Your message dated Mon, 22 Mar 2021 14:18:47 +0000 with message-id <e1loloj-0009kn...@fasolo.debian.org> and subject line Bug#985004: fixed in gemma 0.98.4+dfsg-2 has caused the Debian Bug report #985004, regarding gemma: flaky armhf autopkgtest: regularly times out after 2:47 h to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 985004: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=985004 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: gemma Version: 0.98.3+dfsg-1 Severity: serious Tags: sid bullseye X-Debbugs-CC: debian...@lists.debian.org User: debian...@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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--- Begin Message ---Source: gemma Source-Version: 0.98.4+dfsg-2 Done: Andreas Tille <ti...@debian.org> We believe that the bug you reported is fixed in the latest version of gemma, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 985...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated gemma package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 22 Mar 2021 14:09:15 +0100 Source: gemma Architecture: source Version: 0.98.4+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Closes: 985004 Changes: gemma (0.98.4+dfsg-2) unstable; urgency=medium . * Team upload. * Do only one test for armhf to reduce test time Closes: #985004 Checksums-Sha1: 94e5bac818507dbcffb8ac262cec9391f2de8f0c 2113 gemma_0.98.4+dfsg-2.dsc 0c89e6f41b605d648d35a3588fcea6d670235bab 5260 gemma_0.98.4+dfsg-2.debian.tar.xz 1f9affe1bca79880053f8ca4d36854915d4abdd9 6695 gemma_0.98.4+dfsg-2_amd64.buildinfo Checksums-Sha256: 557f61e9859760561c2dbabc295f088aeade8eac1d08907cca18c3cbbf75810a 2113 gemma_0.98.4+dfsg-2.dsc 89a5d0b7e1267eb42ae5bafe4ee0eec2c09db70032fbc000357a9f8d604c24cc 5260 gemma_0.98.4+dfsg-2.debian.tar.xz 2348e83f5e89d81ec842b4de06f6f0382e0219dfbb72ef59420ce315e11ed18c 6695 gemma_0.98.4+dfsg-2_amd64.buildinfo Files: 3c7ff478b565e0bdf55103c61ae410af 2113 science optional gemma_0.98.4+dfsg-2.dsc 3acf67def392b2ca3545bd7beaec77f9 5260 science optional gemma_0.98.4+dfsg-2.debian.tar.xz a3922eb76c7b20e99901924c3fd7922c 6695 science optional gemma_0.98.4+dfsg-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmBYnfgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtES0A/7BB8yehRIw3tWT34YrEyHDXlfB4r7zBkL 7KmglRn0D2+AQ8hoVyYLXdR80rNV86fCFkDBLBqkOfdrV3qQYPQ7PpzvsfDtMOfH tpVjroXG2wdR3ykmFjWBvSzpCqNHjbBu+yaRACGt9C/hx3GoF6gT2r7r1FATyOc7 hlKHowTqyWZWD8c/APzu5i1NQUrN1J8C7Z7DmVMSeRkbc13HsmQ6+hosem+zypk0 3KUstziXizKzhsBxuBfFvc14++8UVTyISRSQrNEwUVQEgbQ5Fr6JlAH3ZALiBUDq 691A+73/ghLCZ4eJUi5Mlmjoew3PbSna/OP5ufuvkSB7cSyuo7yE+pn6N1B+euba /H5fQ7efZiSeevbGcyoZCGbHsLIuUJt2UFusPMrkXJw8PrLSyzNB9RMP+KZhU6j9 T9mZLBS9RsTJyk6AVBANOieGm048Mlt4QCTt6auQd3RFekp2w76tDGA52t+n0QaI 9NBZxKuQ/EO1wJ63oyZ17ZZhHLYWElm8LsGXd5YivfY0Nkh3hd0ecKBie+js23UI nCL/+TrxzeiG/LQoZfrSaTPLcL4VrcvrUjRvu5Jwm1lI06EftFjSXeqkrM8QigZV DA2eHzNu3ctkjAeVhwtn7gZHFwjHCHc+mqFvGYbrIBP6WUnDM76gAXarDTJYYbKq 4KcdX8L5Leo= =eQU1 -----END PGP SIGNATURE-----
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