1 by 909833 -- http://fam-tille.de

Bug#909833: ants FTBFS with gcc 8

2022-05-04 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/ANTsX/ANTs/issues/1353 Hi, I've started checking whether we can save ants inside Debian. The Debian Med team tries to take over packages from NeuroDebian and take over responsibility. The situation of ants became better since in

Bug#884710: ants: FTBFS: URL using bad/illegal format or missing URL

2022-05-04 Thread Andreas Tille
Control: block -1 by 909833 -- http://fam-tille.de

Bug#1010536: libdcmimage.so.16: cannot open shared object file: No such file or directory

2022-05-04 Thread Andreas Tille
Hi, Am Wed, May 04, 2022 at 03:34:43PM +0200 schrieb Johannes Schauer Marin Rodrigues: > > I asked in #debian-release and Sebastian Ramacher writes: > > 15:27 < Sebastinas> libdcmtk17 will also need Breaks+Replaces on the > libdcmtk16 version with the .so.17 files. > 15:29 < Sebastinas> At lea

Bug#1010536: libdcmimage.so.16: cannot open shared object file: No such file or directory

2022-05-04 Thread Andreas Tille
Hi Johannes, Am Wed, May 04, 2022 at 12:22:50PM +0200 schrieb Johannes Schauer Marin Rodrigues: > Quoting Andreas Tille (2022-05-04 11:25:20) > > Aaargh, sorry for my sloppyness. I did not expect a SONAME bump connected > > with micro-Version bump. An updated package is in new

Bug#1010536: libdcmimage.so.16: cannot open shared object file: No such file or directory

2022-05-04 Thread Andreas Tille
Hi, Am Wed, May 04, 2022 at 10:56:57AM +0200 schrieb Johannes Schauer Marin Rodrigues: > > I'm going to rebuild all reverse dependencies and see if anything breaks > > and report back to you in case I find any FTBFS caused by the new dcmtk > > version. > > the following source package build depe

Bug#1010536: libdcmimage.so.16: cannot open shared object file: No such file or directory

2022-05-04 Thread Andreas Tille
Control: tags -1 pending Aaargh, sorry for my sloppyness. I did not expect a SONAME bump connected with micro-Version bump. An updated package is in new. Kind regards Andreas. -- http://fam-tille.de

Bug#1010276: parasail: compiles something extra (or less) depending on the CPU features available

2022-05-01 Thread Andreas Tille
Am Sun, May 01, 2022 at 01:27:39PM +0200 schrieb Étienne Mollier: > Thank you for the clarification. In any case, I believe the mv > makes a random static library disappear, so I'll replace by cp. > This is looking like a safe maneuver. Uh, that's actually true and should for sure have been a

Bug#1010276: parasail: compiles something extra (or less) depending on the CPU features available

2022-05-01 Thread Andreas Tille
Am Sun, May 01, 2022 at 02:09:21PM +0200 schrieb Étienne Mollier: > > Note that `sort` is locale dependant, so if that's really the proper way > > to do it (tbh doing find|head feels *very* brittle to me… it's probably > > better if you can think of a better way to achieve whatever that piece > > o

Bug#1010276: Bug#1010276: parasail: compiles something extra (or less) depending on the CPU features available

2022-05-01 Thread Andreas Tille
Hi Étienne, Am Sun, May 01, 2022 at 10:50:16AM +0200 schrieb Étienne Mollier: > I'm still looking up this issue, but I wrap up a status to clear > my mind. > > To me, the main topic of the bug is the reproducibility issue[1] > observed on i386, but other architectures may be affected. The > diff

Bug#991566: r-cran-bslib is in NEW now

2022-04-29 Thread Andreas Tille
Hi, just hoping that r-cran-bslib will be accepted soonish to be able to work on this issue. Kind regards Andreas. -- http://fam-tille.de

Bug#997265: Removing opensurgsim from Debian (Was: [simquest/opensurgsim] Build failures with libeigen3-3.4.0 (Issue #5))

2022-04-26 Thread Andreas Tille
22 13:38:05 -0700 From: Harald Scheirich To: simquest/opensurgsim Cc: Andreas Tille , Comment Subject: Re: [simquest/opensurgsim] Build failures with libeigen3-3.4.0 (Issue #5) Sorry there really isn't any work being done using OSS at the moment on our side, any change will have to com

Bug#1009467: [Bioconductor/Biostrings] S.h seems to be deprecated (Issue #66)

2022-04-13 Thread Andreas Tille
Hi Hervé, Am Wed, Apr 13, 2022 at 09:46:59AM -0700 schrieb Hervé Pagès: > @tillea And most importantly, it seems that Debian is building the wrong > version of Bioconductor. The `S.h` file was removed from R 4.2 and they are > reporting a bug for **Biostrings** 2.62.0, which belongs to Bioconduc

Bug#1009467: r-bioc-biostrings: FTBFS: BitMatrix.c:9:10: fatal error: S.h: No such file or directory

2022-04-13 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/Bioconductor/Biostrings/issues/66

Bug#1009462: I think we can remove pyqi (Was: Bug#1009462: pyqi: FTBFS: Only Python 3.8 and 3.9 are supported.E: pybuild pybuild:369: configure: plugin distutils failed with: exit code=1: python3.10 s

2022-04-13 Thread Andreas Tille
Hi, if I remember correctly pyqi was packaged for qiime 1.x. It has no rdepends any more and I think we should remove it. Does anybody think differently? Kind regards Andreas. - Weitergeleitete Nachricht von Lucas Nussbaum - Date: Tue, 12 Apr 2022 20:44:37 +0200 From: Lucas N

Bug#1009120: python-freecontact: build-depends on package that is no longer available on armel.

2022-04-12 Thread Andreas Tille
Control: reassign -1 ftp.debian.org Control: severity -1 normal Control: retitle -1 ROM - Please remove libfreecontact-perl for armel Hi ftpmasters, since the build-dependency libfreecontact-dev is not available on arm armel any more please also remove libfreecontact-perl on armel. Thank you for

Bug#1009119: python-freecontact: build-depends on package that is no longer available on armel.

2022-04-12 Thread Andreas Tille
Control: reassign -1 ftp.debian.org Control: severity -1 normal Control: retitle -1 ROM - Please remove python3-freecontact for armel Hi ftpmasters, since the build-dependency libfreecontact-dev is not available on arm armel any more please also remove python3-freecontact on armel. Thank you for

Bug#991566: r-cran-bookdown is so old that it fails to even start

2022-04-11 Thread Andreas Tille
Control: tags -1 confirmed Control: block -1 by 996965 > I reported this bug upstream, but they closed it saying that the bookdown > package is ways too old to be of any use, and that I should install the > package directly instead. They are right in some sense, but I'd prefer to use > the Deb

Bug#1008356: GenABEL fails to build (Was: Bug#1008356: r-cran-genabel: FTBFS: fexact.c:1025:13: error: ‘PROBLEM’ undeclared (first use in this function))

2022-04-04 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 yu...@bionet.nsc.ru Control: tags -1 pending Hi, the Debian packaged version of GenABEL received a bug report once we switched from R 4.1.2 to 4.1.3 The following patch solves this issue: https://salsa.debian.org/r-pkg-team/r-cran-genabel/-/bl

Bug#1008402: khmer: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13

2022-04-03 Thread Andreas Tille
Hi Stefano, Am Sat, Apr 02, 2022 at 07:03:04PM -0400 schrieb Stefano Rivera: > > > > return _sys.stdout.buffer if 'b' in self._mode else > > > > _sys.stdout > > > E AttributeError: '_io.StringIO' object has no attribute > > > 'buffer' > > I assume the big relevant ch

Bug#1008745: nipy: FTBFS with Python 3.10 as default

2022-04-01 Thread Andreas Tille
Control: tags -1 upstream Control: tags -1 help Control: forwarded -1 https://github.com/nipy/nipy/issues/492

Bug#1005438: pygame: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" --system=custom --test-args "/usr/bin/xvfb-run {interpreter} -m pygame.tests.__main__ --exclude opengl"

2022-03-22 Thread Andreas Tille
Hi, Am Wed, Mar 23, 2022 at 12:19:40AM +1100 schrieb Hugh McMaster: > On Mon, 28 Feb 2022 at 16:40, Hugh McMaster wrote: > > > I did some testing and found that pygame 2.1.0 is the first recent > > version not affected by the FreeType test issue. > > > > I'll keep digging, but I'd strongly sugges

Bug#1005500: argh: FTBFS: doctest.h:1398:92: error: use of deleted function ‘doctest::detail::Expression_lhs >::Expression_lhs(doctest::detail::Expression

2022-03-17 Thread Andreas Tille
Control: tags -1 help Control: tags -1 upstream Control: forwarded -1 https://github.com/adishavit/argh/issues/72

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-03-16 Thread Andreas Tille
22 at 12:36 PM Andreas Tille wrote: > > > Cool! This finally works. Thanks a lot for your patience, Andreas. > > > > Am Sun, Feb 20, 2022 at 09:43:10AM -0800 schrieb Chris Chang: > > > Hmm. Ordinarily, that download link would be fine. I had not updated it > >

Bug#1000336: Upgrading tbb

2022-03-13 Thread Andreas Tille
Hi, Am Mon, Mar 14, 2022 at 12:13:50AM + schrieb Torrance, Douglas: > On Sun 13 Mar 2022 04:50:32 PM EDT, M. Zhou wrote: > > Recently I'm not able to test the build of libtbb-dev's reverse dependencies > > as my build machine was out of access. That blocks my submission of the > > transition

Bug#1007172: r-cran-pki incompatible with OpenSSL 3

2022-03-12 Thread Andreas Tille
Control: forwarded -1 Simon Urbanek Control: tags -1 pending Hi Simon, I'll upload the attached patch which also applies to the new upstream version 0.1-10. Kind regards Andreas. Am Sat, Mar 12, 2022 at 10:37:24AM -0800 schrieb Steve Langasek: > Package: r-cran-pki > Version: 0.1-9-1 > S

Bug#1006380: Blocked by r-cran-jinjar (waiting in new queue)

2022-03-09 Thread Andreas Tille
Control: block -1 by 1005377 The new upstream version of r-cran-emayili needs r-cran-jinjar which is waiting in new queue. Kind regards Andreas. -- http://fam-tille.de

Bug#1005459: Any reason not to upload rdflib 6 to unstable (Was: rdflib: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.10 3.9" returned exit code 13)

2022-02-24 Thread Andreas Tille
Am Thu, Feb 24, 2022 at 01:40:51PM +0100 schrieb Andreas Tille: > > On the other hand in the current situation with two open RC bugs all > other packages are broken anyway and will be removed from testing if > we do not act upon the issue. So may be we should upload to unstable? I&

Bug#1005459: rdflib: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.10 3.9" returned exit code 13

2022-02-24 Thread Andreas Tille
Hi Nilesh, Am Thu, Feb 24, 2022 at 06:00:03PM +0530 schrieb Nilesh Patra: > On 2/24/22 3:36 PM, Andreas Tille wrote: > > I tried to follow your suggestion to upgrade rdflib to version 6 in Git. > > Unfortunately I'm stumbling upon a different issue in the new test > >

Bug#1005459: rdflib: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.10 3.9" returned exit code 13

2022-02-24 Thread Andreas Tille
Control: tags -1 confirmed Control: tags -1 help Hi Jonas, > Please consider releasing rdflib v6 which in my brief testing is > compatible with pyparser v3. I tried to follow your suggestion to upgrade rdflib to version 6 in Git. Unfortunately I'm stumbling upon a different issue in the new tes

Bug#1000336: Upgrading tbb

2022-02-22 Thread Andreas Tille
Am Wed, Feb 23, 2022 at 12:31:07AM -0500 schrieb M. Zhou: > Hello guys. Finally it's all green on our release architectures > https://buildd.debian.org/status/package.php?p=onetbb&suite=experimental > > I shall request the slot for transition once finished the rebuild > of its reverse dependencies

Bug#1005438: pygame: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" --system=custom --test-args "/usr/bin/xvfb-run {interpreter} -m pygame.tests.__main__ --exclude opengl"

2022-02-22 Thread Andreas Tille
Hi Stefano, Am Wed, Feb 23, 2022 at 01:56:11AM + schrieb Stefano Rivera: > Hi Andreas (2022.02.22_07:57:25_+) > > I've put all developers mentioned as Uploader in CC. Given that the > > last non-team upload was two years ago which might have lead to the > > situation that following upstre

Bug#1005438: pygame: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.10 3.9" --system=custom --test-args "/usr/bin/xvfb-run {interpreter} -m pygame.tests.__main__ --exclude opengl"

2022-02-22 Thread Andreas Tille
Control: tags -1 confirmed Hi, I had a look into this issue since a Debian Med package received a testing removal warning. I can confirm the build fails with Segmentation fault in the build time test suite. I realised that this package is lagging quite a bit behind upstream and my personal

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-02-20 Thread Andreas Tille
ignificant enough that a temporary discordance is less disruptive than > making you change your packing process, so I've updated the website source > link to point to the newer code; let me know if you still run into any > problems. > > On Sat, Feb 19, 2022 at 11:53 PM Andreas Tille wr

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-02-19 Thread Andreas Tille
Chang wrote: > > > If you build off the current head, the version string should say "18 Feb > > 2022", not "17 Feb 2022". > > > > On Sat, Feb 19, 2022 at 7:02 AM Andreas Tille wrote: > > > >> Hi again, > >> > >> Am Sa

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-02-19 Thread Andreas Tille
Hi again, Am Sat, Feb 19, 2022 at 12:28:21AM -0800 schrieb Chris Chang: > Ok, new release/tag created. I've built the new version now. The bad news is that it keeps on SEGFAULTing for me: ... (gdb) run Starting program: /usr/lib/plink2/plink2-sse3 --debug --pfile tmp_data --export vcf vcf-dosa

Bug#990201: Update golang-github-appc-cni to 1.0 (was Re: singularity-container: CVE-2021-33622)

2022-02-19 Thread Andreas Tille
Hi, Am Fri, Feb 18, 2022 at 10:19:01PM +0100 schrieb Andreas Tille: > > So I do not know where this error comes from; or if you have something else > > locally. > > I'll simply revert the version bump ... I did so and uploaded to experimental[1]. I think once all precon

Bug#990201: extra vendor/ directory

2022-02-18 Thread Andreas Tille
Hi Benda, Am Sat, Feb 19, 2022 at 11:34:22AM +0800 schrieb Benda Xu: > Many thanks for taking care of the 3.9 series! You are welcome. I was somehow forced to do this since I need a working singularity. ;-) > I am confused of the 'vendor/' directory in tag 'upstream/3.9.5+ds1'. > > The upstre

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-02-18 Thread Andreas Tille
Hi Chris, Am Fri, Feb 18, 2022 at 07:27:20PM -0800 schrieb Chris Chang: > I have confirmed that the original code segfaults when compiled with gcc > 11.2 on my Debian instance, and that it runs to completion after the latest > patch. I have also confirmed that, after the latest patch, all other t

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-02-18 Thread Andreas Tille
there is an > > existing non-inlined version that is used for very old gcc versions, but it > > looks like it may also be needed here. > > > > On Fri, Feb 18, 2022 at 11:40 AM Andreas Tille wrote: > > > >> Hi again, > >> > >> I applied th

Bug#990201: Update golang-github-appc-cni to 1.0 (was Re: singularity-container: CVE-2021-33622)

2022-02-18 Thread Andreas Tille
Hi again, I can confirm I've got version 3.9.4 building thanks to all your help. Am Fri, Feb 18, 2022 at 11:31:23PM +0530 schrieb Nilesh Patra: > | dh_fixperms > | chown -c root.root debian/singularity-container/usr/lib/*/singularity/bin/* > | chown: changing ownership of > 'debian/singularity-c

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-02-18 Thread Andreas Tille
0 schrieb Chris Chang: > Ok, I don't know why that particular line would fail, but I've added > another debug-print before it on GitHub. > > On Fri, Feb 18, 2022 at 4:24 AM Andreas Tille wrote: > > > Hi Chris, > > > > Am Thu, Feb 17, 2022 at 07:13:49PM -

Bug#990201: singularity-container: CVE-2021-33622

2022-02-18 Thread Andreas Tille
;m happy about anybody who joins the fun. But if you are wondering yourself why you are in here it makes no sense to list you, thought. > Andreas Tille writes: > > > I updated singularity-container in Salsa to the latest available CE > > release and added some new Build-Depends.

Bug#990201: singularity-container: CVE-2021-33622

2022-02-18 Thread Andreas Tille
Control: tags -1 help Hi, I updated singularity-container in Salsa to the latest available CE release and added some new Build-Depends. Unfortunately it does not build as you can see in salsa-ci[1]. Any help to get the package build is welcome. I personally have no idea about Go language nor s

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-02-18 Thread Andreas Tille
Hi Chris, Am Thu, Feb 17, 2022 at 07:13:49PM -0800 schrieb Chris Chang: > I was unable to replicate this issue on a Debian EC2 instance. However, > there are very few things that happen between printing "End time:" and > program exit, so I have added a bunch of debug-prints (active when the > --d

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-02-17 Thread Andreas Tille
Am Thu, Feb 17, 2022 at 11:39:30AM -0800 schrieb Chris Chang: > Haven't yet replicated this on any of my usual non-Debian test machines, > but I will spin up a Debian EC2 instance within the next two days and try > to replicate the crash there. Thanks a lot, Andreas. -- http://fam-tille.de

Bug#1002335: python-epimodels: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13

2022-02-17 Thread Andreas Tille
Control: tags -1 upstream Control: forwarded -1 https://github.com/fccoelho/epimodels/issues/4

Bug#1003165: scikit-learn in unstable FTBFS on arm64, armel, armhf, i386, ppc64el and s390x

2022-02-17 Thread Andreas Tille
Hi, Am Wed, Feb 16, 2022 at 12:09:23PM +0100 schrieb John Paul Adrian Glaubitz: > > So, I have skimmed over the build logs and one of the main issues is the use > of > -march flags to enforce a certain baseline [1]: > > powerpc64le-linux-gnu-gcc: error: unrecognized command-line option > ‘-mar

Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

2022-02-16 Thread Andreas Tille
PS to last mail: Here https://salsa.debian.org/med-team/plink2/-/jobs/2479769 is a full test log in our Gitlab CI for the latest version which I just injected into the packaging Git repository but did not upload yet. Kind regards Andreas. -- http://fam-tille.de

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