[med-svn] [Git][med-team/rna-star][master] 4 commits: fix building with new C++ standard
Sascha Steinbiss (@satta)
gitlab at salsa.debian.org
Wed Aug 19 16:09:50 BST 2026
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 <satta at debian.org> Sat, 21 Feb 2026 18:22:54 +0100
+ -- Sascha Steinbiss <satta at debian.org> 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 <moeller at debian.org>,
Andreas Tille <tille at debian.org>,
Sascha Steinbiss <satta at debian.org>,
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 <moeller at debian.org>
- 2016-2019 Sascha Steinbiss <sascha at debian.org>
+ 2016-2026 Sascha Steinbiss <satta at debian.org>
2015-2019 Andreas Tille <tille at debian.org>
License: GPL-3+
Files: debian/tests/*
-Copyright: 2016 Sascha Steinbiss <sascha at steinbiss.name>
+Copyright: 2016 Sascha Steinbiss <satta at debian.org>
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 <satta at debian.org>
+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
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