Bug#1069873: rdkit: FTBFS convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb).

2024-05-28 Thread Andrius Merkys
Control: severity -1 important On Fri, 26 Apr 2024 09:25:06 +0300 Andrius Merkys wrote: Since I need to upload rdkit to experimental to deal with time_t64 transition, I am going to disable latexpdf documentation building for the time being and deal with this issue later. I have disabled

Bug#1071655: pytorch: FTBFS on ppc64el

2024-05-23 Thread Andrius Merkys
Source: pytorch Version: 2.1.2+dfsg-4 Severity: serious Tags: ftbfs Hello, pytorch FTBFS on ppc64el: FAILED: caffe2/CMakeFiles/torch_cpu.dir/__/aten/src/ATen/native/Col2Im.cpp.o /usr/bin/c++ -DAT_PER_OPERATOR_HEADERS -DCAFFE2_BUILD_MAIN_LIB -DFMT_HEADER_ONLY=1 -DHAVE_MALLOC_USABLE_SIZE=1

Bug#1035833: cpptraj: autopkgtest failure everywhere except on amd64

2024-05-17 Thread Andrius Merkys
Control: severity -1 important Control: retitle -1 cpptraj: FTBFS on \!amd64 On Wed, 10 May 2023 02:29:08 +0530 Kiran S Kunjumon wrote: You package cpptraj has an autopkgtest, great. However, it fails everywhere except on amd64. Can you please investigate the situation and fix it? I have

Bug#1035833: cpptraj: autopkgtest failure everywhere except on amd64

2024-05-13 Thread Andrius Merkys
On Wed, 10 May 2023 02:29:08 +0530 Kiran S Kunjumon wrote: === FAILURES === TEST: /tmp/autopkgtest-lxc.kz5vbtvg/downtmp/build.qgE/src/test/Test_SPAM CPPTRAJ: SPAM Test ../MasterTest.sh: line 495: 3218 Killed

Bug#1064311: rdkit: NMU diff for 64-bit time_t transition

2024-04-29 Thread Andrius Merkys
Hi, On Wed, 24 Apr 2024 23:57:17 +0200 Chris Hofstaedtler wrote:> An upload with t64 binaries is required as soon as possible. Given the packages have to go to binary-NEW, you must upload with binaries, and then probably follow up with a source-only upload once they are ACCEPTed. t64

Bug#1065660: antlr4-maven-plugin: please provide debian-versioned maven coordinates

2024-04-26 Thread Andrius Merkys
Control: severity -1 important Control: tags -1 - ftbfs Hi, On 2024-04-25 19:12, Santiago Vila wrote: I noticed that chemicaltagger currently FTBFS and I believe it is because of this problem, so to avoid duplicate reports, I'm raising this one to serious. A build log for chemicaltagger is

Bug#1065660: antlr4-maven-plugin: please provide debian-versioned maven coordinates

2024-04-26 Thread Andrius Merkys
Hi, On 2024-04-25 19:12, Santiago Vila wrote: I noticed that chemicaltagger currently FTBFS and I believe it is because of this problem, so to avoid duplicate reports, I'm raising this one to serious. A build log for chemicaltagger is available here:

Bug#1069873: rdkit: FTBFS convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb).

2024-04-26 Thread Andrius Merkys
Source: rdkit Version: 202309.3-3 Severity: serious Tags: ftbfs sid Hello, rdkit FTBFS with the following error in latexpdf documentation build: Extension error: convert exited with error: [stderr] b'convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb).\n' [stdout] b''

Bug#1064311: rdkit: NMU diff for 64-bit time_t transition

2024-04-25 Thread Andrius Merkys
Hi Chris, On 2024-04-25 00:57, Chris Hofstaedtler wrote: t64 is already in unstable and making its way to testing. So you are a bit late with getting rdkit fixed for t64. An upload with t64 binaries is required as soon as possible. Given the packages have to go to binary-NEW, you must upload

Bug#1063124: libccp4: NMU diff for 64-bit time_t transition

2024-04-25 Thread Andrius Merkys
Hi, On Mon, 05 Feb 2024 07:52:37 + Steve Langasek wrote: If you have any concerns about this patch, please reach out ASAP. Although this package will be uploaded to experimental immediately, there will be a period of several days before we begin uploads to unstable; so if information

Bug#1064311: rdkit: NMU diff for 64-bit time_t transition

2024-04-24 Thread Andrius Merkys
Hi, On Mon, 19 Feb 2024 21:35:16 + Steve Langasek wrote:> Since turning on 64-bit time_t is being handled centrally through a change to the default dpkg-buildflags (https://bugs.debian.org/1037136), it is important that libraries affected by this ABI change all be uploaded close together

Bug#1068942: unblock 1068942 by 1069098

2024-04-18 Thread Andrius Merkys
control: unblock 1068942 by 1069098 Hello, emboss no longer builds on s390x and its binaries have been RMed from s390x, unblocking emboss migration to testing. This in principle should resolve the current bug. Andrius

Bug#1069226: tomogui: FTBFS: RuntimeError: Sphinx is required to build or test the documentation

2024-04-18 Thread Andrius Merkys
Source: tomogui Version: 0.3.1-2 Severity: serious Tags: ftbfs Hello, tomogui FTBFS in sid on amd64: running build_doc Traceback (most recent call last): File "/home/merkys/tomogui-0.3.1/setup.py", line 804, in setup_package() File "/home/merkys/tomogui-0.3.1/setup.py", line 801, in

Bug#1069225: freesas: FTBFS: fatal error: numpy/arrayobject.h: No such file or directory

2024-04-18 Thread Andrius Merkys
Source: freesas Version: 0.9.0-6 Severity: serious Tags: ftbfs Hello, freesas FTBFS in sid on amd64: INFO:root:x86_64-linux-gnu-gcc -Wsign-compare -fwrapv -O2 -Wall -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security

Bug#1069224: nabu: FTBFS: AssertionError: OpenclUnsharpMask: max error is too high with method

2024-04-18 Thread Andrius Merkys
Source: nabu Version: 2023.1.1-3 Severity: serious Tags: ftbfs Hello, nabu FTBFS in sid on amd64: FAILURES

Bug#1066450: opensearch: FTBFS with lucene9/9.10.0+dfsg

2024-04-02 Thread Andrius Merkys
control: retitle -1 opensearch: FTBFS with lucene9/9.10.0+dfsg I have recently updated lucene9. Current FTBFS is caused by missing lucene9 classes. Thus it seems that lucene9 API has changed breaking backwards compatibility. Andrius

Bug#1066296: RE: Bug#1066296: xli: FTBFS: dither.c:77:36: error: implicit declaration of function ‘strlen’ [-Werror=implicit-function-declaration]

2024-03-26 Thread Andrius Merkys
Hi Nilson, On Wed, 13 Mar 2024 17:34:15 + Nilson Silva wrote: Relevant part (hopefully): > cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O

Bug#1061765: Help needed to fix python-coverage-test-runner

2024-02-22 Thread Andrius Merkys
Hi Andreas, On 2024-02-23 09:15, Andreas Tille wrote: I've attempted to fix python-coverage-test-runner in Git since this package is finally responsible for the failure of vmdb2: File "/usr/lib/python3/dist-packages/CoverageTestRunner.py", line 22, in import imp ModuleNotFoundError: No

Bug#1041027: rapidjson FTBFS with googletest 1.13.0

2024-02-08 Thread Andrius Merkys
On Thu, 8 Feb 2024 10:22:10 +0200 Andrius Merkys wrote: I attach a patch which fixes the issue by setting -std=c++14 (as needed by googletest) and commenting out a code line in include/rapidjson/document.h which is gone in the newest upstream commit [1]. [1] https://github.com/Tencent

Bug#1041027: rapidjson FTBFS with googletest 1.13.0

2024-02-08 Thread Andrius Merkys
control: tags -1 + patch On Fri, 14 Jul 2023 11:03:55 +0300 Adrian Bunk wrote: Source: rapidjson Version: 1.1.0+dfsg2-7.1 Severity: serious Tags: ftbfs trixie sid https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rapidjson.html ... In file included from

Bug#1058454: [Debichem-devel] Bug#1058454: Do we really need to support 32bit in abinit and prody (maybe others)

2024-02-01 Thread Andrius Merkys
Hi Andreas, On 2024-01-31 13:08, Andreas Tille wrote: in connection with the time_t transition in Debian Med we are discussing[1] whether we really need 32 bit support for some of our tools or whether we should realistically drop this support to concentrate on problems which are more relevant

Bug#1058127: python-mpiplus: FTBFS: AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?

2024-01-16 Thread Andrius Merkys
Hi Yogeswaran, On 2024-01-16 03:43, Yogeswaran Umasankar wrote: I have removed the hard-coded version number from setup.py. I found that the issue was due to changes in PEP440 version naming convention in versioneer. For this package no need python3-versioneer, upstream has its own

Bug#1058127: python-mpiplus: FTBFS: AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?

2024-01-15 Thread Andrius Merkys
Hi Yogeswaran, On 2024-01-14 18:46, Yogeswaran Umasankar wrote: I created a patch for fixing AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. In the process I have updated it to the latest upstream too. I’ve attached the debdiff for you to check out. I noticed you

Bug#1054974: behave: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13

2024-01-15 Thread Andrius Merkys
Hi, On 2024-01-15 17:34, Christoph Berg wrote: Re: Andrius Merkys The patch proposed in #1042610 does not fix test failure. Interestingly, the failure seems to be nondeterministic: after patching #1042610 some builds succeed. However, I did not manage to find the root cause. The difference

Bug#1054974: behave: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13

2024-01-04 Thread Andrius Merkys
Hi, On Tue, 12 Dec 2023 19:35:09 +0100 s3v wrote: please see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1042610 for a proposed patch. The patch proposed in #1042610 does not fix test failure. Interestingly, the failure seems to be nondeterministic: after patching #1042610 some

Bug#1042610: #1042610: patch works

2024-01-04 Thread Andrius Merkys
Control: tags -1 + patch Hello, I can confirm that the provided patch (+B-D on python3-doc) fixes the bug. However, #1054974 is not fixed, thus behave still FTBFS. Andrius

Bug#1059175: dials: FTBFS: Imported target "DXTBX::DXTBX" includes non-existent path

2023-12-20 Thread Andrius Merkys
Control: tags -1 + patch pending Hi, On 2023-12-21 00:42, Sebastian Ramacher wrote: Source: dials Version: 3.12.1+dfsg3-5 Severity: serious Tags: ftbfs Justification: fails to build from source (but built successfully in the past) X-Debbugs-Cc: sramac...@debian.org

Bug#1056457: [Debichem-devel] Bug#1056457: python-ase's autopkg tests fail with Python 3.12

2023-12-20 Thread Andrius Merkys
Control: tags -1 + patch Hi, On 2023-12-20 20:23, s3v wrote: After applying [1][2][3] from upstream and adding "-p no:warnings":   addopts = -p no:cacheprovider -p no:warnings in ase/test/pytest.ini (DeprecationWarnings from various packages make tests fail), I was able to build your

Bug#1058690: liblatex-tounicode-perl: trying to overwrite .../ltx2unitxt.1.gz, which is also in package texlive-bibtex-extra 2023.20231207-1

2023-12-14 Thread Andrius Merkys
Control: tags -1 + patch Hello, On 2023-12-14 16:07, Vincent Lefevre wrote: Package: liblatex-tounicode-perl Version: 0.54-1 Severity: serious As a consequence of the upgrade of texlive-bibtex-extra to 2023.20231207-3: [...] Selecting previously unselected package liblatex-tounicode-perl.

Bug#1058454: [Debichem-devel] Bug#1058454: prody: autopkgtest regression on i386

2023-12-12 Thread Andrius Merkys
Hi, On 2023-12-12 13:48, Graham Inggs wrote: Source: prody Version: 2.3.1+dfsg-3 Severity: serious Tags: sid trixie User: debian...@lists.debian.org Usertags: regression Hi Maintainer The autopkgtest of prody 2.3.1+dfsg-3 is failing when tested with numpy 1:1.24.2-2 [1]. I've copied what I

Bug#1057951: [Debichem-devel] Bug#1057951: promod3: FTBFS: No such file or directory: 'model.pdb'

2023-12-11 Thread Andrius Merkys
Control: owner -1 ! Hi, On 2023-12-11 14:04, Santiago Vila wrote: # Also happens in bookworm found 1057951 3.2.1+ds-6 thanks El 11/12/23 a las 12:06, Andrius Merkys escribió: I can reproduce this in clean chroot on barriere.d.o. Interestingly, FTBFS happens only when building on two threads

Bug#1057951: [Debichem-devel] Bug#1057951: promod3: FTBFS: No such file or directory: 'model.pdb'

2023-12-11 Thread Andrius Merkys
Control: tags -1 + confirmed Hi, On 2023-12-10 22:51, Santiago Vila wrote: Package: src:promod3 Version: 3.3.1+ds-1 Severity: serious Tags: ftbfs Dear maintainer: During a rebuild of all packages in unstable, your package failed to build:

Bug#1055896: cod-tools: FTBFS: source.c:33:5: error: ‘SPGCONST’ undeclared (first use in this function); did you mean ‘OP_CONST’?

2023-11-14 Thread Andrius Merkys
Control: owner -1 ! Hi, On 2023-11-14 14:27, Gianfranco Costamagna wrote: https://github.com/cod-developers/cod-tools/commit/2e9c0aaa367366883105fa9a7ba3d965495700f8 Just removing SPGCONST from the source.c file is enough, trivial patch attached: Sadly I opened an upstream PR before

Bug#1055447: htsjdk: FTBFS: 35741 tests completed, 9 failed, 10 skipped

2023-11-08 Thread Andrius Merkys
Hi Pierre, On 2023-11-08 12:14, Pierre Gruet wrote: Thanks for the bug report. It was not easy to reproduce this one! Interesting, I ran rebuild two times and both times it failed :) I spotted this issue during ratt-rebuild of a bunch of other packages, did not really give a decent look.

Bug#1055237: does not conform to the standards for library packaging

2023-11-07 Thread Andrius Merkys
Hello, On Thu, 02 Nov 2023 18:10:19 +0100 Pierre Gruet wrote: Recently catch2/3.4.0-1 was uploaded to Debian, great. Yet the binary packages do not follow the layout for libraries that is described in Policy Section 8. For instance I think we should provide a shared library and if there are

Bug#1055153: skeema: FTBFS on mips64el

2023-11-06 Thread Andrius Merkys
Hello, On Wed, 1 Nov 2023 11:49:20 +0100 Sebastian Ramacher wrote: Source: skeema Version: 1.11.0+ds-1 Severity: serious Tags: ftbfs Justification: fails to build from source (but built successfully in the past) I am unable to reproduce this on eller. Most likely the test timeout is due to

Bug#1055447: htsjdk: FTBFS: 35741 tests completed, 9 failed, 10 skipped

2023-11-06 Thread Andrius Merkys
Source: htsjdk Version: 3.0.5+dfsg-1 Severity: serious Justification: FTBFS Tags: sid ftbfs Hi, I noticed htsjdk FTBFS in sid: Gradle Test Executor 1 finished executing tests. Results: FAILURE (35741 tests, 35722 successes, 9 failures, 10 skipped) 35741 tests completed, 9 failed, 10 skipped

Bug#1052877: redmine: FTBFS: make[1]: *** [debian/rules:20: override_dh_auto_configure] Error 7

2023-10-24 Thread Andrius Merkys
Hello, On Tue, 26 Sep 2023 15:30:11 +0200 Lucas Nussbaum wrote:> > bundle install --local --quiet > `/sbuild-nonexistent` is not a directory. > Bundler will use `/tmp/bundler20230926-1767679-427jij1767679' as your home directory temporarily. > Could not find gem 'nokogiri (~> 1.14.0)' in

Bug#1054433: node-puppeteer: website is build with Docusaurus not packaged for debian

2023-10-24 Thread Andrius Merkys
Hi, On 2023-10-23 22:06, Bastien Roucariès wrote: Source: fasttext Source package names in Subject and Source do not match. Please retitle if this is not intentional. Best, Andrius

Bug#1054432: [Pkg-javascript-devel] Bug#1054432: node-puppeteer: website is build with Docusaurus not packaged for debian

2023-10-24 Thread Andrius Merkys
Hi, On 2023-10-23 22:04, Bastien Roucariès wrote: Source: node-katex Source package names in Subject and Source do not match. Please retitle if this is not intentional. Best, Andrius

Bug#1053865: prody: incompatible with python3-biopython > 1.79

2023-10-13 Thread Andrius Merkys
Source: prody Version: 2.3.1+dfsg-3 Severity: serious Justification: FTBFS Tags: sid ftbfs Forwarded: https://github.com/prody/ProDy/issues/1723 Hello, prody FTBFS with python3-biopython > 1.79: == FAIL: testBuildMSAlocal

Bug#1052888: epics-base: FTBFS: make[2]: *** [configure/RULES_TOP:62: runtests] Error 1

2023-10-10 Thread Andrius Merkys
Control: tags -1 + unreproducible On Tue, 26 Sep 2023 15:34:01 +0200 Lucas Nussbaum wrote: Source: epics-base Version: 7.0.7+dfsg1-5 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu...@debian.org Usertags: ftbfs-20230925 ftbfs-trixie Hi, During a rebuild of all packages

Bug#1049872: armel and armhf excluded from asmjit architectures

2023-09-30 Thread Andrius Merkys
control: severity -1 normal Hello, In 0.0~git20230914.917f19d-1 I have excluded armel and armhf architectures from the list of architectures asmjit is built upon. Thus I think the severity should be normal now. Andrius

Bug#1049872: FTBFS on multiple release architectures

2023-09-13 Thread Andrius Merkys
Hi Emanuele, On 2023-09-11 12:07, Emanuele Rocca wrote: On 2023-09-09 08:38, Andrius Merkys wrote: This is news to me. Could you please point out where in Debian Policy I can read more about such requirement? I thought I saw packages dropping support for one or another release architecture

Bug#1049872: FTBFS on multiple release architectures

2023-09-08 Thread Andrius Merkys
Hi Emanuele, On 2023-09-05 16:58, Emanuele Rocca wrote: On 2023-08-28 07:42, Andrius Merkys wrote: On Wed, 16 Aug 2023 14:29:10 +0200 Emanuele Rocca wrote: asmjit does not build correctly on the following architectures: armel, armhf, mips64el, mipsel, s390x. Does this constitute an RC bug

Bug#1049872: FTBFS on multiple release architectures

2023-08-28 Thread Andrius Merkys
Hi, On Wed, 16 Aug 2023 14:29:10 +0200 Emanuele Rocca wrote: asmjit does not build correctly on the following architectures: armel, armhf, mips64el, mipsel, s390x. Does this constitute an RC bug? If not, severity should be lowered. Thanks, Andrius

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

2023-08-17 Thread Andrius Merkys
Hi Andreas, On 2023-08-17 10:49, Andreas Tille wrote: thanks for reporting this issue. You were mentioning you want to come up with a patch. Since you seem to have dived into this issue deeper I assume you will care for this bug. If not please clarify the status (or may be set the "help"

Bug#1042769: provean: incompatible with cd-hit >= 4.8.1-4

2023-07-31 Thread Andrius Merkys
Package: provean Version: 1.1.5+ds-2 Severity: serious Hello, Current provean package is broken: it segfaults while parsing the output of cd-hit. The most recent compatible version of cd-hit seems to be 4.6.4-1. I hope to come up with a patch sooner or later. Andrius

Bug#1039917: [Debichem-devel] Bug#1039917: gemmi breaks finalcif autopkgtest: causes autopkgtest timeout

2023-06-29 Thread Andrius Merkys
Hi, On 2023-06-29 17:06, Paul Gevers wrote: With a recent upload of gemmi the autopkgtest of finalcif fails in testing when that autopkgtest is run with the binary packages of gemmi from unstable. It passes when run with only packages from testing. In tabular form:   

Bug#1000303: liboqs: not yet ready for testing or stable

2023-06-28 Thread Andrius Merkys
Hi Mikael, On Wed, 28 Jun 2023, 10:09 Mikael Frykholm, wrote: > > The upstream wishes to keep the package out of stable distributions for > > now, until the NIST Post-Quantum Cryptography standardization project > > reaches its conclusion > > Is this still true? Can this package be migrated to

Bug#1039087: epic-base: embed yajl

2023-06-27 Thread Andrius Merkys
Hi, On Sun, 25 Jun 2023 15:02:18 + =?utf-8?q?Bastien_Roucari=C3=A8s?= wrote: Your package embed a copy of yajl. I agree with un-embedding. Could you: - compile against the packaged yajl package I spent some time trying, but did not find an unintrusive way to do so. Adding

Bug#1038954: Bug#1037474: transition: openmm

2023-06-26 Thread Andrius Merkys
Hello, On 2023-06-25 21:15, Sebastian Ramacher wrote: python-pdbfixer seems to need a sourceful upload due to the python3-simtk => python3-openmm rename. Sourceful upload does not seem to help: somewhy python3-pdbfixer picks dependency on python3-simtk instead of python3-openmm. I guess this

Bug#1037472: molmodel: FTBFS with gemmi 0.6.2+ds-1

2023-06-13 Thread Andrius Merkys
Source: molmodel Severity: serious Version: 3.1.0-2 Hello, molmodel FTBFS after recent update of gemmi to 0.6.2+ds-1: /home/merkys/molmodel-3.1.0/src/PDBReader.cpp: In function 'gemmi::Structure getStructureFromFile(const std::string&)': /home/merkys/molmodel-3.1.0/src/PDBReader.cpp:98:29:

Bug#1037463: macromoleculebuilder: FTBFS with gemmi 0.6.2+ds-1

2023-06-13 Thread Andrius Merkys
Source: macromoleculebuilder Severity: serious Version: 4.0.0+dfsg-2 Hello, macromoleculebuilder FTBFS after recent update of gemmi to 0.6.2+ds-1: /home/merkys/macromoleculebuilder-4.0.0+dfsg/src/CifOutput.cpp: In function 'void SimTK::CIFOut::reWriteOutCif(const gemmi::Model&, const

Bug#1016958: epics-base: FTBFS without network access

2023-02-28 Thread Andrius Merkys
Hello, On 2023-02-28 12:57, Santiago Vila wrote: Hello. Merely trying network access is already considered RC, so this should really be serious. (I would be willing to test a fix if somebody proposes one). This particular test seems to attempt to communicate to a locally running server

Bug#1030491: prody: FTBFS: AssertionError: 3205 != 3211

2023-02-08 Thread Andrius Merkys
Hi Santiago, On 2023-02-06 19:36, Santiago Vila wrote: This is fully reproducible at least on Hetzner virtual instances of type CX21 and CX31. Thanks for giving this a look. Could you please provide the versions of python3-biopython and python3-numpy on your setup? ci.debian.net uses the

Bug#1028722: [Debichem-devel] Bug#1028722: prody: FTBFS: AssertionError: 3205 != 3211 : selection 'abs(x) == sqrt(sq(x))' for Selection 'all' failed, expected 3211, selected 3205

2023-01-27 Thread Andrius Merkys
Control: severity -1 important Control: tags -1 + moreinfo unreproducible Hello, On 2023-01-27 13:40, Adrian Bunk wrote: On Sat, Jan 14, 2023 at 01:42:10PM +0100, Lucas Nussbaum wrote: Source: prody Version: 2.3.1+dfsg-3 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User:

Bug#1028705: xraylarch: FTBFS: build-dependency not installable: python-numpy-doc

2023-01-16 Thread Andrius Merkys
Control: tags -1 + pending On Sat, 14 Jan 2023 13:54:02 +0100 Lucas Nussbaum wrote:> > The following packages have unmet dependencies: > sbuild-build-depends-main-dummy : Depends: python-numpy-doc but it is not installable > E: Unable to correct problems, you have held broken packages. >

Bug#1026207: marked as pending in python-ase

2023-01-16 Thread Andrius Merkys
Control: tag -1 pending Hello, Bug #1026207 in python-ase 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#1027215: How much do we lose if we remove theano (+keras, deepnano, invesalius)?

2023-01-16 Thread Andrius Merkys
Hello, On 2023-01-14 13:12, Rebecca N. Palmer wrote: theano has been mostly abandoned upstream since 2018.  (The Aesara fork is not abandoned, but includes interface changes including the import name, so would break reverse dependencies not specifically altered for it.) Its reverse

Bug#1023972: Python 3.11 for bookworm?

2023-01-09 Thread Andrius Merkys
Hi Simon, On 2023-01-07 13:24, Simon McVittie wrote: On Sat, 07 Jan 2023 at 10:23:19 +0200, Andrius Merkys wrote: If I may, I would as well be grateful if someone could give a look at: #1023972 [src:python-ase] FTBFS with Python 3.11 due to pathlib.Path.__enter__() deprecation I have no idea

Bug#1023972: marked as pending in python-ase

2023-01-09 Thread Andrius Merkys
Control: tag -1 pending Hello, Bug #1023972 in python-ase 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#1023972: Python 3.11 for bookworm?

2023-01-07 Thread Andrius Merkys
Hello, On 2023-01-07 10:05, Andreas Tille wrote: Am Thu, Jan 05, 2023 at 01:57:43PM +0100 schrieb Thomas Goirand: Please share it in this list! #1023965 [src:pandas] pandas FTBFS with Python 3.11 as supported version #1024031 [src:numba] numba FTBFS with Python 3.11 as supported

Bug#1027828: [Debichem-devel] Bug#1027828: macromoleculebuilder: FTBFS in bullseye (a2x: ERROR: "xsltproc" [...] returned non-zero exit status 5)

2023-01-03 Thread Andrius Merkys
Hi Santiago, On 2023-01-03 22:35, Santiago Vila wrote: Package: src:macromoleculebuilder Version: 3.2+dfsg-2 Severity: serious Tags: ftbfs Control: fixed -1 4.0.0+dfsg-2 Dear maintainer: During a rebuild of all packages in bullseye, your package failed to build I can reproduce the issue.

Bug#1026603: foolscap: FTBFS: AttributeError: module 'inspect' has no attribute 'getargspec'

2022-12-27 Thread Andrius Merkys
Hello, On Tue, 20 Dec 2022 18:11:51 +0100 Lucas Nussbaum > During a rebuild of all packages in sid, your package failed to build on amd64. [skip] > File "/<>/.pybuild/cpython3_3.11/build/foolscap/remoteinterface.py", line 191, in initFromMethod > names, _, _, typeList =

Bug#1026325: [Debichem-devel] Bug#1026325: libchemistry-opensmiles-perl breaks smiles-scripts autopkgtest: output changed

2022-12-18 Thread Andrius Merkys
Control: owner -1 ! Hi Paul, On 2022-12-18 18:48, Paul Gevers wrote: With a recent upload of libchemistry-opensmiles-perl the autopkgtest of smiles-scripts fails in testing when that autopkgtest is run with the binary packages of libchemistry-opensmiles-perl from unstable. It passes when run

Bug#1023972: python-ase: FTBFS with Python 3.11 due to pathlib.Path.__enter__() deprecation

2022-12-15 Thread Andrius Merkys
On Sun, 13 Nov 2022 13:12:15 +0200 Andrius Merkys wrote: python-ase/3.22.1 FTBFS with the following after Python 3.11 support has been added: DeprecationWarning: pathlib.Path.__enter__() is deprecated and scheduled for removal in Python 3.13; Path objects as a context manager is a no-op I

Bug#1025000: python-qtawesome: Includes non-source Font Awesome 5

2022-12-12 Thread Andrius Merkys
Hi, On 2022-12-12 00:17, Bastian Germann wrote: finalcif's source has some fa5 prefixes, so the package might be affected. Andrius, can you please comment on this? Yes, these are calls to qtawesome.icon('fa5.save') and the like. But if fonts can be drop-in-replaced with ones from

Bug#1025000: python-qtawesome: Includes non-source Font Awesome 5

2022-12-09 Thread Andrius Merkys
Hi, On 2022-12-09 09:28, Julian Gilbey wrote: I have seen this and will deal with it soon. Have you contacted the authors of the package to discuss this issue? No, I did not. Anyway, a quick check on testing shows that there are three packages depending on python3-qtawesome: finalcif,

Bug#1025000: python-qtawesome: Includes non-source Font Awesome 5

2022-12-08 Thread Andrius Merkys
Hi Bastian, On Mon, 28 Nov 2022 16:16:19 +0100 Bastian Germann wrote: This package contains three font files /usr/share/python-qtawesome/fonts/fontawesome5-*-webfont.ttf which are licensed freely but are not built from source and cannot be built from source (missing build system). #902981

Bug#1024526: simbody: FTBFS on ppc64el, mips64el

2022-12-04 Thread Andrius Merkys
Control: severity -1 important The upstream says this is a bug in optimization, but they do not have access to these architectures. For now I have RMed the binaries of ppc64el and mips64el, thus the package should be allowed to migrate to testing without them for the time being. Andrius

Bug#1025242: fastapi: FTBFS with python3.11

2022-12-01 Thread Andrius Merkys
Source: fastapi Severity: serious Version: 0.85.0-2 Hello, fastapi FTBFS with added support for python3.11: pybuild --test --test-pytest -i python{version} -p "3.11 3.10" I: pybuild base:240: PYTHONPATH=/<>/build/lib/ python3.11 -m pytest tests/

Bug#1025238: python-uvicorn: FTBFS with python3.11

2022-12-01 Thread Andrius Merkys
Source: python-uvicorn Severity: serious Version: 0.17.6-1 Hello, python-uvicorn FTBFS with added support for python3.11: debian/rules override_dh_auto_test make[1]: Entering directory '/<>' http_proxy= https_proxy= dh_auto_test I: pybuild pybuild:300: cp -r /<>/tests

Bug#1025237: scalene: FTBFS with python3.11

2022-12-01 Thread Andrius Merkys
Source: scalene Severity: serious Version: 1.4.1-1 Hello, scalene FTBFS with added support for python3.11: building 'scalene.pywhere' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2

Bug#1019808: [Debichem-devel] Bug#1019808: marked as pending in openbabel

2022-11-28 Thread Andrius Merkys
Hi Olly, On 2022-11-27 21:09, Olly Betts wrote: This transition is now down to just 3 packages needing updating (one of which accidentally got uploaded over the weekend based on a pre-transition version so we should be down to 2 packages soon). This bug has been tagged as "pending" for over a

Bug#1024986: python-biopython: does not vendor bindings for python3.11 yet

2022-11-28 Thread Andrius Merkys
Hi, On 2022-11-28 10:23, Nilesh Patra wrote: biopython in unstable does not vendor bindings for python3.11, due to which augur and busco fail their autopkgtest. This as well blocks the update of prody to 2.3.1. The issue is fixed in 1.80+dfsg-1~0exp0 in experimental [1][2]. [1]

Bug#1022307: status on t_coffee causing biopython ftbfs

2022-11-23 Thread Andrius Merkys
Hi Nilesh, On 2022-11-23 15:35, Nilesh Patra wrote: That sounds quite a reasonable thing to do, but we probably should also decrese the severity of this bug to "important" to let biopython be in testing once the corresponding tests are skipped. Sure, lowering of severity was implied (but it

Bug#1022307: status on t_coffee causing biopython ftbfs

2022-11-23 Thread Andrius Merkys
Hi, On Tue, 22 Nov 2022 23:54:48 +0100 =?utf-8?Q?=C3=89tienne?= Mollier wrote: Hi, mostly retitling the open entry against biopython for the sake of clarity, and also pinging both bugs to reset auto- removal counters. We don't have much news from t_coffee upstream to day unfortunately.

Bug#953630: [Debichem-devel] Bug#953630: openbabel autopkg tests fail on non-amd64 architectures

2022-11-21 Thread Andrius Merkys
Hi, On 2022-11-20 18:18, Paul Gevers wrote: From the BSP in Tilburg, I uploaded the attached NMU to DELAYED/5. Please let me know if I should delay more or cancel. Thanks, IMO this NMU is fine. Similar logic should be applied to the build time tests in future, since now their failures are

Bug#1024035: marked as pending in pycifrw

2022-11-16 Thread Andrius Merkys
Control: tag -1 pending Hello, Bug #1024035 in pycifrw 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#1024075: [Debichem-devel] Bug#1024075: pymatgen FTBFS with Python 3.11 as supported version

2022-11-14 Thread Andrius Merkys
Control: tags -1 + fixed-upstream Hello, On 2022-11-14 15:54, Adrian Bunk wrote: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat

Bug#1012093: ciftools-java: FTBFS with OpenJDK 17 due to test failures

2022-11-10 Thread Andrius Merkys
Hi Pierre, On 2022-11-10 11:04, Pierre Gruet wrote: But whoops, sorry, this morning I tried to upload 4.0.3-2 with a manual fix as I hadn't seen upstream released 4.0.4 fixing the issue. I launched a dcut cancel command, we will see if it worked... Else my upload will get accepted and I will

Bug#1012093: ciftools-java: FTBFS with OpenJDK 17 due to test failures

2022-11-10 Thread Andrius Merkys
Control: owner -1 ! Control: tags -1 + pending fixed-upstream Hi Pierre, On 2022-11-10 00:05, Pierre Gruet wrote: I investigated the test failure a bit and saw tiny differences between a generated gzip file and a reference one. This reminded me of one similar and innocuous issue [0] so that I

Bug#1019808: marked as pending in openbabel

2022-10-27 Thread Andrius Merkys
Control: tag -1 pending Hello, Bug #1019808 in openbabel 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#1021550: FTBFS: JarCacheTest.cacheMiss Expected exception: java.io.IOException

2022-10-19 Thread Andrius Merkys
Control: tags -1 + unreproducible Control: severity -1 important Hi Pierre, I have successfully built the package even with disabled network. Thus I cannot reproduce the FTBFS in any setup I can think of. As a result I am lowering issue's severity. Feel free to bump it back, but please supply

Bug#1021550: FTBFS: JarCacheTest.cacheMiss Expected exception: java.io.IOException

2022-10-11 Thread Andrius Merkys
Control: tags -1 + moreinfo Hi Pierre, I cannot reproduce this issue. I suspect it may have something to do with network not being present at the build time. Could you please confirm that your build setup has network disabled intentionally? Interestingly, reproducible-builds does not

Bug#1020148: marked as pending in georegression

2022-09-20 Thread Andrius Merkys
Control: tag -1 pending Hello, Bug #1020148 in georegression 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#1016227: marked as pending in openbabel

2022-09-08 Thread Andrius Merkys
Control: tag -1 pending Hello, Bug #1016227 in openbabel 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#1017717: cp2k: FTBFS: symbol lookup error: /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so: undefined symbol: pmix_value_load

2022-08-19 Thread Andrius Merkys
Source: cp2k Version: 9.1-2 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs Hello, cp2k fails to build on amd64: cd tools/manual && \ /home/merkys/cp2k-9.1/exe/*/cp2k.psmp --xml && \ saxonb-xslt -o index.html -ext:on cp2k_input.xml cp2k_input.xsl orted: symbol

Bug#1009281: [Debichem-devel] Bug#1009281: Bug#1009281: Bug#1009281: Should cinfony be removed?

2022-08-06 Thread Andrius Merkys
Hi, On 2022-07-24 21:18, Moritz Mühlenhoff wrote: > Did you get any reply? Otherwise let's go ahead with the removal. I have checked upstream's master branch and it indeed seems to contain at least some porting to Python 3. I have opened a branch on Salsa ('python3') to attempt to package it.

Bug#953630: [Debichem-devel] Bug#953630: openbabel autopkg tests fail on non-amd64 architectures

2022-08-03 Thread Andrius Merkys
Hello, IMO it is high time to revisit this issue. On 2020-03-11 14:33, Matthias Klose wrote: > openbabel autopkg tests areq quiet interesting. Working around the timeout on > arm64 hides the fact that two other tests fail on every non-amd64 > architecture. I agree that the way the autopkgtest

Bug#1012482: rdflib: URLInputSource can be abused to retrieve arbitrary documents if used naïvely

2022-07-31 Thread Andrius Merkys
Hi Nilesh, On Sun, 31 Jul 2022, 12:12 Nilesh Patra, wrote: > rdflib has been removed from testing along with a bunch of other packages. > And it is triggering -rm-s for packages in testing anyway. > > Upstream is not actively working on the issue as I see from the github > Issue > URL. -- Do

Bug#1014492: guzzle: CVE-2022-31090 CVE-2022-31091

2022-07-14 Thread Andrius Merkys
Hi Katharina, On Thu, 7 Jul 2022 10:56:06 +0200 Katharina Drexel wrote: > thanks for the hints. I pushed a new version in the repo > (https://salsa.debian.org/php-team/pear/php-guzzlehttp-guzzle). > TBD: someone should upload it in the debian repo. Is it OK if I upload guzzle? By the way,

Bug#1013085: marked as pending in python-ase

2022-06-27 Thread Andrius Merkys
Control: tag -1 pending Hello, Bug #1013085 in python-ase 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#1013566: [Pkg-javascript-devel] Bug#1013566: node-sockjs: FTBFS: sockjs.coffee:137:9: error: Can't reference 'this' before calling super in derived class constructors

2022-06-27 Thread Andrius Merkys
Hi Yadd, On 2022-06-24 17:10, Yadd wrote: > I prepared a fix, pushed to salsa. Could you take a look ? Thanks a lot, reviewed and uploaded. Best wishes, Andrius

Bug#1012498: finalcif: FTBFS with python3-gemmi 0.5.5+ds

2022-06-08 Thread Andrius Merkys
Source: finalcif Version: 104+dfsg-1 Severity: serious Tags: ftbfs finalcif FTBFS with python3-gemmi 0.5.5+ds: self = @property def is_centrosymm(self) -> bool: """ Whether a structuere is centro symmetric or not. """ if not self.symmops or self.symmops

Bug#1012482: rdflib: URLInputSource can be abused to retrieve arbitrary documents if used naïvely

2022-06-08 Thread Andrius Merkys
Source: rdflib Version: 6.1.1 Severity: critical Tags: security upstream Forwarded: https://github.com/RDFLib/rdflib/issues/1844 Hello, rdflib will attempt to resolve any URL in @context in POSTed JSON-LD messages, leading to various probing and DDoS vectors, see the upstream discussion [1].

Bug#1009402: [Debichem-devel] Bug#1009402: Bug#1009402: molmodel: FTBFS: demangle.hpp:23:33: error: ‘string_view’ in namespace ‘std’ does not name a type

2022-05-30 Thread Andrius Merkys
Hi, On 2022-05-26 16:24, Adrian Bunk wrote: > The remaining problem can be fixed with the same change as > https://salsa.debian.org/debichem-team/macromoleculebuilder/-/blob/master/debian/patches/drop-CMAKE_CXX_STANDARD.patch Thanks for the suggestion - it worked! Best, Andrius

Bug#1009402: [Debichem-devel] Bug#1009402: molmodel: FTBFS: demangle.hpp:23:33: error: ‘string_view’ in namespace ‘std’ does not name a type

2022-04-14 Thread Andrius Merkys
Control: retitle -1 molmodel: FTBFS with tao-pegtl v3 Control: tags -1 + confirmed Control: block -1 by 1009415 Hello, On 2022-04-12 20:47, Lucas Nussbaum wrote: > /usr/include/tao/pegtl/match.hpp:139:15: error: use of deleted function > ‘tao::pegtl::internal::marker

Bug#1009415: [Debichem-devel] Bug#1009415: gemmi: FTBFS: cif.hpp:40:30: error: ‘analysis’ in namespace ‘gemmi::cif::pegtl’ does not name a type

2022-04-13 Thread Andrius Merkys
Control: retitle -1 gemmi: FTBFS with tao-pegtl v3 Control: tags -1 + confirmed Hello, On 2022-04-12 20:45, Lucas Nussbaum wrote: >> /usr/include/tao/pegtl/match.hpp:57:34: error: incomplete type >> ‘gemmi::cif::rules::str_stop’ used in nested name specifier >>57 | -> decltype(

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