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 <[email protected]> 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 <[email protected]> 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 <[email protected]>, Michael R. Crusoe <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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