Bug#991728: unblock: gemma/0.98.4+dfsg-4
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock
X-Debbugs-Cc: 991652@bugs.debian.org
Please unblock package gemma
[ Reason ]
To fix RC bug #991652 some tests that were causes by rounding errors
had to be disabled. The patch to do so was provided by upstream so
we are sure that we are not blindly excluding valid tests.
[ Impact ]
Package would not build from source.
[ Tests ]
Build time tests and autopkgtests are working (now).
[ Risks ]
Gemma is a leaf package so the risk to affect other packages is
low.
[ Checklist ]
[x] all changes are documented in the d/changelog
[x] I reviewed all changes and I approve them
[x] attach debdiff against the package in testing
unblock gemma/0.98.4+dfsg-4
diff -Nru gemma-0.98.4+dfsg/debian/changelog gemma-0.98.4+dfsg/debian/changelog
--- gemma-0.98.4+dfsg/debian/changelog 2021-04-07 16:28:38.000000000 +0200
+++ gemma-0.98.4+dfsg/debian/changelog 2021-07-30 21:53:57.000000000 +0200
@@ -1,3 +1,14 @@
+gemma (0.98.4+dfsg-4) unstable; urgency=medium
+
+ * Team upload.
+ * 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@debian.org> Fri, 30 Jul 2021 21:53:57 +0200
+
gemma (0.98.4+dfsg-3) unstable; urgency=medium
* Team upload.
diff -Nru gemma-0.98.4+dfsg/debian/patches/exclude_assertions_failing_under_some_circumstances.patch gemma-0.98.4+dfsg/debian/patches/exclude_assertions_failing_under_some_circumstances.patch
--- gemma-0.98.4+dfsg/debian/patches/exclude_assertions_failing_under_some_circumstances.patch 2021-04-07 16:28:38.000000000 +0200
+++ gemma-0.98.4+dfsg/debian/patches/exclude_assertions_failing_under_some_circumstances.patch 2021-07-30 21:53:57.000000000 +0200
@@ -51,3 +51,88 @@
}
+--- 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`
Reply to: