[med-svn] [Git][med-team/ivar][master] 4 commits: add forward-build-options.patch

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / ivar


Commits:
4c24e1b4 by Étienne Mollier at 2021-08-28T10:55:34+02:00
add forward-build-options.patch

This addresses ivar not being built with Debian default build options.

- - - - -
86054629 by Étienne Mollier at 2021-08-28T10:56:37+02:00
add gcc-11.patch

This fixes a failure to build from source with Gcc 11.

Closes: #984067

- - - - -
58108eb3 by Étienne Mollier at 2021-08-28T10:59:07+02:00
update changelog

- - - - -
66cbbce4 by Étienne Mollier at 2021-08-28T11:14:39+02:00
d/salsa-ci.yml: allow reprotest to fail, for now

- - - - -


5 changed files:

- debian/changelog
- + debian/patches/forward-build-options.patch
- + debian/patches/gcc-11.patch
- debian/patches/series
- debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+ivar (1.3.1+dfsg-2) UNRELEASED; urgency=medium
+
+  * add forward-build-options.patch; build ivar with Debian build options
+  * add gcc-11.patch; fixes ftbfs with Gcc 11  (Closes: #984067)
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 28 Aug 2021 10:57:25 +0200
+
 ivar (1.3.1+dfsg-1) unstable; urgency=medium
 
   [ Étienne Mollier ]


=====================================
debian/patches/forward-build-options.patch
=====================================
@@ -0,0 +1,33 @@
+Description: inject Debian build options
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2021-08-28
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- ivar.orig/src/Makefile.am
++++ ivar/src/Makefile.am
+@@ -1,6 +1,6 @@
+ LIBS = -lhts -lz -lpthread
+ 
+-CXXFLAGS = -v -g -std=c++11 -Wall -Wextra -Werror
++CXXFLAGS += -v -g -std=c++11 -Wall -Wextra -Werror
+ 
+ # this lists the binaries to produce, the (non-PHONY, binary) targets in
+ # the previous manual Makefile
+--- ivar.orig/tests/Makefile.am
++++ ivar/tests/Makefile.am
+@@ -1,6 +1,6 @@
+ LIBS = -lhts -lz -lpthread
+ 
+-CXXFLAGS = -g -std=c++11 -Wall -Wextra -Werror
++CXXFLAGS += -g -std=c++11 -Wall -Wextra -Werror
+ 
+ TESTS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search
+ check_PROGRAMS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search
+@@ -21,4 +21,4 @@
+ check_primer_trim_edge_cases_SOURCES = test_primer_trim_edge_cases.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
+ check_isize_trim_SOURCES = test_isize_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
+ check_interval_tree_SOURCES = test_interval_tree.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
+-check_amplicon_search_SOURCES = test_amplicon_search.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
+\ No newline at end of file
++check_amplicon_search_SOURCES = test_amplicon_search.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp


=====================================
debian/patches/gcc-11.patch
=====================================
@@ -0,0 +1,22 @@
+Description: fix ftbfs with gcc-11
+ Failure is caused by a mismatch between an instance allocation via "new"
+ operator, and it's freeing via free(3) instead of "delete".  The failure to
+ build from source is caused by the warning -Wno-mismatched-new-delete, which
+ is treated as an error.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984067
+Forwarded: no
+Last-Update: 2021-08-28
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- ivar.orig/src/ivar.cpp
++++ ivar/src/ivar.cpp
+@@ -484,7 +484,7 @@
+       for (int i = 0; i < nfiles; ++i) {
+ 	free(files[i]);
+       }
+-      free(files);
++      delete files;
+     } else {
+       res = common_variants(g_args.prefix, g_args.min_threshold, argv + optind, argc - optind);
+     }


=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
 Fix-warning.patch
+forward-build-options.patch
+gcc-11.patch


=====================================
debian/salsa-ci.yml
=====================================
@@ -2,3 +2,6 @@
 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
+
+variables:
+  SALSA_CI_DISABLE_REPROTEST: 1



View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/f7462dcad6edb5c5b6c206c8e19a9e5bd7a5df63...66cbbce4f6bfda7d9e0f2b5b334f22b55a80a2ba

-- 
View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/f7462dcad6edb5c5b6c206c8e19a9e5bd7a5df63...66cbbce4f6bfda7d9e0f2b5b334f22b55a80a2ba
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