[med-svn] [Git][med-team/cufflinks][master] 9 commits: fix FTBFS with GCC 10
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Nov 2 11:10:21 GMT 2021
Andreas Tille pushed to branch master at Debian Med / cufflinks
Commits:
5f3ad429 by Andreas Tille at 2021-11-02T10:56:57+01:00
fix FTBFS with GCC 10
- - - - -
cd5534ee by Andreas Tille at 2021-11-02T10:56:57+01:00
routine-update: debhelper-compat 13
- - - - -
47f91116 by Andreas Tille at 2021-11-02T10:56:57+01:00
routine-update: Add salsa-ci file
- - - - -
d5754eb7 by Andreas Tille at 2021-11-02T10:56:57+01:00
cme fix dpkg-control
- - - - -
fdee7c12 by Andreas Tille at 2021-11-02T10:56:57+01:00
Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
463404e8 by Andreas Tille at 2021-11-02T10:56:57+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
e0f1b29a by Andreas Tille at 2021-11-02T10:56:57+01:00
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
- - - - -
88fffb27 by Andreas Tille at 2021-11-02T10:56:57+01:00
routine-update: Ready to upload to unstable
- - - - -
daa7a025 by Andreas Tille at 2021-11-02T12:10:06+01:00
Fix autoconf issue
- - - - -
8 changed files:
- debian/changelog
- debian/control
- + debian/patches/gcc-11.patch
- + debian/patches/gcc10.patch
- + debian/patches/no_svnversion.patch
- debian/patches/series
- + debian/salsa-ci.yml
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,27 @@
+cufflinks (2.2.1+dfsg.1-9) UNRELEASED; urgency=medium
+
+ * Fix autoconf issue
+ Closes: #998241
+
+ -- Andreas Tille <tille at debian.org> Tue, 02 Nov 2021 12:00:24 +0100
+
+cufflinks (2.2.1+dfsg.1-8) unstable; urgency=medium
+
+ [ Reiner Herrmann ]
+ * fix FTBFS with GCC 10
+ Closes: #966191
+
+ [ Andreas Tille ]
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Use secure URI in Homepage field.
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
+ * Remove obsolete field Name from debian/upstream/metadata (already present in
+ machine-readable debian/copyright).
+
+ -- Andreas Tille <tille at debian.org> Sun, 02 Aug 2020 10:02:34 +0200
+
cufflinks (2.2.1+dfsg.1-7) unstable; urgency=medium
* Team upload
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Uploaders: Alexandre Mestiashvili <mestia at debian.org>,
Section: non-free/science
XS-Autobuild: yes
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
help2man,
libboost-dev,
@@ -18,16 +18,16 @@ Build-Depends: debhelper-compat (= 12),
python3,
libeigen3-dev
Standards-Version: 4.5.0
-Rules-requires-root: no
Vcs-Browser: https://salsa.debian.org/med-team/cufflinks
Vcs-Git: https://salsa.debian.org/med-team/cufflinks.git
-Homepage: http://cufflinks.cbcb.umd.edu
+Homepage: https://cufflinks.cbcb.umd.edu
+Rules-Requires-Root: no
Package: cufflinks
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- ${python3:Depends},
+ ${python3:Depends}
Recommends: gffread
Enhances: tophat
Description: Transcript assembly, differential expression and regulation for RNA-Seq
=====================================
debian/patches/gcc-11.patch
=====================================
@@ -0,0 +1,67 @@
+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/gcc10.patch
=====================================
@@ -0,0 +1,17 @@
+Author: Reiner Herrmann <reiner at reiner-h.de>
+Description: Fix FTBFS with GCC 10
+ curwin is declared in different source file. declare it as extern
+ to fix multiple definition linker error.
+Bug-Debian: https://bugs.debian.org/966191
+
+--- a/src/locfit/startlf.c
++++ b/src/locfit/startlf.c
+@@ -233,7 +233,7 @@
+ extern lfit lf;
+ extern design des;
+ extern plots pl[];
+-int curwin;
++extern int curwin;
+ vari *vb;
+
+ INT nofit()
=====================================
debian/patches/no_svnversion.patch
=====================================
@@ -0,0 +1,25 @@
+Description: Prevent that AM_INIT_AUTOMAKE is called twice
+Bug-Debian: https://bugs.debian.org/998241
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 02 Nov 2021 12:00:24 +0100
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -6,14 +6,14 @@ m4_include([ax_bam.m4])
+ m4_include([ax_check_zlib.m4])
+ m4_include([ax_check_eigen.m4])
+
+-define([svnversion], esyscmd([sh -c "svnversion|tr -d '\n'"]))dnl
++#define([svnversion], esyscmd([sh -c "svnversion|tr -d '\n'"]))dnl
+ AC_INIT([cufflinks], [2.2.1], [cole at cs.umd.edu])
+-AC_DEFINE(SVN_REVISION, "svnversion", [SVN Revision])
++AC_DEFINE(SVN_REVISION, "Debian package", [Debian package])
+
+ AC_CONFIG_SRCDIR([config.h.in])
+ AC_CONFIG_HEADERS([config.h])
+ AC_CONFIG_AUX_DIR([build-aux])
+-AM_INIT_AUTOMAKE
++# AM_INIT_AUTOMAKE
+
+ #AM_PATH_CPPUNIT(1.10.2)
+
=====================================
debian/patches/series
=====================================
@@ -8,3 +8,6 @@ fix_gcc-7_ftbfs.patch
format-security.patch
lib_eigen.patch
fix_gcc-6.1_issue_in_liblemon_code_copy.patch
+gcc10.patch
+no_svnversion.patch
+# gcc-11.patch
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,5 +1,6 @@
Contact: Cole Trapnell <cole at cs.umd.edu>
-Name: Cufflinks
+Bug-Database: https://github.com/cole-trapnell-lab/cufflinks/issues
+Bug-Submit: https://github.com/cole-trapnell-lab/cufflinks/issues/new
Reference:
- Author: >
Cole Trapnell and Brian A Williams and Geo Pertea and
@@ -42,3 +43,5 @@ Registry:
Entry: cufflinks
- Name: conda:bioconda
Entry: cufflinks
+Repository: https://github.com/cole-trapnell-lab/cufflinks.git
+Repository-Browse: https://github.com/cole-trapnell-lab/cufflinks
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e
--
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e
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