Your message dated Wed, 07 Apr 2021 15:03:31 +0000 with message-id <e1lu9in-000ium...@fasolo.debian.org> and subject line Bug#982692: fixed in gemma 0.98.4+dfsg-3 has caused the Debian Bug report #982692, regarding gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2 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.) -- 982692: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=982692 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: gemma Version: 0.98.4+dfsg-1 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20210213 ftbfs-bullseye Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[2]: Entering directory '/<<PKGBUILDDIR>>' > g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch > -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS > -isystem/usr/local/opt/openblas/include -Og -Wfatal-errors -g -DHAVE_INLINE > -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -Og -Wfatal-errors > -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc > -c -o test/src/unittests-main.o test/src/unittests-main.cpp > g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch > -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS > -isystem/usr/local/opt/openblas/include -Og -Wfatal-errors -g -DHAVE_INLINE > -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -Og -Wfatal-errors > -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc > -c -o test/src/unittests-math.o test/src/unittests-math.cpp > g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS > -isystem/usr/local/opt/openblas/include -Og -Wfatal-errors -g -DHAVE_INLINE > -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -Og -Wfatal-errors > -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc > ./test/src/unittests-main.o ./test/src/unittests-math.o src/bslmm.o > src/bslmmdap.o src/debug.o src/fastblas.o src/gemma.o src/gemma_io.o > src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o > src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl > -lz -lopenblas -o ./bin/unittests-gemma > ./bin/unittests-gemma > Mismatch coordinates (1,0)0:3! > > This example computes real matrix C=alpha*A*B+beta*C using > Intel(R) MKL function dgemm, where A, B, and C are matrices and > alpha and beta are double precision scalars > > Initializing data for matrix multiplication C=A*B for matrix > A(2000x200) and matrix B(200x1000) > > Allocating memory for matrices aligned on 64-byte boundary for better > performance > > Intializing matrix data > > Computing matrix product using Intel(R) MKL dgemm function via CBLAS > interface > > > This example computes real matrix C=alpha*A*B+beta*C using > Intel(R) MKL function dgemm, where A, B, and C are matrices and > alpha and beta are double precision scalars > > Initializing data for matrix multiplication C=A*B for matrix > A(2000x200) and matrix B(200x1000) > > Allocating memory for matrices aligned on 64-byte boundary for better > performance > > Intializing matrix data > > Computing matrix product using Intel(R) MKL dgemm function via CBLAS > interface > > > Computations completed. > > =============================================================================== > All tests passed (23 assertions in 4 test cases) > > rm -vf test/output/* > cd test && ./dev_test_suite.sh | tee ../dev_test.log > run system shunit2 > testLinearModel > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > 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 > 0% > ==== 8% > ======== 16% > ============ 25% > ================ 33% > ==================== 41% > ======================== 49% > ============================ 57% > ================================ 65% > ==================================== 74% > ======================================== 82% > ============================================ 90% > ================================================= 98% > ================================================== 100% > > **** INFO: Done. > ## total computation time = 0.0556125 min > testBXDStandardRelatednessMatrixKSingularError > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > **** INFO: no intercept term is found in the cvt file: a column of 1s is > added. > GSL ERROR: matrix is singular in lu.c at line 449 errno 1 > testBXDStandardRelatednessMatrixK > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > **** INFO: no intercept term is found in the cvt file: a column of 1s is > added. > ## number of total individuals = 198 > ## number of analyzed individuals = 67 > ## number of covariates = 3 > ## number of phenotypes = 1 > ## number of total SNPs/var = 7320 > ## number of analyzed SNPs = 7317 > Calculating Relatedness Matrix ... > 0% > ====== 14% > ============= 27% > ==================== 41% > =========================== 55% > ================================== 68% > ======================================== 82% > =============================================== 96% > ================================================== 100% > > **** INFO: Done. > testBXDLMLikelihoodRatio > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > **** INFO: no intercept term is found in the cvt file: a column of 1s is > added. > ## number of total individuals = 198 > ## number of analyzed individuals = 67 > ## number of covariates = 3 > ## number of phenotypes = 1 > ## number of total SNPs/var = 7320 > ## number of analyzed SNPs = 7317 > 0% > ====== 14% > ============= 27% > ==================== 41% > =========================== 55% > ================================== 68% > ======================================== 82% > =============================================== 96% > ================================================== 100% > > **** INFO: Done. > testBXDLMMLikelihoodRatio > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > **** INFO: no intercept term is found in the cvt file: a column of 1s is > added. > ## number of total individuals = 198 > ## number of analyzed individuals = 67 > ## number of covariates = 3 > ## number of phenotypes = 1 > ## number of total SNPs/var = 7320 > ## number of analyzed SNPs = 7317 > Start Eigen-Decomposition... > **** WARNING: Matrix G has 6 eigenvalues close to zero > pve estimate =2.82146e-06 > se(pve) =0.23116 > 0% > ====== 14% > ============= 27% > ==================== 41% > =========================== 55% > ================================== 68% > ======================================== 82% > =============================================== 96% > ================================================== 100% > ================================================== 100% > > **** INFO: Done. > ASSERT:expected:<3088458213> but was:<3088444823> > testBXDLMM9LikelihoodRatio > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > **** INFO: no intercept term is found in the cvt file: a column of 1s is > added. > ## number of total individuals = 198 > ## number of analyzed individuals = 67 > ## number of covariates = 3 > ## number of phenotypes = 1 > ## number of total SNPs/var = 7320 > ## number of analyzed SNPs = 7317 > Start Eigen-Decomposition... > **** WARNING: Matrix G has 6 eigenvalues close to zero > pve estimate =2.82146e-06 > se(pve) =0.23116 > 0% > ====== 14% > ============= 27% > ==================== 41% > =========================== 55% > ================================== 68% > ======================================== 82% > =============================================== 96% > ================================================== 100% > ================================================== 100% > > **** INFO: Done. > ASSERT:expected:<3088496565> but was:<3088483525> > testCenteredRelatednessMatrixissue188 > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > ## number of total individuals = 1008 > ## number of analyzed individuals = 876 > ## number of covariates = 1 > ## number of phenotypes = 1 > ## number of total SNPs/var = 2000 > ## number of analyzed SNPs = 1850 > Calculating Relatedness Matrix ... > 0% > ========================= 50% > ================================================== 100% > > **** WARNING: K has 75 eigenvalues close to zero in src/gemma.cpp at line 1912 > **** WARNING: K is ill conditioned! in src/gemma.cpp at line 1912 > **** INFO: Done. > testLMMissue188 > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > ## number of total individuals = 1008 > ## number of analyzed individuals = 876 > ## number of covariates = 1 > ## number of phenotypes = 1 > ## number of total SNPs/var = 2000 > ## number of analyzed SNPs = 1850 > **** WARNING: K has 3 eigenvalues close to zero in src/gemma.cpp at line 2590 > **** WARNING: K is ill conditioned! in src/gemma.cpp at line 2590 > Start Eigen-Decomposition... > **** WARNING: Matrix G has 386 eigenvalues close to zero > pve estimate =3.25181e-05 > se(pve) =0.0760733 > 0% > ========================= 50% > ================================================== 100% > > **** INFO: Done. > ASSERT:expected:<338154001.76> but was:<338144655.90> > testCenteredRelatednessMatrixKLOCO1 > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > **** TEST MODE: trim individuals from 1940 to 400 > **** TEST MODE: trim individuals from 1940 to 400 > ## number of total individuals = 400 > ## number of analyzed individuals = 247 > ## number of covariates = 1 > ## number of phenotypes = 1 > ## leave one chromosome out (LOCO) = 1 > ## number of total SNPs/var = 12226 > ## number of considered SNPS = 1000 > ## number of SNPS for K = 11182 > ## number of SNPS for GWAS = 1044 > ## number of analyzed SNPs = 889 > Calculating Relatedness Matrix ... > 0% > ==== 8% > ======== 16% > ============ 25% > ================ 33% > ==================== 41% > ======================== 49% > ============================ 57% > ================================ 65% > ==================================== 74% > ======================================== 82% > ============================================ 90% > ================================================= 98% > ================================================== 100% > > **** INFO: Done. > ## total computation time = 0.0308908 min > testUnivariateLinearMixedModelLOCO1 > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > **** TEST MODE: trim individuals from 1940 to 400 > **** TEST MODE: trim individuals from 1940 to 400 > ## number of total individuals = 400 > ## number of analyzed individuals = 247 > ## number of covariates = 1 > ## number of phenotypes = 1 > ## leave one chromosome out (LOCO) = 1 > ## number of total SNPs/var = 12226 > ## number of considered SNPS = 1000 > ## number of SNPS for K = 11182 > ## number of SNPS for GWAS = 1044 > ## number of analyzed SNPs = 889 > Start Eigen-Decomposition... > **** WARNING: Matrix G has 81 eigenvalues close to zero > pve estimate =7.01411e-06 > se(pve) =0.000282002 > 0% > ==== 8% > ======== 16% > ============ 25% > ================ 33% > ==================== 41% > ======================== 49% > ============================ 57% > ================================ 65% > ==================================== 74% > ======================================== 82% > ============================================ 90% > ================================================= 98% > ================================================== 100% > ================================================== 100% > > **** INFO: Done. > ## total computation time = 0.0255047 min > ASSERT:expected:<15465346.22> but was:<15464740.32> > testPlinkCenteredRelatednessMatrixKLOCO1 > testPlinkUnivariateLinearMixedModelLOCO1 > testCorrelatedPhenotypesMvLLM > GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 > GSL_RNG_SEED=100 > GSL random generator type: mt19937; seed = 100 (option -1); first value = > 2333906440 > Reading Files ... > ## number of total individuals = 1000 > ## number of analyzed individuals = 1000 > ## number of covariates = 1 > ## number of phenotypes = 5 > ## number of total SNPs/var = 100 > ## number of analyzed SNPs = 100 > REMLE estimate for Vg in the null model: > 0.8091 > 0.1435 0.0660 > -0.1456 -0.0664 0.1165 > 0.0907 0.0362 -0.0830 0.0639 > -0.5533 -0.0985 0.1171 -0.0765 0.4131 > se(Vg): > 0.0488 > 0.3422 14.2561 > 0.4678 42.5474 60.0713 > 32.4112 57.9632 53.2384 324.3620 > 78.4902 103.4650 264.6324 763.8744 0.0654 > REMLE estimate for Ve in the null model: > 0.0334 > 0.0267 0.4502 > -0.0529 -0.0883 0.6004 > 0.0683 0.1413 -0.6502 0.8400 > -0.0128 -0.0041 -0.0706 0.0880 0.0419 > se(Ve): > 2425.4682 > 0.8800 0.0349 > 1.3841 0.0300 0.0499 > 0.0327 0.0248 0.0545 0.0626 > 1.6822 0.0284 0.0220 0.0117 0.4277 > REMLE likelihood = -3813.3258 > MLE estimate for Vg in the null model: > 0.8082 > 0.1434 0.0660 > -0.1455 -0.0664 0.1165 > 0.0906 0.0362 -0.0830 0.0639 > -0.5528 -0.0984 0.1170 -0.0764 0.4127 > se(Vg): > 0.0487 > 0.3430 14.2911 > 0.4559 42.5031 63.0295 > 32.3991 57.9657 54.1131 326.3249 > 78.6757 104.0103 265.2345 763.8790 1.8635 > MLE estimate for Ve in the null model: > 0.0334 > 0.0267 0.4497 > -0.0529 -0.0882 0.5997 > 0.0682 0.1412 -0.6495 0.8392 > -0.0128 -0.0040 -0.0705 0.0879 0.0418 > se(Ve): > 2429.2615 > 0.8793 0.0348 > 1.3833 0.0300 0.0499 > 0.0327 0.0247 0.0545 0.0625 > 1.6841 0.0283 0.0220 0.0117 0.4208 > MLE likelihood = -3814.3913 > 0% > ================================================== 100% > > **** INFO: Done. > > Ran 13 tests. > > FAILED (failures=4) > tail -n 1 dev_test.log | grep -q 'OK' > make[2]: *** [Makefile:237: fast-check] Error 1 > make[2]: Leaving directory '/<<PKGBUILDDIR>>' > rm -fr -- /tmp/dh-xdg-rundir-9P32mk69 > dh_auto_test: error: make -j1 check returned exit code 2 The full build log is available from: http://qa-logs.debian.net/2021/02/13/gemma_0.98.4+dfsg-1_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please marking it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with me so that we can identify if something relevant changed in the meantime. About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---Source: gemma Source-Version: 0.98.4+dfsg-3 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 982...@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: Wed, 07 Apr 2021 16:28:38 +0200 Source: gemma Architecture: source Version: 0.98.4+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Closes: 982692 Changes: gemma (0.98.4+dfsg-3) unstable; urgency=medium . * Team upload. * Follow upstream suggestion to comment some tests that might fail due to some floating point rounding Closes: #982692 Checksums-Sha1: ecace02a2263865b550dc28d097ce5f39b118aaf 2113 gemma_0.98.4+dfsg-3.dsc 872c15c8bb4f38276f05a8713cad1ef3aa2beb3f 5820 gemma_0.98.4+dfsg-3.debian.tar.xz 24a7e58d6b3fd9060ee7b491332fd82016e12506 6699 gemma_0.98.4+dfsg-3_amd64.buildinfo Checksums-Sha256: a47feeef34604acac11ba950ac246c32b01ed316438bdc0eb73c57af8fba01fe 2113 gemma_0.98.4+dfsg-3.dsc 55a831ea1eed6ad4bc2dc7414a4fb98b8ac45aa32b471cde2e781b9f4745a5db 5820 gemma_0.98.4+dfsg-3.debian.tar.xz 3c981fa42f024d034460d95aedb4039d0dcdea10353bf48c220ee14019f63054 6699 gemma_0.98.4+dfsg-3_amd64.buildinfo Files: f8dff324c500db965cf3f94fb1f7aced 2113 science optional gemma_0.98.4+dfsg-3.dsc 6f325d03b13c1f6b26f0517ddc42a3dd 5820 science optional gemma_0.98.4+dfsg-3.debian.tar.xz 85678d4efb3bb0211587b92ff1470fb6 6699 science optional gemma_0.98.4+dfsg-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmBtxdARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGIyw//VR5uroFOIpHn84uIaaaiDwHjlUxf8BhI QMykwnz50EsuV/vZXAefuKQ8v7XwG2VxSkUfTrhKdM6iT4gbnjBzkZdFgnn7kj4s xQgG/Oa8F10NApQu4ibX5dREDQ40h4dXWjbiZQ6ojh+OavbfrfMhbGoCnbgVS8Or UaPPQ+KrNPSyyg7p/q9jVsgVXUbJZswPUIpzFwBca/XiiiP27HqAprskOtf4PrC5 /HBSouAXQcJX9A21gqsAfuEqsoJyCWHfi8aLng4NfZ0LvTvVsfDLwAuihJqR9giF 2fphMbhYyclP4eCoQGS3oBuC007sJggjenzjR+w4ZB+M6LjsmkCtAeGxn6SJ/Jyk DEbIa5suAst1CQ7Q1VpdHHIqbUbHnJplDbHSwCqCLN4sLbKYx3OmZxxTJ3xqaDcl 038pymBQm+hj+ktZpFWDsP8G+SFc5+weSI/zKNmuMM858w974LXGEh3T1nEGF95E j1RvrYe9rGyYr5v4wRB2RAfda4LUVoifysOpjMvx0F4V1Tg/qqEuwAuFBpTSd+NI 3GcnjNvfv9w+lpNafdVU1SD6r9XJEv3CgHle8+HjPwhLqXvpO8WXNRnj5296RCRz b/sz4R6JyCLkHwmf8pE/rC+jzPZIdgJ5+ROy07Snl2YTjZzmrt3I9jWJgIa0n+Z9 YfxijPLe3GE= =tQGk -----END PGP SIGNATURE-----
--- End Message ---
