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.
