[med-svn] [Git][med-team/cufflinks][master] 5 commits: Enable build using gcc-11 by forcing -std=c++14
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon Nov 8 13:26:15 GMT 2021
Andreas Tille pushed to branch master at Debian Med / cufflinks
Commits:
fbf4fbca by Andreas Tille at 2021-11-08T14:12:41+01:00
Enable build using gcc-11 by forcing -std=c++14
- - - - -
9b0f65f2 by Andreas Tille at 2021-11-08T14:13:17+01:00
Remove redundant debian/gbp.conf
- - - - -
1cd24bb3 by Andreas Tille at 2021-11-08T14:14:08+01:00
routine-update: Standards-Version: 4.6.0
- - - - -
ed5deb88 by Andreas Tille at 2021-11-08T14:17:50+01:00
cme fix dpkg-control
- - - - -
3f36fa54 by Andreas Tille at 2021-11-08T14:21:26+01:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- − debian/gbp.conf
- − debian/patches/gcc-11.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,13 @@
-cufflinks (2.2.1+dfsg.1-9) UNRELEASED; urgency=medium
+cufflinks (2.2.1+dfsg.1-9) unstable; urgency=medium
* Fix autoconf issue
Closes: #998241
+ * Enable build using gcc-11 by forcing -std=c++14
+ * Remove redundant debian/gbp.conf
+ * Standards-Version: 4.6.0 (routine-update)
+ * cme fix dpkg-control
- -- Andreas Tille <tille at debian.org> Tue, 02 Nov 2021 12:00:24 +0100
+ -- Andreas Tille <tille at debian.org> Mon, 08 Nov 2021 14:18:10 +0100
cufflinks (2.2.1+dfsg.1-8) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -17,7 +17,7 @@ Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
python3,
libeigen3-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/cufflinks
Vcs-Git: https://salsa.debian.org/med-team/cufflinks.git
Homepage: https://cufflinks.cbcb.umd.edu
@@ -31,11 +31,13 @@ Depends: ${shlibs:Depends},
Recommends: gffread
Enhances: tophat
Description: Transcript assembly, differential expression and regulation for RNA-Seq
- Cufflinks assembles transcripts, estimates their abundances, and tests for
- differential expression and regulation in RNA-Seq samples. It accepts aligned
- RNA-Seq reads and assembles the alignments into a parsimonious set of
- transcripts. Cufflinks then estimates the relative abundances of these
- transcripts based on how many reads support each one.
+ Cufflinks assembles transcripts, estimates their abundances, and
+ tests for differential expression and regulation in RNA-Seq samples.
+ It accepts aligned RNA-Seq reads and assembles the alignments into a
+ parsimonious set of transcripts. Cufflinks then estimates the
+ relative abundances of these transcripts based on how many reads
+ support each one.
.
- This package provides the binary of cufflinks and associated tools, i.e.
- compress_gtf, cuffcompare, cuffdiff, cuffmerge, cuffnorm, cuffquant and gtf_to_sam.
+ This package provides the binary of cufflinks and associated tools, i.e..
+ compress_gtf, cuffcompare, cuffdiff, cuffmerge, cuffnorm, cuffquant and
+ gtf_to_sam.
=====================================
debian/gbp.conf deleted
=====================================
@@ -1,4 +0,0 @@
-# This source package is managed with git-buildpackage and pristine-tar.
-
-[DEFAULT]
-pristine-tar = True
=====================================
debian/patches/gcc-11.patch deleted
=====================================
@@ -1,67 +0,0 @@
-Description: Attempt to fix gcc-11 issues with `byte` - but failed
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 02 Nov 2021 12:00:24 +0100
-
---- a/src/gdna.h
-+++ b/src/gdna.h
-@@ -9,7 +9,7 @@ char* reverseComplement(char* seq, int s
-
- bool gDnaInit();
-
--byte gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4)
--char g2bit2base(byte v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T'
-+std::byte gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4)
-+char g2bit2base(std::byte v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T'
-
- #endif
---- a/src/gff.h
-+++ b/src/gff.h
-@@ -16,11 +16,11 @@
- #endif
-
- /*
--const byte exMskMajSpliceL = 0x01;
--const byte exMskMajSpliceR = 0x02;
--const byte exMskMinSpliceL = 0x04;
--const byte exMskMinSpliceR = 0x08;
--const byte exMskTag = 0x80;
-+const std::byte exMskMajSpliceL = 0x01;
-+const std::byte exMskMajSpliceR = 0x02;
-+const std::byte exMskMinSpliceL = 0x04;
-+const std::byte exMskMinSpliceR = 0x08;
-+const std::byte exMskTag = 0x80;
- */
-
- //reserved Gffnames::feats entries -- basic feature types
-@@ -43,7 +43,7 @@ extern const uint gfo_flag_DISCARDED; //
- extern const uint gfo_flag_LST_KEEP; //GffObj from GffReader::gflst is to be kept (not deallocated)
- //when GffReader is destroyed
- extern const uint gfo_flag_LEVEL_MSK; //hierarchical level: 0 = no parent
--extern const byte gfo_flagShift_LEVEL;
-+extern const std::byte gfo_flagShift_LEVEL;
-
- extern bool gff_show_warnings;
-
-@@ -502,18 +502,18 @@ public:
- if (v) flags |= gfo_flag_CHILDREN_PROMOTED;
- else flags &= ~gfo_flag_CHILDREN_PROMOTED;
- }
-- void setLevel(byte v) {
-+ void setLevel(std::byte v) {
- if (v==0) flags &= ~gfo_flag_LEVEL_MSK;
- else flags &= ~(((uint)v) << gfo_flagShift_LEVEL);
- }
-- byte incLevel() {
-+ std::byte incLevel() {
- uint v=((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL);
- v++;
- flags &= ~(v << gfo_flagShift_LEVEL);
- return v;
- }
-- byte getLevel() {
-- return ((byte)((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL));
-+ std::byte getLevel() {
-+ return ((std::byte)((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL));
- }
-
- bool isValidTranscript() {
=====================================
debian/patches/series
=====================================
@@ -10,4 +10,3 @@ lib_eigen.patch
fix_gcc-6.1_issue_in_liblemon_code_copy.patch
gcc10.patch
no_svnversion.patch
-# gcc-11.patch
=====================================
debian/rules
=====================================
@@ -6,6 +6,8 @@ pkg := cufflinks
mandir := $(CURDIR)/debian/$(pkg)/usr/share/man/man1
bindir := $(CURDIR)/debian/$(pkg)/usr/bin
+export DEB_CFLAGS_MAINT_APPEND=-std=c++14
+
%:
dh $@ --with python3
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/compare/daa7a02557702a42b49de1b1768b6344e140f96e...3f36fa5495b7fa61292d8298321f412f1c52bfa3
--
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/compare/daa7a02557702a42b49de1b1768b6344e140f96e...3f36fa5495b7fa61292d8298321f412f1c52bfa3
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