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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