[med-svn] [Git][med-team/rsem][master] 4 commits: stdgnu++11.patch: new: fix ftbfs with boost1.83.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Mon Dec 18 12:59:53 GMT 2023
Étienne Mollier pushed to branch master at Debian Med / rsem
Commits:
d223f7c1 by Étienne Mollier at 2023-12-18T13:53:43+01:00
stdgnu++11.patch: new: fix ftbfs with boost1.83.
boost1.83 looks to require building with gnu++11, but upstream
codebase is still at gnu++98 for now, hence the nature of the patch.
Closes: #1056010
- - - - -
59187720 by Étienne Mollier at 2023-12-18T13:54:23+01:00
d/control: declare compliance to standards version 4.6.2.
- - - - -
89241c5b by Étienne Mollier at 2023-12-18T13:57:36+01:00
d/control: build depend on libncurses-dev.
This replaces the obsolete libncurses5-dev.
- - - - -
7d77511a by Étienne Mollier at 2023-12-18T13:59:04+01:00
ready to upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/stdgnu++11.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,20 @@
-rsem (1.3.3+dfsg-3) UNRELEASED; urgency=medium
+rsem (1.3.3+dfsg-3) unstable; urgency=medium
+ * Team upload.
+
+ [ Andreas Tille ]
* Fix salca-ci since i386 is explicitly excluded by Build-Depends: bowtie2
- -- Andreas Tille <tille at debian.org> Thu, 09 Sep 2021 09:15:53 +0200
+ [ Étienne Mollier ]
+ * stdgnu++11.patch: new: fix ftbfs with boost1.83.
+ boost1.83 looks to require building with gnu++11, but upstream
+ codebase is still at gnu++98 for now, hence the nature of the patch.
+ (Closes: #1056010)
+ * d/control: declare compliance to standards version 4.6.2.
+ * d/control: build depend on libncurses-dev.
+ This replaces the obsolete libncurses5-dev.
+
+ -- Étienne Mollier <emollier at debian.org> Mon, 18 Dec 2023 13:58:36 +0100
rsem (1.3.3+dfsg-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
- libncurses5-dev,
+ libncurses-dev,
libboost-dev,
perl <!nocheck>,
python3:any,
@@ -16,7 +16,7 @@ Build-Depends: debhelper-compat (= 13),
# bowtie is a run-time dependency available on only a few systems, not actually
# needed for building but it prevents the creation of uninstallable packages
bowtie | bowtie2
-Standards-Version: 4.6.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/rsem
Vcs-Git: https://salsa.debian.org/med-team/rsem.git
Homepage: https://deweylab.github.io/RSEM/
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
hardening
use_debian_packaged_samtools.patch
2to3.patch
+stdgnu++11.patch
=====================================
debian/patches/stdgnu++11.patch
=====================================
@@ -0,0 +1,69 @@
+Description: port codebase to gnu++11.
+ Since boost 1.83, it is necessary to build rsem with C++ 2011 standard. This
+ patch bumps the -std=gnu++98 passed by upstream Makefil to -std=gnu++11. It
+ should become unnecessary once upstream bumped to C++ 2011 or later, or when
+ the package will not depend on boost anymore, in case this is in upstream's
+ agenda; there is a merge request open upstream to bump to -std=gnu++17 in the
+ meantime.
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug: https://github.com/deweylab/RSEM/pull/96
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1056010
+Last-Update: 2023-12-18
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- rsem.orig/Makefile
++++ rsem/Makefile
+@@ -12,7 +12,7 @@
+
+ # Compilation variables
+ CXX = g++
+-CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST)
++CXXFLAGS += -std=gnu++11 -Wall -I. -I$(BOOST)
+ CPPFLAGS ?=
+
+ LDFLAGS ?=
+--- rsem.orig/PairedEndHit.h
++++ rsem/PairedEndHit.h
+@@ -26,7 +26,7 @@
+
+ bool PairedEndHit::read(std::istream& in) {
+ conprb = 0.0;
+- return (in>>sid>>pos>>insertL);
++ return ((bool)(in>>sid>>pos>>insertL));
+ }
+
+ void PairedEndHit::write(std::ostream& out) {
+--- rsem.orig/SingleHit.h
++++ rsem/SingleHit.h
+@@ -43,7 +43,7 @@
+
+ bool SingleHit::read(std::istream& in) {
+ conprb = 0.0;
+- return (in>>sid>>pos);
++ return ((bool)(in>>sid>>pos));
+ }
+
+ void SingleHit::write(std::ostream& out) {
+--- rsem.orig/buildReadIndex.cpp
++++ rsem/buildReadIndex.cpp
+@@ -37,15 +37,15 @@
+ streampos pos = fin.tellg();
+ success = true;
+
+- success = (getline(fin, line));
++ success = ((bool)getline(fin, line));
+ if (!success) continue;
+- success = (getline(fin, line));
++ success = ((bool)getline(fin, line));
+ if (!success) continue;
+
+ if (hasQ) {
+- success = (getline(fin, line));
++ success = ((bool)getline(fin, line));
+ if (!success) continue;
+- success = (getline(fin, line));
++ success = ((bool)getline(fin, line));
+ if (!success) continue;
+ }
+
View it on GitLab: https://salsa.debian.org/med-team/rsem/-/compare/4a95720a688cb39826c581821ff4ae120450c82d...7d77511a9b2e955a9f35904b1c7dc8ce1806a289
--
View it on GitLab: https://salsa.debian.org/med-team/rsem/-/compare/4a95720a688cb39826c581821ff4ae120450c82d...7d77511a9b2e955a9f35904b1c7dc8ce1806a289
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20231218/e6110060/attachment-0001.htm>
More information about the debian-med-commit
mailing list