Andreas Tille pushed to branch master at Debian Med / gemma
Commits: d57a77f0 by Andreas Tille at 2021-04-07T16:20:35+02:00 Revert changes to enable a smallest changes upload to fix bug #982692 - - - - - e4e9da9d by Andreas Tille at 2021-04-07T16:28:07+02:00 Follow upstream suggestion to comment some tests that might fail due to some floating point rounding - - - - - e665bff6 by Andreas Tille at 2021-04-07T16:39:30+02:00 Upload to unstable - - - - - 6 changed files: - debian/changelog - + debian/patches/exclude_assertions_failing_under_some_circumstances.patch - − debian/patches/hardening.patch - debian/patches/series - debian/rules - debian/tests/run-sample-analysis Changes: ===================================== debian/changelog ===================================== @@ -1,9 +1,11 @@ -gemma (0.98.4+dfsg-3) UNRELEASED; urgency=medium +gemma (0.98.4+dfsg-3) unstable; urgency=medium * Team upload. - * Enable hardening + * Follow upstream suggestion to comment some tests that might fail due + to some floating point rounding + Closes: #982692 - -- Andreas Tille <[email protected]> Mon, 22 Mar 2021 14:38:26 +0100 + -- Andreas Tille <[email protected]> Wed, 07 Apr 2021 16:28:38 +0200 gemma (0.98.4+dfsg-2) unstable; urgency=medium ===================================== debian/patches/exclude_assertions_failing_under_some_circumstances.patch ===================================== @@ -0,0 +1,53 @@ +Description: Follow upstream suggestion to comment some tests that might fail due + to some floating point rounding +Bug-Debian: https://bugs.debian.org/982692 +Author: Andreas Tille <[email protected]> +Last-Update: Wed, 07 Apr 2021 16:25:29 +0200 + +--- a/test/dev_test_suite.sh ++++ b/test/dev_test_suite.sh +@@ -79,7 +79,7 @@ testBXDLMMLikelihoodRatio() { + + outfn=output/$outn.assoc.txt + assertEquals "73180" `wc -w < $outfn` +- assertEquals "3088458213" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn` ++ #assertEquals "3088458213" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn` + } + + testBXDLMM9LikelihoodRatio() { +@@ -96,7 +96,7 @@ testBXDLMM9LikelihoodRatio() { + + outfn=output/$outn.assoc.txt + assertEquals "80498" `wc -w < $outfn` +- assertEquals "3088496565" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn` ++ #assertEquals "3088496565" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn` + } + + testCenteredRelatednessMatrixissue188() { +@@ -113,7 +113,7 @@ testLMMissue188() { + $gemma $gemmaopts -b data/issue188/2000 -lmm 2 -k output/$outn.cXX.txt -maf 0.01 -o $outn -n 1 + assertEquals 0 $? + outfn=output/$outn.assoc.txt +- assertEquals "338154001.76" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` ++ #assertEquals "338154001.76" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + } + + testCenteredRelatednessMatrixKLOCO1() { +@@ -147,7 +147,7 @@ testUnivariateLinearMixedModelLOCO1() { + assertEquals 0 $? + outfn=output/$outn.assoc.txt + assertEquals "68" `wc -l < $outfn` +- assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` ++ #assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + } + + testPlinkCenteredRelatednessMatrixKLOCO1() { +@@ -188,7 +188,7 @@ testPlinkUnivariateLinearMixedModelLOCO1 + assertEquals 0 $? + outfn=output/$outn.assoc.txt + assertEquals "68" `wc -l < $outfn` +- assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` ++ #assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` + } + + ===================================== debian/patches/hardening.patch deleted ===================================== @@ -1,23 +0,0 @@ -Description: Propagate LDFLAGS to enable hardening -Author: Andreas Tille <[email protected]> -Last-Update: Mon, 22 Mar 2021 14:38:26 +0100 - ---- a/Makefile -+++ b/Makefile -@@ -219,14 +219,14 @@ debug: $(OUTPUT) - $(shell bash $(VGEN) $(GUIX_PROFILE) > src/version.h) - - $(OUTPUT): $(OBJS) -- $(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT) -+ $(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT) $(LDFLAGS) - - $(OBJS): $(HDR) - - .SUFFIXES : .cpp .c .o $(SUFFIXES) - - ./bin/unittests-gemma: $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(OBJS) -- $(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma -+ $(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma $(LDFLAGS) - - unittests: all ./bin/unittests-gemma - ./bin/unittests-gemma ===================================== debian/patches/series ===================================== @@ -1,4 +1,4 @@ +exclude_assertions_failing_under_some_circumstances.patch Reproducible_builds.patch no-lquadmath.patch Makefile.patch -hardening.patch ===================================== debian/rules ===================================== @@ -1,7 +1,7 @@ #!/usr/bin/make -f export DH_VERBOSE = 1 -export DEB_BUILD_MAINT_OPTIONS = hardening=+all +#export DEB_BUILD_MAINT_OPTIONS = hardening=+all export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen export DEB_CXXFLAGS_MAINT_APPEND = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen ===================================== debian/tests/run-sample-analysis ===================================== @@ -17,6 +17,8 @@ gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt \ -a mouse_hs1940.anno.txt -gk -o mouse_hs1940 hostarch=$(dpkg-architecture -qDEB_HOST_ARCH) + +# Ignore single test on armhf and i386 (see bug #972553) if [ "$hostarch" = "armhf" ] ; then echo "Do only one test for $hostarch to reduce test time (see bug #985004)" exit 0 View it on GitLab: https://salsa.debian.org/med-team/gemma/-/compare/f7047363b8fcaf1eefde9caa80d5ae88076f808a...e665bff6d93fa88e71353d9bc8f41629758247d7 -- View it on GitLab: https://salsa.debian.org/med-team/gemma/-/compare/f7047363b8fcaf1eefde9caa80d5ae88076f808a...e665bff6d93fa88e71353d9bc8f41629758247d7 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
