[Debian-med-packaging] Bug#952190: gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2
Lucas Nussbaum
lucas at debian.org
Sun Feb 23 13:06:57 GMT 2020
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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