Your message dated Sun, 29 Nov 2020 06:48:38 +0000 with message-id <e1kjgvi-0001fg...@fasolo.debian.org> and subject line Bug#952190: fixed in gemma 0.98.3+dfsg-1 has caused the Debian Bug report #952190, 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.) -- 952190: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=952190 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: gemma Version: 0.98.1+dfsg-1 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20200222 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 -fdebug-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 -g -DHAVE_INLINE -pthread -Wall > -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -Og -g > -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 > -Icontrib/catch-1.9.7 -Isrc -c -o test/src/unittests-main.o > test/src/unittests-main.cpp > g++ -g -O2 -fdebug-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 -g -DHAVE_INLINE -pthread -Wall > -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -Og -g > -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 > -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 -g -DHAVE_INLINE -pthread -Wall > -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -Og -g > -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 > -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/eigenlib.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 (24 assertions in 4 test cases) > > rm -vf test/output/* > cd test && ./dev_test_suite.sh | tee ../dev_test.log > run system shunit2 > testLinearModel > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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 = 0.0628087 min > ASSERT:expected:<4053667109.69> but was:<4053667109.67> > testBXDStandardRelatednessMatrixKSingularError > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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 266 errno 1 > testBXDStandardRelatednessMatrixK > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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. > ASSERT:expected:<-116.11> but was:<-116.13> > testBXDLMLikelihoodRatio > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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. > ASSERT:expected:<3089042886.28> but was:<3089042886.08> > testBXDLMMLikelihoodRatio > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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... > pve estimate =0.00100086 > se(pve) =0.204165 > 0% > ====== 14% > ============= 27% > ==================== 41% > =========================== 55% > ================================== 68% > ======================================== 82% > =============================================== 96% > ================================================== 100% > ================================================== 100% > > **** INFO: Done. > ASSERT:expected:<3088458212.93> but was:<3088458212.86> > testCenteredRelatednessMatrixissue188 > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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. > ASSERT:expected:<193.80> but was:<193.78> > testLMMissue188 > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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 2588 > **** WARNING: K is ill conditioned! in src/gemma.cpp at line 2588 > Start Eigen-Decomposition... > **** WARNING: Matrix G has 3 eigenvalues close to zero > pve estimate =0.631857 > se(pve) =0.0548406 > 0% > ========================= 50% > ================================================== 100% > > **** INFO: Done. > testCenteredRelatednessMatrixKLOCO1 > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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 = 0.0318409 min > testUnivariateLinearMixedModelLOCO1 > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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... > pve estimate =0.678775 > se(pve) =0.0717914 > 0% > ==== 8% > ======== 16% > ============ 25% > ================ 33% > ==================== 41% > ======================== 49% > ============================ 57% > ================================ 65% > ==================================== 74% > ======================================== 82% > ============================================ 90% > ================================================= 98% > ================================================== 100% > ================================================== 100% > > **** INFO: Done. > ## total computation time = 0.0264891 min > testPlinkCenteredRelatednessMatrixKLOCO1 > testPlinkUnivariateLinearMixedModelLOCO1 > testCorrelatedPhenotypesMvLLM > GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018 > 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): > 0.0736 > 0.0355 0.0299 > 0.0421 0.0264 0.0422 > 0.0444 0.0279 0.0430 0.0479 > 0.0516 0.0254 0.0295 0.0313 0.0389 > 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): > 0.0378 > 0.0252 0.0329 > 0.0299 0.0281 0.0456 > 0.0332 0.0319 0.0494 0.0583 > 0.0266 0.0186 0.0215 0.0242 0.0208 > 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): > 0.0735 > 0.0355 0.0298 > 0.0420 0.0264 0.0421 > 0.0443 0.0278 0.0430 0.0478 > 0.0515 0.0254 0.0295 0.0313 0.0388 > 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 0.8391 > -0.0128 -0.0040 -0.0705 0.0879 0.0418 > se(Ve): > 0.0378 > 0.0252 0.0329 > 0.0298 0.0281 0.0455 > 0.0331 0.0318 0.0493 0.0582 > 0.0265 0.0185 0.0215 0.0242 0.0207 > MLE likelihood = -3814.3913 > 0% > ================================================== 100% > > **** INFO: Done. > > Ran 12 tests. > > FAILED (failures=5) > tail -n 1 dev_test.log | grep -q 'OK' > make[2]: *** [Makefile:231: fast-check] Error 1 > make[2]: Leaving directory '/<<PKGBUILDDIR>>' > dh_auto_test: error: make -j1 check returned exit code 2 The full build log is available from: http://qa-logs.debian.net/2020/02/22/gemma_0.98.1+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! 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.
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--- Begin Message ---Source: gemma Source-Version: 0.98.3+dfsg-1 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 952...@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: SHA256 Format: 1.8 Date: Sat, 28 Nov 2020 23:07:55 +0100 Source: gemma Architecture: source Version: 0.98.3+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Closes: 952190 Changes: gemma (0.98.3+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream release Closes: #952190 * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Use secure URI in Homepage field. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Checksums-Sha1: 931b7595da51dcbe45943dcd0afb54fd974b3d32 2113 gemma_0.98.3+dfsg-1.dsc d2f5e30b41a8c4ad82776b559cc8bb3361899c4d 42620448 gemma_0.98.3+dfsg.orig.tar.xz 9cf6340721a44c3b9260020a165d02363a1c77df 5132 gemma_0.98.3+dfsg-1.debian.tar.xz 853d954c55c3bc247d74c36935ae43ba60831e83 6822 gemma_0.98.3+dfsg-1_amd64.buildinfo Checksums-Sha256: 137b151e720cf60cca0d71a68e24102699cf31868c51ee0060e1dc63b980d40b 2113 gemma_0.98.3+dfsg-1.dsc db160fd13a95725a4cacf8db0e33fb7955f3738fb909fad06655782068458fde 42620448 gemma_0.98.3+dfsg.orig.tar.xz d1681697ca925141bc0f8b6bbf9e68e114e22418f03cdd4fdcfe26fdac4f28ee 5132 gemma_0.98.3+dfsg-1.debian.tar.xz 2ddb7012f752e4305f13ccab459a13f852ffd9643bc59e576cdf9e1751a32e73 6822 gemma_0.98.3+dfsg-1_amd64.buildinfo Files: 980afbd1c6e5f563469bb17c57db1187 2113 science optional gemma_0.98.3+dfsg-1.dsc a7cf6fcaf5d52e05566c0528a2f0c5c3 42620448 science optional gemma_0.98.3+dfsg.orig.tar.xz b14043bccd9c0a7adefb0fb42b5cd3cd 5132 science optional gemma_0.98.3+dfsg-1.debian.tar.xz a15788bee1fa3d8d3e62cea69fc8dc7b 6822 science optional gemma_0.98.3+dfsg-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/DP3QRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHSDw/9Hfl+3DRfi92nS6aUyPJJUjLaw30jPlBP MIccXFh6zlqyDtK6C9qbQvPEZCV4XJVonXl4t0l7PAXVwlTHsn+B2bymUXuzMUWw GMkMWoJ83LY/rmqoHOn9VeFfH4AXr7qv4vVTo7wTAG9leHvYqBt5cT51V+L6y0yy gWnjA5sULZ93X27FTAxZdArlc42K2ZokXMDxjpOKqgmcUjUBnuuTNyx5xF3vluve b1gJ7fSIIPqBTuixWt9DuvGO2W1VO4de9ZoYA8I6To5RWYHoXlz/EztPHMBB7Cpx BTURnq1KIcpdxQ2mliRaMBuVmEt9gXp6yBy+ItALXJjtJf8AKFbblp1dVBLy3iQC hCFOj8jnljoy5qYa2Ky7RsuwPhJsJuho9YEgKZ2gWGyEUYPGU1T0gfo3yPlaDkVv z3R/fXOSzIuTgnLXu9auvLLkKvSgSjDKpMgsuC+c4hp6S4POWJ7K+DPKzTdEZWWE +eOiGl4MOOdfZnIxc26v7c1wydi5RZoDYnAX5Fq6jCgbR+8MI6hOnEcdI9bgEF3G YGnmzd+/z4+9mL979yQHI6v49ORFiU0n/yMyP36YFiR1YSDaiz11wj6mfeniJZW2 t++YLO9zzy4+TBgqQxxlApNs9XJmo/hKSJiM417ks1jf8dePFAtB8s3k73tzW3at FOPC4H89yFo= =883/ -----END PGP SIGNATURE-----
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