WARNING: (guile-user): imported module (guix build utils) overrides core binding `delete' starting phase `separate-from-pid1' build process now running as PID 18 phase `separate-from-pid1' succeeded after 0.0 seconds starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/5h1qy58jckhsxpvygm3s2f5szdkjkcjv-perl-5.36.0/bin:/gnu/store/p555rn79h1p6aqyl5kk7dwjzjfmgrq5b-shunit2-2.1.8/bin:/gnu/store/5cy1x75wy5cg0jzhbydck5r0wlfyv79f-which-2.21/bin:/gnu/store/my28256isi11qxynvvwr1mhlzfpnszwi-gsl-2.8/bin:/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/bin:/gnu/store/219fsiidadr6pc6bs4dym6wnmx4599rv-tar-1.35/bin:/gnu/store/zxi7miw74iwd4hhwxl736biv35xb689r-gzip-1.14/bin:/gnu/store/i4d9xwml7bq2d8ahkdmya3va8jjn3skg-bzip2-1.0.8/bin:/gnu/store/959nv0bhy0bbnhjzam9jp5vdq2k1s1n5-file-5.46/bin:/gnu/store/mvkvfd07rkfcbgkm6cnz65wf3hpssrbx-diffutils-3.12/bin:/gnu/store/2yhmp56pijfiwql4r360a9bzy4qw9dx8-patch-2.7.6/bin:/gnu/store/mkyrz3q61w91zji4y0ifkq6kjb4il4pi-findutils-4.10.0/bin:/gnu/store/m2pljzzsl56krbhvjki7wl8fdf9jdf8s-gawk-5.3.0/bin:/gnu/store/xikl61gcn30gz9bdwqp85c4r3ghjq08w-zstd-1.5.6/bin:/gnu/store/mj86ysrfzcil7bbk80hpwfp9mzchgdms-sed-4.9/bin:/gnu/store/jjs0rzim62kprxlnfjbw1pa7gf4fk2pv-grep-3.11/bin:/gnu/store/wr1f53i0phrm1kmj8x7i6iz0kf95sskp-xz-5.4.5/bin:/gnu/store/bx30pvvnm2ga19ah3aw2dsp32c92d6jj-coreutils-9.1/bin:/gnu/store/1hfa6nhqr5ixs2j68bmvn1i4rz9rzx19-make-4.4.1/bin:/gnu/store/5bccyn63h9dchddf947j6w6ia8vz6va5-bash-minimal-5.2.37/bin:/gnu/store/f0fnqg45llbljjxhm7hfbky0nds89wis-ld-wrapper-0/bin:/gnu/store/09bj4p5zcjma6h254lhf85z65srgmkyw-binutils-2.44/bin:/gnu/store/bpswla55k8725gg5mmzy2apiclr5wkx4-gcc-14.3.0/bin:/gnu/store/7qwp1164axvx185i2gm0ixxcykb9x2nd-glibc-2.41/bin:/gnu/store/7qwp1164axvx185i2gm0ixxcykb9x2nd-glibc-2.41/sbin' environment variable `PERL5LIB' set to `/gnu/store/5h1qy58jckhsxpvygm3s2f5szdkjkcjv-perl-5.36.0/lib/perl5/site_perl' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/vzw0aqcsllafzk7cffmxs69m7naba7ic-catch2-1.12.2/include:/gnu/store/my28256isi11qxynvvwr1mhlzfpnszwi-gsl-2.8/include:/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include:/gnu/store/r9bjfamkk65a2sx4lfxpz5gb56hfg5rw-zlib-1.3.1/include:/gnu/store/i4d9xwml7bq2d8ahkdmya3va8jjn3skg-bzip2-1.0.8/include:/gnu/store/959nv0bhy0bbnhjzam9jp5vdq2k1s1n5-file-5.46/include:/gnu/store/m2pljzzsl56krbhvjki7wl8fdf9jdf8s-gawk-5.3.0/include:/gnu/store/wr1f53i0phrm1kmj8x7i6iz0kf95sskp-xz-5.4.5/include:/gnu/store/1hfa6nhqr5ixs2j68bmvn1i4rz9rzx19-make-4.4.1/include:/gnu/store/09bj4p5zcjma6h254lhf85z65srgmkyw-binutils-2.44/include:/gnu/store/bpswla55k8725gg5mmzy2apiclr5wkx4-gcc-14.3.0/include:/gnu/store/7qwp1164axvx185i2gm0ixxcykb9x2nd-glibc-2.41/include:/gnu/store/b0kf4xxm614xymigyyza9invl0dz0qjq-linux-libre-headers-6.12.17/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/vzw0aqcsllafzk7cffmxs69m7naba7ic-catch2-1.12.2/include:/gnu/store/my28256isi11qxynvvwr1mhlzfpnszwi-gsl-2.8/include:/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include:/gnu/store/r9bjfamkk65a2sx4lfxpz5gb56hfg5rw-zlib-1.3.1/include:/gnu/store/i4d9xwml7bq2d8ahkdmya3va8jjn3skg-bzip2-1.0.8/include:/gnu/store/959nv0bhy0bbnhjzam9jp5vdq2k1s1n5-file-5.46/include:/gnu/store/m2pljzzsl56krbhvjki7wl8fdf9jdf8s-gawk-5.3.0/include:/gnu/store/wr1f53i0phrm1kmj8x7i6iz0kf95sskp-xz-5.4.5/include:/gnu/store/1hfa6nhqr5ixs2j68bmvn1i4rz9rzx19-make-4.4.1/include:/gnu/store/09bj4p5zcjma6h254lhf85z65srgmkyw-binutils-2.44/include:/gnu/store/bpswla55k8725gg5mmzy2apiclr5wkx4-gcc-14.3.0/include/c++:/gnu/store/bpswla55k8725gg5mmzy2apiclr5wkx4-gcc-14.3.0/include:/gnu/store/7qwp1164axvx185i2gm0ixxcykb9x2nd-glibc-2.41/include:/gnu/store/b0kf4xxm614xymigyyza9invl0dz0qjq-linux-libre-headers-6.12.17/include' environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/vzw0aqcsllafzk7cffmxs69m7naba7ic-catch2-1.12.2/include:/gnu/store/my28256isi11qxynvvwr1mhlzfpnszwi-gsl-2.8/include:/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include:/gnu/store/r9bjfamkk65a2sx4lfxpz5gb56hfg5rw-zlib-1.3.1/include:/gnu/store/i4d9xwml7bq2d8ahkdmya3va8jjn3skg-bzip2-1.0.8/include:/gnu/store/959nv0bhy0bbnhjzam9jp5vdq2k1s1n5-file-5.46/include:/gnu/store/m2pljzzsl56krbhvjki7wl8fdf9jdf8s-gawk-5.3.0/include:/gnu/store/wr1f53i0phrm1kmj8x7i6iz0kf95sskp-xz-5.4.5/include:/gnu/store/1hfa6nhqr5ixs2j68bmvn1i4rz9rzx19-make-4.4.1/include:/gnu/store/09bj4p5zcjma6h254lhf85z65srgmkyw-binutils-2.44/include:/gnu/store/bpswla55k8725gg5mmzy2apiclr5wkx4-gcc-14.3.0/include:/gnu/store/7qwp1164axvx185i2gm0ixxcykb9x2nd-glibc-2.41/include:/gnu/store/b0kf4xxm614xymigyyza9invl0dz0qjq-linux-libre-headers-6.12.17/include' environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/vzw0aqcsllafzk7cffmxs69m7naba7ic-catch2-1.12.2/include:/gnu/store/my28256isi11qxynvvwr1mhlzfpnszwi-gsl-2.8/include:/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include:/gnu/store/r9bjfamkk65a2sx4lfxpz5gb56hfg5rw-zlib-1.3.1/include:/gnu/store/i4d9xwml7bq2d8ahkdmya3va8jjn3skg-bzip2-1.0.8/include:/gnu/store/959nv0bhy0bbnhjzam9jp5vdq2k1s1n5-file-5.46/include:/gnu/store/m2pljzzsl56krbhvjki7wl8fdf9jdf8s-gawk-5.3.0/include:/gnu/store/wr1f53i0phrm1kmj8x7i6iz0kf95sskp-xz-5.4.5/include:/gnu/store/1hfa6nhqr5ixs2j68bmvn1i4rz9rzx19-make-4.4.1/include:/gnu/store/09bj4p5zcjma6h254lhf85z65srgmkyw-binutils-2.44/include:/gnu/store/bpswla55k8725gg5mmzy2apiclr5wkx4-gcc-14.3.0/include/c++:/gnu/store/bpswla55k8725gg5mmzy2apiclr5wkx4-gcc-14.3.0/include:/gnu/store/7qwp1164axvx185i2gm0ixxcykb9x2nd-glibc-2.41/include:/gnu/store/b0kf4xxm614xymigyyza9invl0dz0qjq-linux-libre-headers-6.12.17/include' environment variable `LIBRARY_PATH' set to `/gnu/store/5h1qy58jckhsxpvygm3s2f5szdkjkcjv-perl-5.36.0/lib:/gnu/store/my28256isi11qxynvvwr1mhlzfpnszwi-gsl-2.8/lib:/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/lib:/gnu/store/r9bjfamkk65a2sx4lfxpz5gb56hfg5rw-zlib-1.3.1/lib:/gnu/store/i4d9xwml7bq2d8ahkdmya3va8jjn3skg-bzip2-1.0.8/lib:/gnu/store/959nv0bhy0bbnhjzam9jp5vdq2k1s1n5-file-5.46/lib:/gnu/store/m2pljzzsl56krbhvjki7wl8fdf9jdf8s-gawk-5.3.0/lib:/gnu/store/wr1f53i0phrm1kmj8x7i6iz0kf95sskp-xz-5.4.5/lib:/gnu/store/09bj4p5zcjma6h254lhf85z65srgmkyw-binutils-2.44/lib:/gnu/store/7qwp1164axvx185i2gm0ixxcykb9x2nd-glibc-2.41/lib:/gnu/store/xjwrdjnmszbjlr63jhmqg1i75sv38xwq-glibc-2.41-static/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/7qwp1164axvx185i2gm0ixxcykb9x2nd-glibc-2.41/lib/locale' environment variable `TZDIR' unset phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'C.UTF-8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/VERSION' -> `./VERSION' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/.guix-dev' -> `./.guix-dev' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/guix.scm' -> `./guix.scm' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/LICENSE' -> `./LICENSE' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/.guix.dag.svg' -> `./.guix.dag.svg' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/RELEASE-NOTES.md' -> `./RELEASE-NOTES.md' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/.travis.yml' -> `./.travis.yml' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/README.md' -> `./README.md' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/.guix-dev-gcc-older' -> `./.guix-dev-gcc-older' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/.guix-dev-static' -> `./.guix-dev-static' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/Makefile' -> `./Makefile' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/.gitignore' -> `./.gitignore' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/cfw.gif' -> `./cfw.gif' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/INSTALL.md' -> `./INSTALL.md' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/bin/.gitignore' -> `./bin/.gitignore' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/scripts/gen_version_info.cmd' -> `./scripts/gen_version_info.cmd' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/scripts/gen_version_info.sh' -> `./scripts/gen_version_info.sh' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/test_suite.sh' -> `./test/test_suite.sh' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/dev_test_suite.sh' -> `./test/dev_test_suite.sh' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/lengthy_test_suite.sh' -> `./test/lengthy_test_suite.sh' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/dev_tests.rb' -> `./test/dev_tests.rb' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/lib/test-helpers.rb' -> `./test/lib/test-helpers.rb' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/performance/releases.org' -> `./test/performance/releases.org' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/src/unittests-math.cpp' -> `./test/src/unittests-math.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/src/unittests-main.cpp' -> `./test/src/unittests-main.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/issue243/multivariate_2traits.bed' -> `./test/data/issue243/multivariate_2traits.bed' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/issue243/multivariate_2traits.fam' -> `./test/data/issue243/multivariate_2traits.fam' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/issue243/multivariate_2traits.bim' -> `./test/data/issue243/multivariate_2traits.bim' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/issue26/mydata.bed' -> `./test/data/issue26/mydata.bed' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/correlated_phenotypes/Genotypes_gemma.csv' -> `./test/data/correlated_phenotypes/Genotypes_gemma.csv' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/correlated_phenotypes/Kinship_eigenval_gemma.txt' -> `./test/data/correlated_phenotypes/Kinship_eigenval_gemma.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/correlated_phenotypes/Kinship_eigenvec_gemma.txt' -> `./test/data/correlated_phenotypes/Kinship_eigenvec_gemma.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/correlated_phenotypes/Ysim_reg_gemma.txt' -> `./test/data/correlated_phenotypes/Ysim_reg_gemma.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/issue188/2000.bim' -> `./test/data/issue188/2000.bim' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/issue188/2000.bed' -> `./test/data/issue188/2000.bed' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/test/data/issue188/2000.fam' -> `./test/data/issue188/2000.fam' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/lm.h' -> `./src/lm.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/prdt.cpp' -> `./src/prdt.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/prdt.h' -> `./src/prdt.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/gemma_io.h' -> `./src/gemma_io.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/lapack.h' -> `./src/lapack.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/debug.h' -> `./src/debug.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/lmm.h' -> `./src/lmm.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/gemma_io.cpp' -> `./src/gemma_io.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/gzstream.h' -> `./src/gzstream.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/fastopenblas.h' -> `./src/fastopenblas.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/version.h' -> `./src/version.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/bslmmdap.h' -> `./src/bslmmdap.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/logistic.h' -> `./src/logistic.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/param.h' -> `./src/param.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/mvlmm.h' -> `./src/mvlmm.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/gemma.h' -> `./src/gemma.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/ldr.h' -> `./src/ldr.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/debug.cpp' -> `./src/debug.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/vc.cpp' -> `./src/vc.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/lapack.cpp' -> `./src/lapack.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/main.cpp' -> `./src/main.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/mvlmm.cpp' -> `./src/mvlmm.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/ldr.cpp' -> `./src/ldr.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/varcov.cpp' -> `./src/varcov.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/bslmmdap.cpp' -> `./src/bslmmdap.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/gemma.cpp' -> `./src/gemma.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/vc.h' -> `./src/vc.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/logistic.cpp' -> `./src/logistic.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/param.cpp' -> `./src/param.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/fastblas.h' -> `./src/fastblas.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/mathfunc.cpp' -> `./src/mathfunc.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/varcov.h' -> `./src/varcov.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/bslmm.h' -> `./src/bslmm.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/fastblas.cpp' -> `./src/fastblas.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/gzstream.cpp' -> `./src/gzstream.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/lmm.cpp' -> `./src/lmm.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/lm.cpp' -> `./src/lm.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/mathfunc.h' -> `./src/mathfunc.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/eigenlib.h' -> `./src/eigenlib.h' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/src/bslmm.cpp' -> `./src/bslmm.cpp' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/BXD_snps.txt' -> `./example/BXD_snps.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/mouse_hs1940.anno.txt' -> `./example/mouse_hs1940.anno.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/HLC.bed' -> `./example/HLC.bed' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/mouse_hs1940_snps.txt' -> `./example/mouse_hs1940_snps.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/HLC_covariates.txt' -> `./example/HLC_covariates.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/demo.txt' -> `./example/demo.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/mouse_hs1940.fam' -> `./example/mouse_hs1940.fam' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/HLC.bim' -> `./example/HLC.bim' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/HLC.simu.pheno.txt' -> `./example/HLC.simu.pheno.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/mouse_hs1940.bim' -> `./example/mouse_hs1940.bim' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/mouse_hs1940.geno.txt.gz' -> `./example/mouse_hs1940.geno.txt.gz' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/BXD_pheno.txt' -> `./example/BXD_pheno.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/mouse_hs1940_snps_anno.txt' -> `./example/mouse_hs1940_snps_anno.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/BXD_geno.txt.gz' -> `./example/BXD_geno.txt.gz' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/mouse_hs1940.pheno.txt' -> `./example/mouse_hs1940.pheno.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/BXD_covariates.txt' -> `./example/BXD_covariates.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/mouse_hs1940.bed' -> `./example/mouse_hs1940.bed' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/BXD_covariates2.txt' -> `./example/BXD_covariates2.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/example/HLC.fam' -> `./example/HLC.fam' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/.github/ISSUE_TEMPLATE/bug_report.md' -> `./.github/ISSUE_TEMPLATE/bug_report.md' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/doc/manual.pdf' -> `./doc/manual.pdf' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/doc/compile_GEMMA_win64.txt' -> `./doc/compile_GEMMA_win64.txt' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/doc/manual.bib' -> `./doc/manual.bib' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/doc/manual.tex' -> `./doc/manual.tex' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/doc/README.md' -> `./doc/README.md' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/doc/Makefile' -> `./doc/Makefile' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/doc/developers/design.org' -> `./doc/developers/design.org' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/doc/developers/profiling.md' -> `./doc/developers/profiling.md' `/gnu/store/9s23prqg7zg4hfwd75f8ang9fwm8xbfr-gemma-0.98.5-checkout/doc/example/data-munging.org' -> `./doc/example/data-munging.org' phase `unpack' succeeded after 0.3 seconds starting phase `prepare-build' phase `prepare-build' succeeded after 0.0 seconds starting phase `bootstrap' no 'configure.ac' or anything like that, doing nothing phase `bootstrap' succeeded after 0.0 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' patch-shebang: ./scripts/gen_version_info.sh: changing `/bin/bash' to `/gnu/store/5bccyn63h9dchddf947j6w6ia8vz6va5-bash-minimal-5.2.37/bin/bash' patch-shebang: ./test/dev_test_suite.sh: changing `/bin/sh' to `/gnu/store/5bccyn63h9dchddf947j6w6ia8vz6va5-bash-minimal-5.2.37/bin/sh' patch-shebang: ./test/lengthy_test_suite.sh: changing `/bin/sh' to `/gnu/store/5bccyn63h9dchddf947j6w6ia8vz6va5-bash-minimal-5.2.37/bin/sh' patch-shebang: ./test/test_suite.sh: changing `/bin/sh' to `/gnu/store/5bccyn63h9dchddf947j6w6ia8vz6va5-bash-minimal-5.2.37/bin/sh' phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `build' g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmm.o src/bslmm.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmmdap.o src/bslmmdap.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/debug.o src/debug.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/fastblas.o src/fastblas.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma.o src/gemma.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma_io.o src/gemma_io.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gzstream.o src/gzstream.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lapack.o src/lapack.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/ldr.o src/ldr.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lm.o src/lm.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lmm.o src/lmm.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/logistic.o src/logistic.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/main.o src/main.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/mathfunc.o src/mathfunc.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/mvlmm.o src/mvlmm.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/param.o src/param.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/prdt.o src/prdt.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/varcov.o src/varcov.cpp g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/vc.o src/vc.cpp In file included from /gnu/store/bpswla55k8725gg5mmzy2apiclr5wkx4-gcc-14.3.0/include/c++/vector:66, from src/vc.cpp:33: In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void ReadFile_cor(const std::string&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::map, unsigned int>&, const std::map, unsigned int>&, const std::map, double>&, const std::map, unsigned int>&, size_t, const double&, const double&, const double&, gsl_matrix*, gsl_matrix*, gsl_vector*, size_t&, size_t&, size_t&, size_t&)’ at src/vc.cpp:1200:37: /gnu/store/bpswla55k8725gg5mmzy2apiclr5wkx4-gcc-14.3.0/include/c++/bits/stl_vector.h:1144:41: warning: ‘bin’ may be used uninitialized [-Wmaybe-uninitialized] 1144 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ src/vc.cpp: In function ‘void ReadFile_cor(const std::string&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::map, unsigned int>&, const std::map, unsigned int>&, const std::map, double>&, const std::map, unsigned int>&, size_t, const double&, const double&, const double&, gsl_matrix*, gsl_matrix*, gsl_vector*, size_t&, size_t&, size_t&, size_t&)’: src/vc.cpp:1024:52: note: ‘bin’ was declared here 1024 | size_t n_nb, nsamp1, nsamp2, n12, bin_size = 10, bin; | ^~~ g++ -DOPENBLAS -isystem/gnu/store/19833iz2cagslalkgw0i834n0qv8qhx4-openblas-0.3.30/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc 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/main.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl -lz -lopenblas -o ./bin/gemma phase `build' succeeded after 15.6 seconds starting phase `check' WARNING: THIS TEST SUITE IS NO LONGER USED run system shunit2 egrep: warning: egrep is obsolescent; using grep -E testBslmm1 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 1 (option 1); first value = 1791095845 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 =0.590431 se(pve) =0.0480392 Calculating UtX... initial value of h = 0.590431 initial value of rho = 0.41375 initial value of pi = 0.00269142 initial value of |gamma| = 29 0% 0.00 ==== 9% 0.18 ========= 18% 0.18 ============= 27% 0.18 ================== 36% 0.18 ====================== 45% 0.17 =========================== 55% 0.17 =============================== 64% 0.17 ==================================== 73% 0.16 ======================================== 82% 0.16 ============================================= 91% 0.16 ================================================== 100% 0.16 **** INFO: Done. testBslmm2 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 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 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm3 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 1 (option 1); first value = 1791095845 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% 0.22 ========= 18% 0.22 ============= 27% 0.21 ================== 36% 0.21 ====================== 45% 0.21 =========================== 55% 0.21 =============================== 64% 0.21 ==================================== 73% 0.21 ======================================== 82% 0.21 ============================================= 91% 0.21 ================================================== 100% 0.21 **** INFO: Done. testBslmm4 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 Adding Breeding Values ... Start Eigen-Decomposition... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm5 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 100 (option 100); first value = 2333906440 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixKFullLOCO1 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModelFullLOCO1 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 10768 Start Eigen-Decomposition... pve estimate =0.593114 se(pve) =0.0332587 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. ## total computation time = 3.1714 min testCenteredRelatednessMatrixK GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 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. testUnivariateLinearMixedModel GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 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. ## total computation time = 4.26642 min testLinearMixedModelPhenotypes GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 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. testPlinkStandardRelatednessMatrixK GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 427 ## number of analyzed individuals = 427 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 358499 ## number of analyzed SNPs = 273349 Calculating Relatedness Matrix ... 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% ====== 14% ====== 14% ======= 14% ======= 15% ======= 15% ======= 15% ======= 15% ======= 16% ======= 16% ======== 16% ======== 16% ======== 17% ======== 17% ======== 17% ======== 18% ======== 18% ========= 18% ========= 18% ========= 19% ========= 19% ========= 19% ========= 20% ========= 20% ========== 20% 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================================================== 100% **** INFO: Done. testPlinkLinearMixedModelCovariates GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 427 ## number of analyzed individuals = 427 ## number of covariates = 2 ## number of phenotypes = 1 ## number of total SNPs/var = 358499 ## number of analyzed SNPs = 223070 Start Eigen-Decomposition... pve estimate =0.365545 se(pve) =0.47481 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% 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ASSERT:expected:<223243> but was:<223071> ASSERT:expected:<89757159113.94> but was:<89689177955.28> shunit2:ERROR testPlinkLinearMixedModelCovariates() returned non-zero return code. Ran 12 tests. FAILED (failures=3) error: in phase 'check': uncaught exception: %exception #<&invoke-error program: "./test_suite.sh" arguments: () exit-status: 1 term-signal: #f stop-signal: #f> phase `check' failed after 526.1 seconds command "./test_suite.sh" failed with status 1 build process 18 exited with status 256