Re: New kissplice version (2.6.0) and packaging changes
Hello, I've added more buildsystem changes as 3 commits, see commit messages for details : - update dependencies - final removal of gcc10 patch (fixed by upstream changes) - replacing the redirection script with a symlink for bcalm The new gcc compilation errors you noticed are related to an internal hashmap library ; its code did not age well. Replacing it with something more modern is planned long-term. In the meantime I fixed the most worrying warnings in a patch release of kissplice (2.6.1). I merged the new release in the salsa repository using `gbp import-orig --uscan`, and this was sufficient to fix the compilation error. Unfortunately while using gbp import-orig I did not notice that my upstream branch was not up-to-date with the gitlab one. The result is that my upstream branch (merged to master) has diverged with origin/upstream and cannot be pushed. What is the best way to fix this rookie mistake ? Force push to upstream, or merge commit ? Looking at the git history this kind of error already happened around the 2.5.0 release... The CI now fails because of dh_installdocs : https://salsa.debian.org/med-team/kissplice/-/jobs/2642625 . The current CMake setup will compile and install a user_guide.pdf to /usr/share/doc/kissplice/user_guide.pdf . Should the entry in debian/docs be simply removed ? Regards, François Gindraud - Mail original - > De: "Andreas Tille" > À: "Francois Gindraud" > Cc: "debian-med" > Envoyé: Vendredi 1 Avril 2022 14:04:28 > Objet: Re: New kissplice version (2.6.0) and packaging changes > Hi Francois, > > Am Thu, Mar 31, 2022 at 11:28:16AM +0200 schrieb Francois Gindraud: >> The new version of kissplice (2.6.0) has been published upstream. >> Due to internal build system and infrastructure changes, the packaging >> infrastructure requires a few changes. >> I had initially contacted Andreas Tille to signal that ahead of time ( [ >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2022-March/098822.html >> | >> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2022-March/098822.html >> ] ). >> >> I've prepared a commit with changes to [ >> https://salsa.debian.org/med-team/kissplice | >> https://salsa.debian.org/med-team/kissplice ] which should handle all >> build-system changes. >> >> I have not retrieved the new version from the upstream gitlab, as it seems to >> rely on automated git scripts I am not familiar with. > > Huh, a simple `git clone` should work. > >> In his reply, Andreas said to simply push my changes to master, but this >> seem to >> require access that I do not yet have. I've sent an access request to >> DebianMed. > > Ups, sorry, it seems the new gitlab did not sent any information mail > about the pending access request. I confirmed now. Please note that > I've meanwhile pushed some changes for the new upstream version. Please > also note that it does not build due to gcc errors: > > https://salsa.debian.org/med-team/kissplice/-/jobs/2627463 > > I've deactivated the gcc-10.patch > > > https://salsa.debian.org/med-team/kissplice/-/blob/master/debian/patches/gcc10.patch > > which did not apply any more but it might read that the code you are > using now is not fit for gcc-12. > > Kind regards > > Andreas. > > -- > http://fam-tille.de
Bug#1008128: marked as done (ITP: gatk-fermilite -- interface to call Heng Li's fermi-lite assembler from Java code)
Your message dated Tue, 05 Apr 2022 18:00:13 + with message-id and subject line Bug#1008128: fixed in gatk-fermilite 1.2.1+dfsg-1 has caused the Debian Bug report #1008128, regarding ITP: gatk-fermilite -- interface to call Heng Li's fermi-lite assembler from Java code to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1008128: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1008128 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems --- Begin Message --- Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: gatk-fermilite Version : 1.2.1 Upstream Author : Broad Institute * URL : https://github.com/broadinstitute/gatk-fermilite-jni * License : BSD-3-clause Programming Lang: Java, C Description : interface to call Heng Li's fermi-lite assembler from Java code Fml-asm (fermi-lite assembler) is a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size, based on the fermi-lite library. gatk-fermilite provides a Java library and a shared library to allow one to use fermilite from Java code. The package will be team-maintained inside Debian-med team. It is needed as a dependency of the packaging target gatk. --- End Message --- --- Begin Message --- Source: gatk-fermilite Source-Version: 1.2.1+dfsg-1 Done: Pierre Gruet We believe that the bug you reported is fixed in the latest version of gatk-fermilite, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1008...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Pierre Gruet (supplier of updated gatk-fermilite package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Format: 1.8 Date: Fri, 25 Mar 2022 21:43:37 +0100 Source: gatk-fermilite Binary: libgatk-fermilite-java libgatk-fermilite-jni libgatk-fermilite-jni-dbgsym Architecture: source all amd64 Version: 1.2.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: libgatk-fermilite-java - interface to call Heng Li's fermi-lite assembler from Java code libgatk-fermilite-jni - interface to call Heng Li's fermi-lite assembler from Java code ( Closes: 1008128 Changes: gatk-fermilite (1.2.1+dfsg-1) unstable; urgency=medium . * Initial release (Closes: #1008128) Checksums-Sha1: 6567afc6ca03af777ed743e633f22ef9d4cc28a2 2209 gatk-fermilite_1.2.1+dfsg-1.dsc 23608342ed1796d5e329645e6dcd8dcadbe4a3cd 12080 gatk-fermilite_1.2.1+dfsg.orig.tar.xz e0824a4359577685210fc9c4d93830cc345d9ef2 7432 gatk-fermilite_1.2.1+dfsg-1.debian.tar.xz 7a0938d235be49838952f30a096df2da2152898f 11706 gatk-fermilite_1.2.1+dfsg-1_amd64.buildinfo f9756d6383b7d9f87133858cd66785faa2aa71cc 11996 libgatk-fermilite-java_1.2.1+dfsg-1_all.deb 818c65da9d893440238f262180c72f5b6536e80d 12876 libgatk-fermilite-jni-dbgsym_1.2.1+dfsg-1_amd64.deb 5b8d95b80b66587e4bddec99336b15fbeef4e825 4704 libgatk-fermilite-jni_1.2.1+dfsg-1_amd64.deb Checksums-Sha256: 65442ef1a9755ee84ba435871825fd832cb6a2c4ef854c83bbeacf84d2dc37fa 2209 gatk-fermilite_1.2.1+dfsg-1.dsc c451f5e2a09a0472ec44d6707974086e6bbf8e5c02f35b619d2fc7bf5a503ab2 12080 gatk-fermilite_1.2.1+dfsg.orig.tar.xz b419e1f12fae3086c3a511a2c2e186f1d99bba6c73352f13fc07929575b77541 7432 gatk-fermilite_1.2.1+dfsg-1.debian.tar.xz 7691cc4947e6165870d0261ce3b066d1a6703094418b10ff2a0fbb58ce842d79 11706 gatk-fermilite_1.2.1+dfsg-1_amd64.buildinfo cd3555283cefdea1dd6806800aaf848da9e1d02a97ad0444a2e4f76a3b019775 11996 libgatk-fermilite-java_1.2.1+dfsg-1_all.deb 6fa9e5b0e926f232d55967d94086f3cabfeb9e1d7ac8f2a5597caaa12f94d43e 12876 libgatk-fermilite-jni-dbgsym_1.2.1+dfsg-1_amd64.deb 0acbe4cbdecd6d075db26d6d325f09d1ff1b2fa54969bb2c9ffe801546644dbd 4704 libgatk-fermilite-jni_1.2.1+dfsg-1_amd64.deb Files: 9f3c6936c9c3269b2bd8c25b03faf405 2209 java optional gatk-fermilite_1.2.1+dfsg-1.dsc ccac31ec944a7bb326f0dcbd5e667cf7 12080 java optional gatk-fermilite_1.2.1+dfsg.orig.tar.xz aa9ad090abfc68501acdc2f1efb341ed 7432 java optional gatk-fermilite_1.2.1+dfsg-1.debian.tar.xz f1c
