[Debian-med-packaging] Bug#985004: gemma: flaky armhf autopkgtest: regularly times out after 2:47 h

Paul Gevers elbrus at debian.org
Thu Mar 11 20:08:15 GMT 2021


Source: gemma
Version: 0.98.3+dfsg-1
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: flaky

Dear maintainer(s),

Your package has an autopkgtest, great. However, I looked into
the history of your autopkgtest [1,2] and I noticed it fails regularly
on armhf, while sporadically a rerun passes. I copied some of the output
at the bottom of this report.

Because the unstable-to-testing migration software now blocks on
regressions in testing, flaky tests, i.e. tests that flip between
passing and failing without changes to the list of installed packages,
are causing people unrelated to your package to spend time on these
tests.

Paul

[1] https://ci.debian.net/packages/g/gemma/testing/armhf/
[2] https://ci.debian.net/packages/g/gemma/unstable/armhf/

https://ci.debian.net/data/autopkgtest/testing/armhf/g/gemma/10238800/log.gz

https://ci.debian.net/data/autopkgtest/testing/armhf/g/gemma/10042898/log.gz

autopkgtest [20:25:33]: test run-sample-analysis: [-----------------------
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =    12226
## number of analyzed SNPs         =    10768
Calculating Relatedness Matrix ...
                                                   0%
====                                               8%
========                                           16%
============                                       25%
================                                   33%
====================                               41%
========================                           49%
============================                       57%
================================                   65%
====================================               74%
========================================           82%
============================================       90%
=================================================  98%
================================================== 100%
**** INFO: Done.
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =    12226
## number of analyzed SNPs         =    10768
Start Eigen-Decomposition...
pve estimate =0.608801
se(pve) =0.032774
                                                   0%
====                                               8%
========                                           16%
============                                       25%
================                                   33%
====================                               41%
========================                           49%
============================                       57%
================================                   65%
====================================               74%
========================================           82%
============================================       90%
=================================================  98%
================================================== 100%
================================================== 100%
**** INFO: Done.
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1197
## number of covariates = 1
## number of phenotypes = 2
## number of total SNPs/var        =    12226
## number of analyzed SNPs         =    10758
Start Eigen-Decomposition...
REMLE estimate for Vg in the null model:
1.3940	
-0.2267	2.0817	
se(Vg):
0.1567	
0.1363	0.2359	
REMLE estimate for Ve in the null model:
0.3489	
0.0491	0.4144	
se(Ve):
0.0206	
0.0166	0.0267	
REMLE likelihood = -2855.1664
MLE estimate for Vg in the null model:
1.3959	
-0.2267	2.0854	
se(Vg):
0.1568	
0.1365	0.2361	
MLE estimate for Ve in the null model:
0.3483	
0.0490	0.4136	
se(Ve):
0.0206	
0.0166	0.0266	
MLE likelihood = -2856.0280
                                                   0%
====                                               8%
========                                           16%
============                                       25%
================                                   33%
====================                               41%
========================                           49%
============================                       57%
================================                   65%
====================================               74%
========================================           82%
============================================       90%
=================================================  98%
================================================== 100%
**** INFO: Done.
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1940
## number of individuals with full phenotypes = 1197
## number of covariates = 1
## number of phenotypes = 2
## number of observed data = 2990
## number of missing data = 890
Start Eigen-Decomposition...
REMLE estimate for Vg in the null model:
1.39393
-0.226693	2.08168
REMLE estimate for Ve in the null model:
0.348902
0.0490447	0.414434
Predicting Missing Phentypes ...
**** INFO: Done.
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1940
## number of covariates = 1
## number of phenotypes = 2
## number of total SNPs/var        =    12226
## number of analyzed SNPs         =    10783
Start Eigen-Decomposition...
REMLE estimate for Vg in the null model:
1.3918	
-0.1223	2.0525	
se(Vg):
0.1163	
0.1015	0.1769	
REMLE estimate for Ve in the null model:
0.2245	
0.0365	0.3270	
se(Ve):
0.0101	
0.0088	0.0150	
REMLE likelihood = -4007.1538
MLE estimate for Vg in the null model:
1.3928	
-0.1222	2.0542	
se(Vg):
0.1163	
0.1015	0.1768	
MLE estimate for Ve in the null model:
0.2243	
0.0365	0.3266	
se(Ve):
0.0101	
0.0088	0.0150	
MLE likelihood = -4007.6761
                                                   0%
====                                               8%
========                                           16%
============                                       25%
================                                   33%
====================                               41%
========================                           49%
============================                       57%
================================                   65%
====================================               74%
========================================           82%
============================================       90%
=================================================  98%
================================================== 100%
**** INFO: Done.
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 757
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =    12226
## number of analyzed SNPs         =    10775
Start Eigen-Decomposition...
pve estimate =0.372151
se(pve) =0.0522377
Calculating UtX...
initial value of h = 0.372151
initial value of rho = 0.393216
initial value of pi = 0.00194896
initial value of |gamma| = 21
                                                   0%    0.00
====                                               9%    0.26
=========                                          18%    0.25
=============                                      27%    0.24
==================                                 36%    0.23
======================                             45%    0.23
===========================                        55%    0.23
===============================                    64%    0.23
====================================               73%    0.23
========================================           82%    0.22
=============================================      91%    0.22
================================================== 100%    0.22
**** INFO: Done.
GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 757
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =    12226
## number of analyzed SNPs         =    10775
## number of cases = 409
## number of controls = 348
Start Eigen-Decomposition...
pve estimate =0.372151
se(pve) =0.0522377
Calculating UtX...
initial value of h = 0.372151
initial value of rho = 0.393216
initial value of pi = 0.00194896
initial value of |gamma| = 21
                                                   0%    0.00
====                                               9%    0.12
=========                                          18%    0.12
=============                                      27%    0.12
==================                                 36%    0.12
======================                             45%    0.11
autopkgtest [23:12:14]: ERROR: timed out on command "su -s /bin/bash
debci -c set -e; export USER=`id -nu`; . /etc/profile >/dev/null 2>&1 ||
true;  . ~/.profile >/dev/null 2>&1 || true;
buildtree="/tmp/autopkgtest-lxc.jk2tfva2/downtmp/build.HjL/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.jk2tfva2/downtmp/run-sample-analysis-artifacts";
export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.jk2tfva2/downtmp/run-sample-analysis-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.jk2tfva2/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.jk2tfva2/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=32; unset
LANGUAGE LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE   LC_MONETARY
LC_MESSAGES LC_PAPER LC_NAME LC_ADDRESS   LC_TELEPHONE LC_MEASUREMENT
LC_IDENTIFICATION LC_ALL;rm -f /tmp/autopkgtest_script_pid; set -C; echo
$$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f
/tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd "$buildtree"; chmod
+x
/tmp/autopkgtest-lxc.jk2tfva2/downtmp/build.HjL/src/debian/tests/run-sample-analysis;
touch /tmp/autopkgtest-lxc.jk2tfva2/downtmp/run-sample-analysis-stdout
/tmp/autopkgtest-lxc.jk2tfva2/downtmp/run-sample-analysis-stderr;
/tmp/autopkgtest-lxc.jk2tfva2/downtmp/build.HjL/src/debian/tests/run-sample-analysis
2> >(tee -a
/tmp/autopkgtest-lxc.jk2tfva2/downtmp/run-sample-analysis-stderr >&2) >
>(tee -a
/tmp/autopkgtest-lxc.jk2tfva2/downtmp/run-sample-analysis-stdout);"
(kind: test)
autopkgtest [23:12:14]: test run-sample-analysis: -----------------------]

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