[med-svn] [Git][med-team/jellyfish][master] 9 commits: Enable build on 32bit architectures
Andreas Tille
gitlab at salsa.debian.org
Thu Dec 3 13:28:50 GMT 2020
Andreas Tille pushed to branch master at Debian Med / jellyfish
Commits:
33f8785f by Andreas Tille at 2020-12-03T09:33:43+01:00
Enable build on 32bit architectures
- - - - -
ee2fd389 by Andreas Tille at 2020-12-03T11:44:06+01:00
Ignore tests on 32 bit architectures since test data are to big
- - - - -
d226e82c by Andreas Tille at 2020-12-03T12:34:35+01:00
Move some arch dependant binaries from examples to jellyfish package
- - - - -
320aaf83 by Andreas Tille at 2020-12-03T13:30:15+01:00
Enable dh_missing --fail-missing
- - - - -
46bc0941 by Andreas Tille at 2020-12-03T13:30:36+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
bd527589 by Andreas Tille at 2020-12-03T13:30:36+01:00
routine-update: debhelper-compat 13
- - - - -
15da0f35 by Andreas Tille at 2020-12-03T13:55:12+01:00
Do not install binaries in example package
- - - - -
375142c7 by Andreas Tille at 2020-12-03T14:13:11+01:00
Move test_all binary to jellyfish binary as well to allow jellyfish-examples beeing architecture all
- - - - -
16bac881 by Andreas Tille at 2020-12-03T14:26:09+01:00
Upload to unstable
- - - - -
10 changed files:
- debian/changelog
- debian/control
- − debian/jellyfish-examples.install
- debian/jellyfish.install
- debian/jellyfish.manpages
- debian/libjellyfish-perl.install
- + debian/patches/fix-32-bit.patch
- debian/patches/series
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,20 @@
-jellyfish (2.3.0-7) UNRELEASED; urgency=medium
+jellyfish (2.3.0-7) unstable; urgency=medium
+ [ Michael R. Crusoe ]
* For jellyfish-examples drop 'jellyfish' to a recommends from a depends.
- -- Michael R. Crusoe <crusoe at debian.org> Fri, 05 Jun 2020 08:59:38 +0200
+ [ Nilesh Patra ]
+ * Enable build on 32bit architectures
+ Closes: #962184
+
+ [ Andreas Tille ]
+ * Ignore tests on 32 bit architectures since test data are to big
+ * Move some arch dependant binaries from examples to jellyfish package
+ * Enable dh_missing --fail-missing
+ * Standards-Version: 4.5.1 (routine-update)
+ * debhelper-compat 13 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Thu, 03 Dec 2020 14:13:45 +0100
jellyfish (2.3.0-6) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Shaun Jackman <sjackman at debian.org>,
Michael R. Crusoe <crusoe at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
d-shlibs,
yaggo,
pkg-config,
@@ -20,7 +20,7 @@ Build-Depends: debhelper-compat (= 12),
libhts-dev,
dos2unix,
samtools
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
Homepage: https://www.cbcb.umd.edu/software/jellyfish/
=====================================
debian/jellyfish-examples.install deleted
=====================================
@@ -1,3 +0,0 @@
-bin/.libs/generate_sequence usr/lib/jellyfish/bin
-bin/.libs/test_all usr/lib/jellyfish/bin
-bin/.libs/fastq2sam usr/lib/jellyfish/bin
=====================================
debian/jellyfish.install
=====================================
@@ -1 +1,4 @@
-bin/.libs/jellyfish usr/bin
+usr/bin
+bin/.libs/fastq2sam usr/lib/jellyfish/bin
+bin/.libs/generate_sequence usr/lib/jellyfish/bin
+bin/.libs/test_all usr/lib/jellyfish/bin
=====================================
debian/jellyfish.manpages
=====================================
@@ -1 +1 @@
-doc/jellyfish.man
+debian/*/usr/share/man/man1/jellyfish.1
=====================================
debian/libjellyfish-perl.install
=====================================
@@ -1 +1,2 @@
-debian/tmp/usr/lib/*/perl5
+usr/lib/*/perl5
+usr/lib/perl/*/*.pm usr/share/perl5
=====================================
debian/patches/fix-32-bit.patch
=====================================
@@ -0,0 +1,38 @@
+Date: Thu, 3 Dec 2020 04:05:11 +0530
+From: Nilesh Patra <npatra974 at gmail.com>
+Bug-Debian: https://bugs.debian.org/962184
+Description: Enable build on 32bit architectures
+
+--- a/include/jellyfish/rectangular_binary_matrix.hpp
++++ b/include/jellyfish/rectangular_binary_matrix.hpp
+@@ -118,7 +118,7 @@
+ uint64_t *p = _columns;
+ while(*p == 0 && p < _columns + _c)
+ ++p;
+- return (p - _columns) == _c;
++ return static_cast<unsigned int>(p - _columns) == _c;
+ }
+
+ // Randomize the content of the matrix
+--- a/include/jellyfish/mer_dna.hpp
++++ b/include/jellyfish/mer_dna.hpp
+@@ -693,7 +693,7 @@
+
+ char buffer[mer.k() + 1];
+ is.read(buffer, mer.k());
+- if(is.gcount() != mer.k())
++ if(static_cast<unsigned int>(is.gcount()) != mer.k())
+ goto error;
+ buffer[mer.k()] = '\0';
+ if(!mer.from_chars(buffer))
+--- a/unit_tests/test_mer_dna.cc
++++ b/unit_tests/test_mer_dna.cc
+@@ -466,7 +466,7 @@
+
+ // Get bits by right-shifting
+ typename TypeParam::Type cm(m);
+- for(unsigned int j = 1; j < start; j += 2)
++ for(unsigned long int j = 1; start>=0 && j < static_cast<unsigned int>(start); j += 2)
+ cm.shift_right(0); // Shift by 2 bits
+ typename TypeParam::Type::base_type y = cm.word(0);
+ if(start & 0x1)
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ portability.patch
fix_replacement_of_-L_option.patch
test_needs_bash
python3
+fix-32-bit.patch
=====================================
debian/rules
=====================================
@@ -88,3 +88,18 @@ override_dh_auto_build:
#override_dh_auto_test:
# BIG=1 dh_auto_test
# false
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ifeq ($(DEB_HOST_ARCH_BITS),32)
+ echo "Test data are to big for 32bit architectures thus no testing is done"
+else
+ dh_auto_test
+endif
+endif
+
+override_dh_missing:
+ # Python files are just installed
+ rm -rf debian/tmp/usr/lib/python3/dist-packages
+ # Necessary Perl files are just installed
+ rm -rf debian/tmp/usr/lib/perl/5.32.0
+ dh_missing
=====================================
debian/tests/run-unit-test
=====================================
@@ -5,6 +5,13 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
+
+if [ $(dpkg-architecture -qDEB_HOST_ARCH_BITS) -eq 32 ] ; then
+ echo "Test data are to big for 32bit architectures thus no testing is done"
+ jellyfish --help
+ exit 0
+fi
+
cd $AUTOPKGTEST_TMP
mkdir tests
cp -a /usr/share/doc/jellyfish-examples/examples/* tests
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/70d728530580b566ba058a690ea9ea54d01d5220...16bac881c9e287541a635ae89856cd2599e12c91
--
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/70d728530580b566ba058a690ea9ea54d01d5220...16bac881c9e287541a635ae89856cd2599e12c91
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