Sascha Steinbiss pushed to branch master at Debian Med / rna-star
Commits: 4322b3a8 by Sascha Steinbiss at 2026-08-19T17:08:44+02:00 fix building with new C++ standard - - - - - dd6b0836 by Sascha Steinbiss at 2026-08-19T17:09:15+02:00 improve d/copyright - - - - - 3cfc70d9 by Sascha Steinbiss at 2026-08-19T17:09:27+02:00 bump Standards-Version - - - - - 5fdf499b by Sascha Steinbiss at 2026-08-19T17:09:35+02:00 remove obsolete Priority from d/control - - - - - 5 changed files: - debian/changelog - debian/control - debian/copyright - + debian/patches/cpp11.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,8 +1,13 @@ -rna-star (2.7.11b+dfsg-3) UNRELEASED; urgency=medium +rna-star (2.7.11b+dfsg-3) unstable; urgency=medium * Update salsa-ci.yml to current Debian Med version. + * Add patch to fix building with new C++ standard. (Closes: #1143695) + * Bump copyright date for debian/ directory. + * Use correct email address in d/copyright. + * Bump Standards-Version. + * Remove obsolete Priority from d/control. - -- Sascha Steinbiss <[email protected]> Sat, 21 Feb 2026 18:22:54 +0100 + -- Sascha Steinbiss <[email protected]> Wed, 19 Aug 2026 09:27:56 +0200 rna-star (2.7.11b+dfsg-2) unstable; urgency=medium ===================================== debian/control ===================================== @@ -4,7 +4,6 @@ Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]>, Sascha Steinbiss <[email protected]>, Section: science -Priority: optional Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, architecture-is-little-endian, @@ -12,7 +11,7 @@ Build-Depends: debhelper-compat (= 13), xxd, zlib1g-dev, libsimde-dev -Standards-Version: 4.6.2 +Standards-Version: 4.7.4 Vcs-Browser: https://salsa.debian.org/med-team/rna-star Vcs-Git: https://salsa.debian.org/med-team/rna-star.git Homepage: https://github.com/alexdobin/STAR/ ===================================== debian/copyright ===================================== @@ -38,12 +38,12 @@ License: MIT Files: debian/* Copyright: 2015-2019 Steffen Moeller <[email protected]> - 2016-2019 Sascha Steinbiss <[email protected]> + 2016-2026 Sascha Steinbiss <[email protected]> 2015-2019 Andreas Tille <[email protected]> License: GPL-3+ Files: debian/tests/* -Copyright: 2016 Sascha Steinbiss <[email protected]> +Copyright: 2016 Sascha Steinbiss <[email protected]> License: GPL-3+ License: GPL-3+ ===================================== debian/patches/cpp11.patch ===================================== @@ -0,0 +1,35 @@ +Description: Fix C++ compatibility issues with operator>> on char* + The operator>> for char* seems to no longer work in later C++ standards. +Author: Sascha Steinbiss <[email protected]> +Forwarded: https://github.com/alexdobin/STAR/pull/2703 +Last-Update: 2026-08-19 +--- a/source/ReadAlignChunk_processChunks.cpp ++++ b/source/ReadAlignChunk_processChunks.cpp +@@ -163,12 +163,10 @@ + if (P.outSAMreadID=="Number") { + chunkInSizeBytesTotal[imate] += sprintf(chunkIn[imate] + chunkInSizeBytesTotal[imate], ">%llu", P.iReadAll); + } else { +- P.inOut->readIn[imate] >> (chunkIn[imate] + chunkInSizeBytesTotal[imate]); ++ P.inOut->readIn[imate].getline(chunkIn[imate] + chunkInSizeBytesTotal[imate], DEF_readNameSeqLengthMax + 1); + chunkInSizeBytesTotal[imate] += strlen(chunkIn[imate] + chunkInSizeBytesTotal[imate]); + }; + +- P.inOut->readIn[imate].ignore(DEF_readNameSeqLengthMax,'\n'); +- + chunkInSizeBytesTotal[imate] += sprintf(chunkIn[imate] + chunkInSizeBytesTotal[imate], " %llu %c %i \n", P.iReadAll, 'N', P.readFilesIndex); + }; + +--- a/source/readLoad.cpp ++++ b/source/readLoad.cpp +@@ -16,7 +16,10 @@ + istringstream line1str(line1); + + readName[0]=0;//clear char array +- line1str >> readName; //TODO check that it does not overflow the array ++ string readNameStr; ++ line1str >> readNameStr; ++ strncpy(readName, readNameStr.c_str(), DEF_readNameLengthMax-1); ++ readName[DEF_readNameLengthMax-1] = 0; // ensure null-termination + if (strlen(readName)>=DEF_readNameLengthMax-1) { + ostringstream errOut; + errOut << "EXITING because of FATAL ERROR in reads input: read name is too long:" << readInStream.gcount()<<"\nRead Name="<<readName<<"\nDEF_readNameLengthMax="<<DEF_readNameLengthMax<<'\n'; ===================================== debian/patches/series ===================================== @@ -6,3 +6,4 @@ do-not-enforce-avx2.patch gcc-12.patch packaged_simde fix_typos.patch +cpp11.patch View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/b84b2d0a971aa7958f2803c8786624abb407dd15...5fdf499b72d3b515aa91c86823b5be60e94cd293 -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/b84b2d0a971aa7958f2803c8786624abb407dd15...5fdf499b72d3b515aa91c86823b5be60e94cd293 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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