Bug#1093245: [Debichem-devel] Bug#1093245: libinchi1.07: InChI trust released InChI version 1.07.2

control: reassign -1 src:inchi control: owner -1 ! Hi Norwid, On 2025-01-16 23:08, Norwid Behrnd via Debichem-devel wrote: InChI trust admitted version 1.07.2 into its main branch of development.[1] Hence I would like to suggest an update of DebiChem's package. If suitable, this could resolve

Bug#1093086: [Debichem-devel] Bug#1093086: Bug#1093086: rdkit: FTBFS on big-endian architectures

Hi, On 2025-01-16 09:45, Michael Banck wrote: I opened an upstream issue yesterday evening and somebody mentioned interest in looking at it, so maybe let's wait a day or two whether they get a fix/PR, but yeah, otherwise we should drop big-endian at least temporarily. Thanks for forwarding the

Bug#1093086: [Debichem-devel] Bug#1093086: Bug#1093086: Bug#1093086: Bug#1093086: rdkit: FTBFS on big-endian architectures

Control: found -1 202409.4-1 Hi Michael, On 2025-01-15 19:44, Michael Banck wrote: I did not have a problem building it, so I uploaded 202409.4-1, let's see how that one goes on the autobuilders. Thanks a lot for uploading 202409.4-1. Interestingly, the problem with 'convert' does not resurf

Bug#1093086: [Debichem-devel] Bug#1093086: rdkit: FTBFS on big-endian architectures

Hello, On 2025-01-15 09:54, Andrius Merkys wrote: From a quick glance it seems that a lot of problems are related to Python pickle reading. Upstream has made some fixes related to endianness in version 202409.4 [1], thus packaging the newer upstream version might mitigate the problem. [1

Bug#1093086: rdkit: FTBFS on big-endian architectures

Source: rdkit Version: 202409.2-3 Severity: serious Tags: ftbfs Hello, rdkit FTBFS in sid on s390x and ppc64. This manifests in the failure of many tests: The following tests FAILED: 8 - testDataStructs (Subprocess aborted) 9 - testFPB (Subprocess aborted) 10 - te

Bug#1092922: moreinfo needed

Hi Paul, On Mon, 13 Jan 2025 10:57:12 -0500 Paul Tagliamonte wrote: Raw output from the removal, comments inline: > Checking reverse dependencies... > # Broken Build-Depends: > coot: librdkit-dev > python3-rdkit I processed the other RoM bug, the remaining binary packages aren't buildi

Bug#1092923: RM: coot [armhf] -- ROM; unsatisfiable deps on rdkit

Package: ftp.debian.org Severity: normal Control: block 1092922 by -1 Hello, Please remove coot binaries for armhf as its dependency rdkit is no longer built on 32bit architectures. Andrius

Bug#1092922: RM: rdkit [armel armhf i386] -- ROM; no longer built for 32bit

Package: ftp.debian.org Severity: normal Hello, Please remove rdkit binaries for armel, armhf and i386 as it is no longer built on 32bit architectures. Andrius

Bug#1083076: [Debichem-devel] Bug#1083076: Bug#1083076: Bug#1083076: 1083076 affects armel too

Hi Michael, On 2025-01-11 22:01, Michael Banck wrote: On Mon, Dec 23, 2024 at 01:27:35PM +0200, Andrius Merkys wrote: Since the freeze is drawing near, and rdkit is blocking a lot of packages, I would suggest considering shipping rdkit without 32bit support in trixie. This would cause all its

Bug#1092271: tahoe-lafs: please remove python3-mock from the build-dependencies

Control: tags -1 + pending Hi, On Mon, 06 Jan 2025 19:27:38 +0100 Alexandre Detiste wrote: This software has been adapted upstream to use the newer unittest.mock from the standard library. The one "python3-mock" line can now be removed from debian/control I removed python3-mock and pushed

Bug#1059316: epics-base: CVE-2023-33460

Hi Moritz, On 2025-01-03 15:25, Moritz Mühlenhoff wrote: I had a closer look, turns out the embedded/forked copy of yajl is actually so old, that epics-base isn't affected. Closing. Thanks for giving this a deeper look! Andrius

Bug#1092006: epics-base: procedure to update debian/control

Hi Santiago, On 2025-01-03 14:25, Santiago Vila wrote: Hi. While including the diff from Niels today I noticed that debian/control depends on debian/control.in in this way: debian/control: debian/control.in debian/rules     [commands to generate debian/control]     [...] override_dh_

Bug#1089319: epics-base: diff for NMU version 7.0.8.1+dfsg1-6.1

On 2025-01-03 10:58, Santiago Vila wrote: AFAIK, NMUs may only be cancelled by whoever makes them. If I use -7 as version (with credit for the changes, of course), then Niels can cancel the NMU or just forget about it and let it to be autorejected (as dak will detect that 6.1 < 7). Great, thank

Bug#1089319: epics-base: diff for NMU version 7.0.8.1+dfsg1-6.1

Hi Santiago, On 2025-01-03 10:48, Santiago Vila wrote: I'd like to see a team upload of this one including the changes from Niels, and also a pending CVE (#1059316). Would I still allowed to do that? This sounds even better. I have never cancelled a DELAYED upload myself, but if you know how

Bug#1089319: epics-base: diff for NMU version 7.0.8.1+dfsg1-6.1

Hi Niels, On 2025-01-02 19:22, Niels Thykier wrote: I've prepared an NMU for epics-base (versioned as 7.0.8.1+dfsg1-6.1) and uploaded it to DELAYED/5. Please feel free to tell me if I should delay it longer. I am OK with DELAYED/5. Could you please push your changes to salsa as well? Thanks,

Bug#1091856: libjson-validator-perl: Requires cache symlink for v3.0 schema

Hello, On 2025-01-01 19:03, gregor herrmann wrote: Control: tag -1 + confirmed On Wed, 01 Jan 2025 17:23:13 +0200, Wouter Verhelst wrote: Running 'strace -ff -o foo ; grep Validator.cache foo*' outputs: foo.146500:newfstatat(AT_FDCWD, "/usr/share/perl5/JSON/Validator/cache/a516498b60c53096b

Bug#1091570: simbody: FTBFS on i386: tests fail

Control: tags -1 + confirmed Hello, On 2024-12-28 18:37, Lucas Nussbaum wrote: The following tests FAILED: 5 - RandomTest (Failed) I can confirm this test fails. I tried building with DEB_BUILD_OPTIONS=noopt, but got the same result, so this is unrelated to optimization. The cod

Bug#1091895: ITP: exprtk -- C++ Mathematical Expression Toolkit Library Documentation

Package: wnpp Owner: Andrius Merkys Severity: wishlist * Package name: exprtk Version : 0.0.3 Upstream Author : Arash Partow * URL : https://github.com/ArashPartow/exprtk * License : Expat Programming Lang: C++ Description : C++ Mathematical

Bug#1091225: python-deadlib: please provide cgi module

Hi, On Thu, 26 Dec 2024, 18:02 Emmanuel Arias, wrote: > Please let us know if python3-legacy-cgi worked for you. If yes please > mark the bugs as done. > Sure, will get to it ASAP, will report and close the bug if successful. Andrius >

Bug#1091225: python-deadlib: please provide cgi module

Hi! On 2024-12-23 18:09, Alexandre Detiste wrote: You must feel stalked 🙂 :D python3-legacy-cgi is there waiting for you Awesome, thanks a lot, I will try it! Best, Andrius

Bug#1091225: python-deadlib: please provide cgi module

Source: python-deadlib Version: 3.13.0-3 Severity: wishlist Control: block 1079794 by -1 Hello, Please provide the 'cgi' module. This is needed to update tahoe-lafs to its newest upstream release (#1079794). Andrius

Bug#1083076: [Debichem-devel] Bug#1083076: 1083076 affects armel too

Hi, On Thu, 28 Nov 2024 18:40:07 +0100 Michael Banck wrote: On Thu, Nov 28, 2024 at 09:40:01AM +0200, Andrius Merkys wrote: > The same issue persists on armel too. I think we should add autopkgtest to > possibly identify other architectures having this issue. Looks like to be a general

Bug#1090086: RM: bespokesynth [mips64el] -- ROM; unsatisfiable build-depends on juce-modules-source

Package: ftp.debian.org Severity: normal Hello, Please remove bespokesynth binaries for mips64el. Build dependency on juce-modules-source is no longer satisfiable there. Andrius

Bug#1089231: dials: autopkgtest regression in testing

Hello, On 2024-12-07 15:56, Graham Inggs wrote: 219s from .pinkindexer import PinkIndexer 219s /usr/lib/python3/dist-packages/dials/algorithms/indexing/lattice_search/pinkindexer.py:5: in 219s import gemmi 219s E ModuleNotFoundError: No module named 'gemmi' dials autopkgtest apparently does

Bug#1061479: mk-origtargz: support lz compression

control: tags -1 + patch control: forwarded -1 https://salsa.debian.org/debian/devscripts/-/merge_requests/441 Hello, I have prepared a patch implementing this functionality. Andrius

Bug#1088896: [Debichem-devel] Bug#1088896: smiles-scripts: FTBFS: scripts/smi_isomorphism: -(1) XXXXXXX: different number of moieties [...], 1 vs. 2

Control: tags -1 + confirmed Control: owner -1 ! Hello, On 2024-12-02 18:48, Santiago Vila wrote: Package: src:smiles-scripts Version: 0.2.0+dfsg1-6 Severity: serious Tags: ftbfs Dear maintainer: During a rebuild of all packages in unstable, your package failed to build This happens due to

Bug#1088671: lintian: New check requested: 'nproc' used in debian/rules instead of DEB_BUILD_OPTION_PARALLEL

Hi Michael, On 2024-11-29 12:30, Michael R. Crusoe wrote: It would be great if there was a check for calling `nproc` from debian/rules. Fair point. I looked at codesearch.debian.net for regex 'path:debian/rules \bnproc\b', all hits seem to be true positives. Andrius

Bug#1083076: 1083076 affects armel too

control: retitle -1 python3-rdkit: SEGFAULT on import on armhf and armel Hello, The same issue persists on armel too. I think we should add autopkgtest to possibly identify other architectures having this issue. Andrius

Bug#1083076: found in rdkit/202409.2-2 as well

control: found -1 202409.2-2 Hello, The issue with segmentation fault on armhf persists in rdkit/202409.2-2 as well. Andrius

Bug#1088334: transition: openstructure

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition Hello, I would like to request a transition slot for openstructure (experimental -> unstable) due to soname bump. Current ben tracker [1] is OK. openstructure has a single reverse depe

Bug#1088028: megahit: consider unembedding parallel-hashmap

Source: megahit Version: 1.2.9-5 Severity: wishlist Hello, megahit embeds a copy of parallel-hashmap, a header-only library provided in Debian package libparallel-hashmap-dev. Please consider unembedding parallel-hashmap to reduce the redundant code copies in Debian. Andrius

Bug#1088027: salmon: consider unembedding parallel-hashmap

Source: salmon Version: 1.10.2+ds1-1 Severity: wishlist Hello, salmon embeds a copy of parallel-hashmap, a header-only library provided in Debian package libparallel-hashmap-dev. Please consider unembedding parallel-hashmap to reduce the redundant code copies in Debian. Andrius

Bug#1088026: spades: consider unembedding parallel-hashmap

Source: spades Version: spades_3.15.5+dfsg-7 Severity: wishlist Hello, spades embeds a copy of parallel-hashmap, a header-only library provided in Debian package libparallel-hashmap-dev. Please consider unembedding parallel-hashmap to reduce the redundant code copies in Debian. Andrius

Bug#1088025: apache-opennlp: run upstream test suite

Source: apache-opennlp Version: 2.5.0-1 Severity: normal Hello, In 2.5.0-1 I have disabled the upstream test suite as it was failing due to some unpackaged or too old dependencies in the testing subsystem. This is to remind me (and others) to investigate deeper and enable the tests again. A

Bug#1088024: python-docx-template: (autopkg)tests run for default Python only

Source: python-docx-template Version: 0.19.0+dfsg-1 Severity: normal Hello, Due to the upstream test suite running Python as an external subprocess, there is no easy way to vary the Python interpreter for it. One possibility would be to patch the test runner to take the interpreter name from

Bug#1085136: python3-mongomock: It no longer seems to work with the current pymongo

Hi, On Tue, 15 Oct 2024 11:39:58 +0200 "Salvo \"LtWorf\" Tomaselli" wrote: Dear Maintainer, unfortunately pymongo changed API This python code no longer works from mongomock import gridfs gridfs.enable_gridfs_integration() I am not familiar with the package. There seems to be a new upstrea

Bug#1087550: cmake-data: FindZLIB.cmake fails to populate ZLIB_INCLUDE_DIRS and ZLIB_LIBRARIES

Package: cmake-data Version: 3.31.0-1 Severity: important Affects: macromoleculebuilder Control: block 1086362 by -1 Hello, FindZLIB.cmake does not populate the declared result variables ZLIB_INCLUDE_DIRS, ZLIB_LIBRARIES and so on. In fact, it seems as if it does not find ZLIB at all (ZLIB_FOU

Bug#1086353: apache-opennlp: FTBFS: autobuilder hangs

Control: tags -1 + confirmed On 10/30/24 13:15, Santiago Vila wrote: [INFO] --- [INFO]  T E S T S [INFO] --- E: Build killed with signal TERM after 60 minutes of inactivity ---

Bug#1086704: ITP: ossia-score -- ossia score is a sequencer for audio-visual artists, designed to enable the creation of interactive shows, museum installations, intermedia digital artworks, interacti

Hi Jean-Michaël. On 11/4/24 15:35, Jean-Michaël Celerier wrote: Description : ossia score is a sequencer for audio-visual artists, designed to enable the creation of interactive shows, museum installations, intermedia digital artworks, interactive music and more in an intuitive user interf

Bug#1068692: python-pycddl: RFP -> ITP

control: retitle -1 ITP: python-pycddl -- deserialize CBOR control: owner -1 ! Hello, I have made considerable progress in packaging python-pycddl. Thus I am taking on the ITP. Andrius

Bug#1085644: ITP: rust-cddl -- Parser for the Concise data definition language - rust source code

Package: wnpp Owner: Andrius Merkys Severity: wishlist Control: block 1068692 by -1 * Package name: rust-cddl Version : 0.9.4 Upstream Author : Andrew Weiss * URL : https://cddl.anweiss.tech * License : Expat Programming Lang: Rust Description

Bug#1085441: RM: juce [mips64el] -- ROM; does not build on mips64el

Hi, On Sat, 19 Oct 2024, 17:51 IOhannes m zmoelnig, wrote: > please remove the mips64el binary packages produced by src:juce > Thanks for taking care of this! Best, Andrius >

Bug#1084629: espresso, wannier90: 'pipes' used in shared code

Control: tags -1 + patch Hello, espresso and wannier90 share an embedded library called 'testcode'. This library uses 'pipes', and this is the only deprecated module in both these source packages. I managed to successfully replace 'pipes' with 'shlex' [1] and will apply the same patch to both

Bug#1083076: python3-rdkit: SEGFAULT on import on armhf

Package: python3-rdkit Version: 202309.3-7 Severity: important Hello, python3-rdkit encounters SEGFAULT on import on armhf: $ python3 Python 3.12.6 (main, Sep 7 2024, 14:20:15) [GCC 14.2.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> from rdkit import Ch

Bug#1082878: [Debichem-devel] Bug#1082878: python3-gemmi: Please add the dist-info data's

Hello, On 2024-09-27 19:23, Picca Frédéric-Emmanuel wrote: While preparing the new version of dials, I discoverd that the gemmi dependency was not automatically generated during the packaging process. Indeed, python3-gemmi does not provide the necessary dist-info. Could you be so kind to add

Bug#1081606: debian/maven.rules help needed for cdk

Hi Emmanuel, On 2024-09-28 00:51, Emmanuel Bourg wrote: Le 27/09/2024 à 14:47, Andrius Merkys a écrit : cdk-data is an artifact of the same project, however, I cannot make maven detect it. I am almost sure the problem is due to some misconfiguration in debian/maven.rules, but I cannot find

Bug#1082747: cod-tools: FTBFS (only) on riscv64

Hello, I am one of the upstream developers of cod-tools. Thanks a lot everyone for tracking down the issue and coming up with a patch. On 2024-09-29 22:52, Santiago Vila wrote: El 29/9/24 a las 20:21, Aurelien Jarno escribió: 1) Defining the rule with an absolute path: I would have gone wi

Bug#1081606: debian/maven.rules help needed for cdk

Hello, I am trying to enable tests for cdk package on branch on salsa [1]. Build is failing with the following: [INFO] [INFO] BUILD FAILURE [INFO] ---

Bug#1082612: lintian: Argument "v0.902.0" isn't numeric in numeric lt (<) at /usr/share/lintian/lib/Lintian/Check/Debian/Upstream/Metadata.pm line 106

control: tags -1 + patch control: owner -1 ! On 2024-09-23 20:10, gregor herrmann wrote: On Mon, 23 Sep 2024 11:47:30 +0300, Andrius Merkys wrote: A simple fix would be to parse both versions using Perl version package from libversion-perl and then compare. Ack. An example can be seen at

Bug#1082747: cod-tools: FTBFS (only) on riscv64

Hi, On 2024-09-25 18:30, gregor herrmann wrote: I noticed that cod-tools 3.10.0+dfsg-1.1 fails to build but only on riscv64: https://buildd.debian.org/status/package.php?p=cod-tools https://buildd.debian.org/status/logs.php?pkg=cod-tools I care about this issue because 1) I uploaded the -1.1 N

Bug#1082612: lintian: Argument "v0.902.0" isn't numeric in numeric lt (<) at /usr/share/lintian/lib/Lintian/Check/Debian/Upstream/Metadata.pm line 106

Hi, On 2024-09-23 20:10, gregor herrmann wrote: On Mon, 23 Sep 2024 11:47:30 +0300, Andrius Merkys wrote: When running lintian on wannier90_3.1.0+ds-9.dsc which I have just uploaded, I got the following warning: Warning in processable ./wannier90_3.1.0+ds-9.dsc: Argument "v0.902.0&q

Bug#1082731: expect: unbuffer fails with "can't find package Expect"

Package: expect Version: 5.45.4-3 Severity: important Affects: src:pdb-tools Hello, When installed on clear chroot, unbuffer fails to start with: can't find package Expect while executing "package require Expect" (file "/usr/bin/unbuffer" line 6) I noticed this when building pdb-tools

Bug#1077055: [Debichem-devel] Bug#1077055: Bug#1077055: postgresql-16-rdkit: inchi support not included in rdkit build

Hi David, On 2024-09-24 17:09, David Lounsbrough wrote: I ran this inside my Docker container, it says the latest version of the package is installed: # apt-get -s install postgresql-16-rdkit Reading package lists... Done Building dependency tree... Done Reading state information... Done postg

Bug#1077055: [Debichem-devel] Bug#1077055: Bug#1077055: postgresql-16-rdkit: inchi support not included in rdkit build

Hi, On 2024-09-24 16:30, David Lounsbrough wrote: Hi, I am simply standing up a Postgres database with this package installed in it. This is the entire Dockerfile I am using: ``` FROM postgres:16 AS postgres-env RUN apt-get update && \   apt-get install -yq postgresql-16-rdkit && \   apt-ge

Bug#1075155: libccp4: ftbfs with GCC-14

control: severity -1 important Hello, I have added -Wno-incompatible-pointer-types to CFLAGS for now, avoiding FTBFS in order to let all reverse dependencies migrate before the freeze. The upstream is informed about the issue, -Wno-incompatible-pointer-types should be removed as soon as prope

Bug#1082109: [Debichem-devel] Bug#1082109: Bug#1082109: inchi: support for .sdf (v3000 dialect) is not functional

control: reassign -1 src:inchi control: owner -1 ! control: tags -1 + confirmed Dear Norwid, I managed to get inchi-1 executable to build and ensured that it passes the test with pyridine.sdf which you have described. Will upload the fixed package soon. Best, Andrius

Bug#1077055: [Debichem-devel] Bug#1077055: postgresql-16-rdkit: inchi support not included in rdkit build

Control: tags -1 + moreinfo Hi David, On Thu, 25 Jul 2024 12:05:55 -0500 David Lounsbrough wrote: To reproduce, I simply ran this Dockerfile: FROM postgres:16 AS postgres-env RUN apt-get update && \ apt-get install -yq postgresql-16-rdkit && \ apt-get clean Then when I try to build a

Bug#1082109: [Debichem-devel] Bug#1082109: Bug#1082109: inchi: support for .sdf (v3000 dialect) is not functional

Dear Norwid, On 2024-09-23 12:29, Norwid Behrnd via Debichem-devel wrote: In the more general case of a .mol/.sdf file about models with multiple atoms and at least one explicit bond, the reference executable of InChI 1.07.1 is able to process data in the v3000 dialect. Their executable publish

Bug#1082612: lintian: Argument "v0.902.0" isn't numeric in numeric lt (<) at /usr/share/lintian/lib/Lintian/Check/Debian/Upstream/Metadata.pm line 106

Package: lintian Version: 2.118.2 Hello, When running lintian on wannier90_3.1.0+ds-9.dsc which I have just uploaded, I got the following warning: Warning in processable ./wannier90_3.1.0+ds-9.dsc: Argument "v0.902.0" isn't numeric in numeric lt (<) at /usr/share/lintian/lib/Lintian/Check/D

Bug#1082109: [Debichem-devel] Bug#1082109: inchi: support for .sdf (v3000 dialect) is not functional

Hi Norwid, On 2024-09-18 16:13, Norwid Behrnd via Debichem-devel wrote: The compiled reference executable of InChI 1.07.1[1] for Linux 64bit assigns InChI for .sdf in either v2000, or v3000 dialect. While replying to an issue report,[2] I noticed `inchi_main` as packaged by DebiChem currently s

Bug#1078202: restfuldb: diff for NMU version 0.16.0+dfsg-1.1

Hi, On 2024-09-17 00:55, gregor herrmann wrote: I've prepared an NMU for restfuldb (versioned as 0.16.0+dfsg-1.1) and uploaded it to DELAYED/5. Please feel free to tell me if I should delay it longer. Thanks a lot for taking care of this issue. DELAYED/5 is fine with me. Andrius

Bug#1078097: cod-tools: diff for NMU version 3.10.0+dfsg-1.1

Hi, On 2024-09-17 00:48, gregor herrmann wrote: I've prepared an NMU for cod-tools (versioned as 3.10.0+dfsg-1.1) and uploaded it to DELAYED/5. Please feel free to tell me if I should delay it longer. Thanks a lot for taking care of this issue. DELAYED/5 is fine with me. Andrius

Bug#1081843: libstar-parser-perl: homepage defunct

Control: tags -1 + patch Hi, On 2024-09-15 16:51, Ben Tris wrote: The current homepage seems not to exist. http://pdb.sdsc.edu/STAR/ No alternative found. This has one nice simple page. https://www.iucr.org/resources/cif/software/starparser I agree that iucr.org webpage for starparser would

Bug#1081606: cdk: run upstream tests during build

Source: cdk Severity: wishlist Forwarded: https://salsa.debian.org/java-team/cdk/-/tree/with-tests Tags: help Hello, cdk includes an extensive testsuite. To ensure the built package's integrity, it would be nice to run the testsuite during build. According to git log, there were several unsucc

Bug#1075155: libccp4: ftbfs with GCC-14

control: forwarded -1 c...@dl.ac.uk Hello, I re-forwarded the issue to ccp4@ and got reply that the upstream has recorded the bug in their internal issue tracker. Andrius

Bug#1079981: transition: inchi

Hi Sebastian, On 2024-09-08 22:10, Sebastian Ramacher wrote: On 2024-09-08 14:21:57 +0300, Andrius Merkys wrote: inchi has migrated to testing and all its binary reverse dependencies seem to have switched from libinchi1 to libinchi1.07. However, transition tracker [1] shows the reverse

Bug#585905: cassandra: ITP -> RFP

retitle 585905 RFP: cassandra -- highly scalable distributed datastore noowner 585905 thanks Hello, I am giving up my efforts to package cassandra. My latest packaging attempt (year 2019) can be found at salsa [1]. In short, I managed to collect all the dependencies, but I failed to get cassan

Bug#1009673: RM: swagger-core -- RoM; not needed

severity 1009673 normal retitle 1009673 RM: swagger-core -- RoM; not needed reassign 1009673 ftp.debian.org affects 1009673 + src:swagger-core thanks Hello, Two years ago I offered src:swagger-core for adoption. Since no one was interested, and it has no reverse dependencies, I am asking for it

Bug#1079981: transition: inchi

Hi, inchi has migrated to testing and all its binary reverse dependencies seem to have switched from libinchi1 to libinchi1.07. However, transition tracker [1] shows the reverse dependencies as partially migrated - what could be the issue with them? Andrius [1] https://release.debian.org/tr

Bug#1080517: [Debichem-devel] Bug#1080517: jni-inchi: FTBFS with inchi 1.07.1

Hi, An upload of -8 has failed somewhy, I will retry ASAP. Andrius

Bug#1080050: Should mbdyn be removed from unstable?

Control: severity -1 normal Control: retitle -1 RM: mbdyn -- RoM; rc-buggy Control: reassign -1 ftp.debian.org Control: affects -1 + src:mbdyn Hello, On 2024-08-30 07:32, Helmut Grohne wrote: I suggest removing mbdyn from Debian for the following reasons: * It accumulated one RC-bug: + #9

Bug#1080035: ITP: jna-inchi -- wrapper to access InChI from Java

Package: wnpp Owner: Andrius Merkys Severity: wishlist Control: block -1 by 1079981 * Package name: jna-inchi Version : 1.2.1 Upstream Author : Daniel Lowe * URL : https://github.com/dan2097/jna-inchi * License : LGPL-2.1+ Programming Lang: Java

Bug#964773: 964773: inchi to become free software again

control: tags -1 - wontfix control: owner -1 ! On Fri, 15 Mar 2024 13:12:14 +0200 Andrius Merkys wrote:> An update: the upcoming inchi release is going to be licensed under Expat [1]. Thus an opportunity may appear to build rdkit with inchi support. rdkit builds successfully with libin

Bug#1079981: transition: inchi

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition Hello, I would like to request a transition slot for inchi (experimental -> unstable) due to soname bump. Current ben tracker [1] is OK. Rebuild results for reverse dependencies: * jni

Bug#1079894: rust-abnf-core: seemingly incorrect homepage

Source: rust-abnf-core Version: 0.6.0-3 Hello, Homepage field in debian/control seems off: it points to https://github.com/duesee/imap-codec while debian/watch points to https://github.com/duesee/abnf-core. Andrius

Bug#1079604: epics-base:FTBFS:build failure (not support riscv64)

Hi Yue, On 2024-08-25 08:24, Yue Gui wrote: Dear epics-base Maintainer, The package epics-base build failed on arch riscv64.The crucial buildd log below: [snip] My solution to this issue: Add riscv64 support for this package. I have completed the development of the patch for supporting the

Bug#1064024: juce: FTBFS on mips64el: Failed to build juceaide

Hello, It seems that the global offset table gets exceeded for mips64el even with -mxgot. As the trixie freeze is drawing near I would suggest RMing juce binaries (and their reverse dependencies) for mips64el for the time being. Andrius

Bug#1079794: tahoe-lafs: package new upstream release 1.19.0

Source: tahoe-lafs Severity: wishlist Control: block -1 by 1068692 Hello, New upstream release 1.19.0 is out. This bug is to track the process of updating tahoe-lafs to it. Andrius

Bug#1075155: libccp4: ftbfs with GCC-14

control: forwarded -1 ccp4-...@dl.ac.uk Hello, The actual log excerpt reporting build failure is the following: fortran/cmtzlib_f.c: In function 'lrhist_': fortran/cmtzlib_f.c:279:43: error: passing argument 2 of 'ccp4_lrhist' from incompatible pointer type [-Wincompatible-pointer-types] 27

Bug#1076519: #1076519: inchi packaging status

control: owner -1 ! control: forwarded -1 https://salsa.debian.org/debichem-team/inchi/-/tree/package/1.07 Hello, I started working on packaging inchi 1.07.1 in a branch on salsa.debian.org. Right now I am working on refreshing patches. Andrius

Bug#1077055: [Debichem-devel] Bug#1077055: postgresql-16-rdkit: inchi support not included in rdkit build

Hi David, On 7/25/24 18:51, David Lounsbrough via Debichem-devel wrote: I wanted to ask if there's a reason that `inchi` support is not enabled for this package. You can read more about the attempts to enable InChI support in rdkit in [1]. In short, inchi package in Debian seems incompatible

Bug#1076519: [Debichem-devel] Bug#1076519: libinchi1: new version 1.07 of InChI (now MIT license scheme)

provides the software equivalent to version 1.03/June 15, 2010. While Andrius Merkys thankfully packaged this version in 2019, there already was the request to provide the community a package corresponding to a more recent version of InChI. However, starting with version 1.04 (September 2011

Bug#1074897: cura-engine: ftbfs with GCC-14

Control: retitle -1 rapidjson: causes FTBFS with GCC-14 Control: block 1075335 by -1 Control: block 1075439 by -1 Hello, When building other packages with rapidjson-dev with GCC-14, the following failure occurs: /usr/include/rapidjson/document.h: In member function ‘rapidjson::GenericStringR

Bug#1075834: [Debichem-devel] Bug#1075834: Bug#1075834: python3-ase: new upstream release available

Hi, On 7/8/24 21:11, Graham Inggs wrote: On Sat, 6 Jul 2024 at 02:45, Drew Parsons wrote: debian/watch is broken. gitlab access to the tarballs is confusing, and I wasn't able to find a simple fix for debian/watch Apparently, this changed in gitlab in March, 2024 [1]. version=4 opts="searchm

Bug#1056457: spglib 2.2.0-3 builds for all supported Python versions

Hello, Since 2.2.0-3 spglib builds for all supported Python versions. Thus the autopkgtest for all supported Python versions can be turned back on. Andrius

Bug#1073561: [Debichem-devel] Bug#1073561: openbabel: FTBFS: failing tests test_tautomer_2[27]

control: tags -1 + unreproducible control: severity -1 normal On 2024-06-30 18:53, Michael Banck wrote: Hi, On Sat, Jun 29, 2024 at 10:21:02PM +0300, Adrian Bunk wrote: On Mon, Jun 17, 2024 at 04:58:46PM +0300, Andrius Merkys wrote: Source: openbabel Version: 3.1.1+dfsg-9 Severity: serious

Bug#1073494: ITP: openapi-schema-validator -- Validate schema against the OpenAPI Schema Specifications

On 2024-06-27 23:20, Julian Gilbey wrote: It's the other way round, but I'll add you anyway. Thanks! Best, Andrius

Bug#1073455: [Debichem-devel] Bug#1073455: openstructure: FTBFS: TypeError: unsupported operand type(s) for -: 'NoneType' and 'float'

control: forwarded -1 openstructure-us...@maillist.unibas.ch On 2024-06-16 16:08, Lucas Nussbaum wrote: == ERROR: testSpearmanCorrel (__main__.TestTable.testSpearmanCorrel) ---

Bug#1073494: ITP: openapi-schema-validator -- Validate schema against the OpenAPI Schema Specifications

Hi Julian, On 2024-06-17 19:34, Julian Gilbey wrote: Super, thanks! I'll add you now. Would you also like to be added to python-openapi-spec-validator? I gather python-openapi-spec-validator is a dependency of python-openapi-schema-validator, right? If so, you can add me. It will be team

Bug#1073494: ITP: openapi-schema-validator -- Validate schema against the OpenAPI Schema Specifications

On 2024-06-16 17:43, Julian Gilbey wrote: * Package name: openapi-schema-validator Version : 0.6.2 Upstream Author : Artur Maciag * URL : https://github.com/python-openapi/openapi-schema-validator * License : BSD-3-clause Programming Lang: Python Descr

Bug#1073561: openbabel: FTBFS: failing tests test_tautomer_2[27]

Source: openbabel Version: 3.1.1+dfsg-9 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs Hi, openbabel FTBFS both in unstable (if a fix for #1073327 is applied) and testing with the following: 99% tests passed, 2 tests failed out of 229 Total Test time (real) = 317.34 sec The f

Bug#1073327: [Debichem-devel] Bug#1073327: openbabel: FTBFS: xml.cpp:245:39: error: invalid conversion from ‘const xmlError*’ {aka ‘const _xmlError*’} to ‘xmlError*’ {aka ‘_xmlError*’} [-fpermissive]

Hello, On 2024-06-16 15:48, Lucas Nussbaum wrote: /<>/src/formats/xml/xml.cpp:245:39: error: invalid conversion from ‘const xmlError*’ {aka ‘const _xmlError*’} to ‘xmlError*’ {aka ‘_xmlError*’} [-fpermissive] 245 | xmlError* perr = xmlGetLastError(); |

Bug#1006482: lintian: non-standard-dir-in-var var/db/

Hi, On 2024-06-17 15:09, Maytham Alsudany wrote: Control: tags -1 + moreinfo On Sat, 26 Feb 2022 10:07:32 +0200 Martin-Éric Racine wrote: Lintian incorrectly reports /var/db/ as non-standard-dir-in-var. /var/db Data bank

Bug#1072576: coot: save its states in HOME.

On 2024-06-11 07:54, Paul Emsley wrote: I have been a bit sloppy with my file names and you should not be. Let's call the "refmac-dictionary" the "ccp4-monomer-library" OK, I will rename it to 'ccp4-monomer-library'. This is where it lives: https://github.com/MonomerLibrary/monomers Looki

Bug#1072576: coot: save its states in HOME.

Hi, On 2024-06-11 07:50, Paul Emsley wrote: OK, so 1.1.09 should now read and save the state and config files in an XDG Base Directory compliant manner. Thanks. I will update the Debian package ASAP. I have cleaned up some of the terminal output (it is verbose because doing so helps me diagn

Bug#1057556: elpa: FTBFS: not enough slots available

Control: owner -1 ! On Fri, 31 May 2024 14:46:28 +0200 Santiago Vila wrote:> Instead of patch-2.txt and patch-3.txt, the following more simple patch would also fix the issue (I've tested it on single-cpu systems and also on m6a.large instances from AWS, which have 1 core and two threads). (S

Bug#1072576: coot: save its states in HOME.

On 2024-06-05 10:13, Andrius Merkys wrote: The REFMAC dictionary packaged in Debian as refmac-dictionary needs some adjustment to make usable by coot and make the messages above go away. I have the fix for refmac-dictionary at hand, by the way. I will upload it soon. Andrius

Bug#1072576: coot: save its states in HOME.

Control: tags -1 + confirmed Hi, On 2024-06-04 17:31, Picca Frédéric-Emmanuel wrote: While using coot I found that it save it's states in these files DEBUG:: saving state to filename 0-coot.state.py State file 0-coot.state.py written. State file 0-coot-history.py written. State file 0-coot-his

Bug#1072618: coot: layla fails to start unless LD_LIBRARY_PATH is specified

Package: coot Version: 1.1.08+dfsg-3 Severity: important Forwarded: https://github.com/pemsley/coot/issues/120 layla executable fails to start unless LD_LIBRARY_PATH is given for it to locate the coot private libraries, e.g.: $ LD_LIBRARY_PATH=/usr/lib/ layla A thin wrapper is needed to set t

Bug#1072564: nmu: cctbx_2023.12+ds2+~3.17.0+ds1-4 clipper_ 2.1.20201109-2 libpdb-redo_3.0.5-2 ssm_1.4.0-2

Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: binnmu Hello, I want to request binNMU on packages which are affected by libccp4 soname change due to time_t64 transition: nmu cctbx_2023.12+ds2+~3.17.0+ds1-4 . ANY . unstable . -m "Rebuild

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