[Debian-med-packaging] Bug#991652: gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2
Andreas Tille
andreas at fam-tille.de
Sat Jul 31 06:04:51 BST 2021
On Fri, Jul 30, 2021 at 10:42:49PM +0200, Pjotr Prins wrote:
> ASSERT:expected:<2247> but was:<2246>
Builds on my machine now, waiting for Salsa CI before uploading.
Thanks a lot for your quick support
Andreas.
> is a round off :/. Can you comment out that line? I can resend the
> patch tomorrow otherwise.
>
> Pj.
>
> On Fri, Jul 30, 2021 at 10:08:45PM +0200, Andreas Tille wrote:
> > Dear Pjotr,
> >
> > thanks a lot for your input. I've applied your changes but there is one
> > remaining failure. I've attached the build log. Did I possibly made some
> > mistake when merging your patch?
> >
> > Kind regards
> >
> > Andreas.
> >
> > On Fri, Jul 30, 2021 at 12:29:57PM +0200, Pjotr Prins wrote:
> > > Dear Andreas,
> > >
> > > I have merged the reproducible patch from the Debian source tree and
> > > changed/disabled some other tests (attached). The problem is that
> > > different AMD64 CPUs together with OpenBlas simply give different
> > > results (mostly SIMD differences).
> > >
> > > I tested the current tests on both Intel and AMD that I have and these
> > > tests pass right now.
> > >
> > > If one is left that still fails, simply disable it.
> > >
> > > I'll revamp the GEMMA testing soon. I have to.
> > >
> > > Attached
> > >
> > > Pj.
> > >
> >
> > > From f90317c64e80c94ba0b5f644d3dc4f502677f8e8 Mon Sep 17 00:00:00 2001
> > > From: Pjotr Prins <pjotr.public01 at thebird.nl>
> > > Date: Fri, 30 Jul 2021 05:01:55 -0500
> > > Subject: [PATCH] Merging the test changes from the Debian tree and changing
> > > some other tests to enhance reproducibility.
> > >
> > > ---
> > > Makefile | 4 ++--
> > > test/dev_test_suite.sh | 10 +++++-----
> > > test/test_suite.sh | 20 ++++++++++----------
> > > 3 files changed, 17 insertions(+), 17 deletions(-)
> > >
> > > diff --git a/Makefile b/Makefile
> > > index 0cf3097..499b325 100644
> > > --- a/Makefile
> > > +++ b/Makefile
> > > @@ -201,8 +201,8 @@ ifdef WITH_LAPACK
> > > endif
> > > endif
> > >
> > > -HDR = $(wildcard src/*.h) ./src/version.h
> > > -SOURCES = $(wildcard src/*.cpp)
> > > +HDR = $(sort $(wildcard src/*.h)) ./src/version.h
> > > +SOURCES = $(sort $(wildcard src/*.cpp))
> > >
> > > # all
> > > OBJS = $(SOURCES:.cpp=.o)
> > > diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh
> > > index 676e0b3..c596679 100755
> > > --- a/test/dev_test_suite.sh
> > > +++ b/test/dev_test_suite.sh
> > > @@ -79,7 +79,7 @@ testBXDLMMLikelihoodRatio() {
> > >
> > > outfn=output/$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`
> > > }
> > >
> > >
> > > diff --git a/test/test_suite.sh b/test/test_suite.sh
> > > index cc244c0..892faa4 100755
> > > --- 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`
> > > --
> > > 2.21.0
> > >
> >
> >
> > --
> > http://fam-tille.de
>
>
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