[med-svn] [Git][med-team/gemma][master] 2 commits: Revert changes that are not in unstable yet
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Jul 30 20:53:54 BST 2021
Andreas Tille pushed to branch master at Debian Med / gemma
Commits:
a7c52420 by Andreas Tille at 2021-07-30T21:50:49+02:00
Revert changes that are not in unstable yet
- - - - -
d6e3931d by Andreas Tille at 2021-07-30T21:53:37+02:00
Apply patch from upstream who explained:
changed/disabled some other tests (attached). The problem is that
different AMD64 CPUs together with OpenBlas simply give different
results (mostly SIMD differences).
- - - - -
7 changed files:
- debian/changelog
- debian/patches/exclude_assertions_failing_under_some_circumstances.patch
- − debian/patches/hardening.patch
- debian/patches/series
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test → debian/tests/run-sample-analysis
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,13 @@
gemma (0.98.4+dfsg-4) UNRELEASED; urgency=medium
* Team upload.
- * Enable hardening
+ * Apply patch from upstream who explained:
+ changed/disabled some other tests (attached). The problem is that
+ different AMD64 CPUs together with OpenBlas simply give different
+ results (mostly SIMD differences).
+ Closes: #991652
- -- Andreas Tille <tille at debian.org> Wed, 07 Apr 2021 16:31:37 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 30 Jul 2021 21:52:30 +0200
gemma (0.98.4+dfsg-3) unstable; urgency=medium
=====================================
debian/patches/exclude_assertions_failing_under_some_circumstances.patch
=====================================
@@ -51,3 +51,88 @@ Last-Update: Wed, 07 Apr 2021 16:25:29 +0200
}
+--- a/test/test_suite.sh
++++ b/test/test_suite.sh
+@@ -27,7 +27,7 @@ testBslmm2() {
+ -gk 1 -o $outn
+ assertEquals 0 $?
+ outfn=output/$outn.cXX.txt
+- assertEquals "579.50" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ assertEquals "580" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn`
+ }
+
+ testBslmm3() {
+@@ -76,7 +76,7 @@ testBslmm5() {
+ -o $outn -seed 100
+ assertEquals 0 $?
+ outfn=output/$outn.prdt.txt
+- assertEquals "571.08" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ # assertEquals "571.08" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ }
+
+ testCenteredRelatednessMatrixKFullLOCO1() {
+@@ -88,7 +88,7 @@ testCenteredRelatednessMatrixKFullLOCO1() {
+ assertEquals 0 $?
+ outfn=output/$outn.cXX.txt
+ assertEquals "1940" `wc -l < $outfn`
+- assertEquals "2246.49" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ assertEquals "2247" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn`
+ }
+
+ testUnivariateLinearMixedModelFullLOCO1() {
+@@ -106,7 +106,7 @@ testUnivariateLinearMixedModelFullLOCO1() {
+ assertEquals 0 $?
+ outfn=output/$outn.assoc.txt
+ assertEquals "951" `wc -l < $outfn`
+- assertEquals "267507852.03" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ # assertEquals "267507852.03" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ }
+
+ testCenteredRelatednessMatrixK() {
+@@ -118,7 +118,7 @@ testCenteredRelatednessMatrixK() {
+ assertEquals "1940" `wc -l < $outfn`
+ assertEquals "3763600" `wc -w < $outfn`
+ assertEquals "0.335" `head -c 5 $outfn`
+- assertEquals "1119.60" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ assertEquals "1120" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn`
+ }
+
+ testUnivariateLinearMixedModel() {
+@@ -134,7 +134,7 @@ testUnivariateLinearMixedModel() {
+ assertEquals 0 $?
+ outfn=output/mouse_hs1940_CD8_lmm.assoc.txt
+ assertEquals "129228" `wc -w < $outfn`
+- assertEquals "4038540440.81" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ # assertEquals "4038540440.81" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ }
+
+ testLinearMixedModelPhenotypes() {
+@@ -149,7 +149,7 @@ testLinearMixedModelPhenotypes() {
+
+ outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
+ assertEquals "139867" `wc -w < $outfn`
+- assertEquals "4029037056.58" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ # assertEquals "4029037056.58" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ }
+
+ testPlinkStandardRelatednessMatrixK() {
+@@ -161,7 +161,7 @@ testPlinkStandardRelatednessMatrixK() {
+ -gk 2 -o $testname
+ assertEquals 0 $?
+ assertEquals "427" `wc -l < $outfn`
+- assertEquals "-358.05" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ assertEquals "-358" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }' $outfn`
+ }
+
+ # Test for https://github.com/genetics-statistics/GEMMA/issues/58
+@@ -178,8 +178,8 @@ testPlinkLinearMixedModelCovariates() {
+ -o $testname
+ assertEquals 0 $?
+ outfn=output/$testname.assoc.txt
+- assertEquals "223243" `wc -l < $outfn`
+- assertEquals "89757159113.94" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
++ # assertEquals "223243" `wc -l < $outfn`
++ # assertEquals "89757159113.94" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ }
+
+ shunit2=`which shunit2`
=====================================
debian/patches/hardening.patch deleted
=====================================
@@ -1,23 +0,0 @@
-Description: Propagate LDFLAGS to enable hardening
-Author: Andreas Tille <tille at debian.org>
-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 $(LDFLAGS)
-
- unittests: all ./bin/unittests-gemma
- ./bin/unittests-gemma
=====================================
debian/patches/series
=====================================
@@ -2,4 +2,3 @@ exclude_assertions_failing_under_some_circumstances.patch
Reproducible_builds.patch
no-lquadmath.patch
Makefile.patch
-hardening.patch
=====================================
debian/rules
=====================================
@@ -1,7 +1,7 @@
#!/usr/bin/make -f
export DH_VERBOSE = 1
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen
export DEB_CXXFLAGS_MAINT_APPEND = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
-Tests: run-unit-test
+Tests: run-sample-analysis
Depends: @
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test → debian/tests/run-sample-analysis
=====================================
@@ -4,7 +4,6 @@ pkg=gemma
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}/example/* $AUTOPKGTEST_TMP
@@ -19,6 +18,7 @@ gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt \
hostarch=$(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/2b70cd9471612c66868457eebd590c8ca4b61b50...d6e3931d303df439800636ac47745599a1d6038a
--
View it on GitLab: https://salsa.debian.org/med-team/gemma/-/compare/2b70cd9471612c66868457eebd590c8ca4b61b50...d6e3931d303df439800636ac47745599a1d6038a
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