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

Andreas Tille tille at debian.org
Fri Mar 12 06:02:53 GMT 2021


Hi,

I recommend to remove armhf from the list of architectures.
This kind of software is possibly not used on armhf and
upstream (in CC) will probably confirm this.

Kind regards
    Andreas.

On Thu, Mar 11, 2021 at 09:08:15PM +0100, Paul Gevers wrote:
> 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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