Hi, On 14/02/21 at 22:38 +0100, Étienne Mollier wrote: > Hi Lucas, > > I couldn't reproduce the issue in gemma neither on mostly clean > chroot running on my native hardware. > > Lucas Nussbaum, on 2021-02-13 18:12:12 +0100: > > The full build log is available from: > > http://qa-logs.debian.net/2021/02/13/gemma_0.98.4+dfsg-1_unstable.log > [...] > > > > 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. > > You will find a diff in attachment. I see error accumulation in > test results, some orders of magnitude in some cases. The only > two meaningful difference I could find is the kernel version, > and the fact that things are running on either regular or > virtualised environment, after reducing possible sources of > inconsistencies. (I had some remains of perl 5.30 and libisl22 > in my old chroot initially, but making sure they were gone > didn't bring much changes.) > > Note I truncated the end of the diff after the failure for the > sake of brevity; let me know if that was a mistake. > > > 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. > > GSL is involved. Maybe a next step would be to try on a virtual > machine. What are the CPU flags on EC2 VM instances usually ? > > Here is my cpu at t time for reference: > > Architecture: x86_64 > CPU op-mode(s): 32-bit, 64-bit > Byte Order: Little Endian > Address sizes: 43 bits physical, 48 bits virtual > CPU(s): 6 > On-line CPU(s) list: 0-5 > Thread(s) per core: 1 > Core(s) per socket: 6 > Socket(s): 1 > NUMA node(s): 1 > Vendor ID: AuthenticAMD > CPU family: 23 > Model: 113 > Model name: AMD Ryzen 5 3600 6-Core Processor > Stepping: 0 > Frequency boost: enabled > CPU MHz: 3853.218 > CPU max MHz: 3600.0000 > CPU min MHz: 2200.0000 > BogoMIPS: 7185.83 > Virtualization: AMD-V > L1d cache: 192 KiB > L1i cache: 192 KiB > L2 cache: 3 MiB > L3 cache: 32 MiB > NUMA node0 CPU(s): 0-5 > Vulnerability Itlb multihit: Not affected > Vulnerability L1tf: Not affected > Vulnerability Mds: Not affected > Vulnerability Meltdown: Not affected > Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass > disabled via prctl and seccomp > Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and > __user pointer sanitization > Vulnerability Spectre v2: Mitigation; Full AMD retpoline, IBPB > conditional, STIBP disabled, RSB filling > Vulnerability Srbds: Not affected > Vulnerability Tsx async abort: Not affected > Flags: fpu vme de pse tsc msr pae mce > cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse > sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm > constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid > aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 > movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm > extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs > skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc > mwaitx cpb cat_l3 cdp_l3 hw_pstate sme ssbd mba sev ibpb stibp > vmmcall sev_es fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx > smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves > cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf > xsaveerptr rdpru wbnoinvd arat npt lbrv svm_lock nrip_save > tsc_scale vmcb_clean flushbyasid decodeassists pausefilter > pfthreshold avic v_vmsave_vmload vgif umip rdpid overflow_recov > succor smca
I tried again and could reproduce the failure. I attached the new build log and the content of /proc/cpuinfo. If this doesn't shed some light, I can try on some other machines. Let me know. Lucas
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-11-206.eu-central-1.compute.internal +==============================================================================+ | gemma 0.98.4+dfsg-1 (amd64) Fri, 19 Feb 2021 14:46:41 +0000 | +==============================================================================+ Package: gemma Version: 0.98.4+dfsg-1 Source Version: 0.98.4+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-1434b2eb-9477-4863-881a-09fc0a218636' with '<<CHROOT>>' I: NOTICE: Log filtering will replace 'build/gemma-mfu544/resolver-1Z9KbY' with '<<RESOLVERDIR>>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'gemma' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gemma.git Please use: git clone https://salsa.debian.org/med-team/gemma.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 42.5 MB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main gemma 0.98.4+dfsg-1 (dsc) [2117 B] Get:2 http://127.0.0.1:12990/debian sid/main gemma 0.98.4+dfsg-1 (tar) [42.5 MB] Get:3 http://127.0.0.1:12990/debian sid/main gemma 0.98.4+dfsg-1 (diff) [5152 B] Fetched 42.5 MB in 0s (106 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/gemma-mfu544/gemma-0.98.4+dfsg' with '<<PKGBUILDDIR>>' I: NOTICE: Log filtering will replace 'build/gemma-mfu544' with '<<BUILDDIR>>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B] Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [412 B] Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [497 B] Fetched 1866 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils catch debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-10 groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libeigen3-dev libelf1 libfile-stripnondeterminism-perl libgfortran-10-dev libgfortran5 libglib2.0-0 libgsl-dev libgsl25 libgslcblas0 libicu67 libmagic-mgc libmagic1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf sensible-utils shunit2 zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-10-multilib gfortran-10-doc libcoarrays-dev groff libeigen3-doc libmpfrc++-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils catch debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-10 groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libeigen3-dev libelf1 libfile-stripnondeterminism-perl libgfortran-10-dev libgfortran5 libglib2.0-0 libgsl-dev libgsl25 libgslcblas0 libicu67 libmagic-mgc libmagic1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-main-dummy sensible-utils shunit2 zlib1g-dev 0 upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 44.6 MB of archives. After this operation, 230 MB of additional disk space will be used. 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up shunit2 (2.1.6-1.2) ... Setting up libicu67:amd64 (67.1-6) ... Setting up libgslcblas0:amd64 (2.6+dfsg-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libgsl25:amd64 (2.6+dfsg-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.66.7-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.3) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up catch (1.12.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libgfortran-10-dev:amd64 (10.2.1-6) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.3+b1) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libopenblas0-pthread:amd64 (0.3.13+ds-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libeigen3-dev (3.3.9-2) ... Setting up gfortran-10 (10.2.1-6) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libopenblas0:amd64 (0.3.13+ds-2) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libopenblas-pthread-dev:amd64 (0.3.13+ds-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:10.2.1-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up dh-autoreconf (20) ... Setting up libopenblas-dev:amd64 (0.3.13+ds-2) ... Setting up debhelper (13.3.3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-9) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.35.1-7 dpkg-dev_1.20.7.1 g++-10_10.2.1-6 gcc-10_10.2.1-6 libc6-dev_2.31-9 libstdc++-10-dev_10.2.1-6 libstdc++6_10.2.1-6 linux-libc-dev_5.10.13-1 Package versions: adduser_3.118 apt_2.2.0 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11 base-passwd_3.5.49 bash_5.1-2 binutils_2.35.1-7 binutils-common_2.35.1-7 binutils-x86-64-linux-gnu_2.35.1-7 bsdextrautils_2.36.1-7 bsdutils_1:2.36.1-7 build-essential_12.9 bzip2_1.0.8-4 catch_1.12.1-1 coreutils_8.32-4+b1 cpp_4:10.2.1-1 cpp-10_10.2.1-6 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.3 debian-archive-keyring_2019.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dpkg_1.20.7.1 dpkg-dev_1.20.7.1 dwz_0.13+20210201-1 e2fsprogs_1.46.1-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1 g++-10_10.2.1-6 gcc_4:10.2.1-1 gcc-10_10.2.1-6 gcc-10-base_10.2.1-6 gcc-9-base_9.3.0-22 gettext_0.21-4 gettext-base_0.21-4 gfortran_4:10.2.1-1 gfortran-10_10.2.1-6 gpgv_2.2.27-1 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.0 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6 libatomic1_10.2.1-6 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.1-7 libblkid1_2.36.1-7 libbz2-1.0_1.0.8-4 libc-bin_2.31-9 libc-dev-bin_2.31-9 libc6_2.31-9 libc6-dev_2.31-9 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6 libcom-err2_1.46.1-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7 libctf0_2.35.1-7 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.256 libdebhelper-perl_13.3.3 libdpkg-perl_1.20.7.1 libeigen3-dev_3.3.9-2 libelf1_0.183-1 libext2fs2_1.46.1-1 libfakeroot_1.25.3-1.1 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-6 libgcc-s1_10.2.1-6 libgcrypt20_1.8.7-3 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran-10-dev_10.2.1-6 libgfortran5_10.2.1-6 libglib2.0-0_2.66.7-1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-7 libgomp1_10.2.1-6 libgpg-error0_1.38-2 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.7-2 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libitm1_10.2.1-6 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 liblsan0_10.2.1-6 liblz4-1_1.9.3-1 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-7 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libnettle8_3.7-2 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopenblas-dev_0.3.13+ds-2 libopenblas-pthread-dev_0.3.13+ds-2 libopenblas0_0.3.13+ds-2 libopenblas0-pthread_0.3.13+ds-2 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-4 libpam-modules-bin_1.4.0-4 libpam-runtime_1.4.0-4 libpam0g_1.4.0-4 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-2 libpipeline1_1.5.3-1 libquadmath0_10.2.1-6 libseccomp2_2.5.1-1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-7 libss2_1.46.1-1 libssl1.1_1.1.1j-1 libstdc++-10-dev_10.2.1-6 libstdc++6_10.2.1-6 libsub-override-perl_0.09-2 libsystemd0_247.3-1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libtsan0_10.2.1-6 libubsan1_10.2.1-6 libuchardet0_0.0.7-1 libudev1_247.3-1 libunistring2_0.9.10-4 libuuid1_2.36.1-7 libxml2_2.9.10+dfsg-6.3+b1 libxxhash0_0.8.0-2 libzstd1_1.4.8+dfsg-2 linux-libc-dev_5.10.13-1 login_1:4.8.1-1 logsave_1.46.1-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.36.1-7 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-2 perl-base_5.32.1-2 perl-modules-5.32_5.32.1-2 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 shunit2_2.1.6-1.2 sysvinit-utils_2.96-5 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-7 xz-utils_5.2.5-1.0 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gemma Binary: gemma, gemma-doc Architecture: any all Version: 0.98.4+dfsg-1 Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Steffen Moeller <[email protected]> Homepage: https://www.xzlab.org/software.html Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/gemma Vcs-Git: https://salsa.debian.org/med-team/gemma.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2 Package-List: gemma deb science optional arch=any gemma-doc deb doc optional arch=all Checksums-Sha1: 85c82ad902b91a62f37dc6db462f178ed64c156c 42535920 gemma_0.98.4+dfsg.orig.tar.xz 73457690c96895a5444690b21a835bdf9dfae5d6 5152 gemma_0.98.4+dfsg-1.debian.tar.xz Checksums-Sha256: ea2833c102e94894b5b6c65f6d9deaa717cc4502e842057f594273bf36fbd702 42535920 gemma_0.98.4+dfsg.orig.tar.xz ce7674e11f3744a50ae2e32b6b23501b5f271c38958a7681b78cf80dd01c26b2 5152 gemma_0.98.4+dfsg-1.debian.tar.xz Files: 81a168398df11339385afb0643057463 42535920 gemma_0.98.4+dfsg.orig.tar.xz 0f1db7a9d2829256ac137b377ad66d8e 5152 gemma_0.98.4+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmAZsbEUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafFNGBAAjgaYQC9B5nXKX5Odi3Lu7zHCcgLW TiyMGllQMYtVTJRPsFt3KypnTYHFdtsxLkF9TX/i9huaQ1K+j4D5iBHt5yU56PR8 Tc5WQDLYTfLtTaDqgblt2FOeZN5f5pIFs24MM3RcOp3TQLDaMVPiGMmmRpd3hD+6 JXVh699xdvkYuj+rlPT3xevem73SyVkVR/ktmpyCnINgWpVTnFhirVZ7Z46lnjJ5 TjURQYpNhFJ/buTGftnQqj5by2EjeFIHvWdqU0Kmz9dnhsieTI0EIoS79hcy0IAo ObwetXTKd/a2+BbeA3davE3p22O/f3Z1tPYEAZegBDE6RxPAdXKOd4n3/+ITc/1N tO+UxO7lXSw/sZlFoBuMHiUoHE28mMpLDEX4iOS447n1UnZzFPI04raSajlSItUD Ror/hLi80eR91I3YNshFxBxsmtA1Kis7W4XGuZVwwqDakEZKT9mA7v9wkwlwGcfP F9yqsR+Mu+6SnCOGMa0g9ZCoJFFdL5zYksH47tPT5aRFgwdD61gbRPWZjlkGvZNG 5cmE3MQSV03sUxZAffYUmhqX+jUmfB99rXmB8rwDxc/qC3uwXqNa1ytLYgMgbZqr xBOq/de6fc4Yp2Svo3CYcSRhM8xy7AGoMtt1px466TYGmuc3dBlTGdbEf/dovGyb 536y31pxW8O8ohs= =foV+ -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.FkbA9ArT/trustedkeys.kbx': General error gpgv: Signature made Tue Feb 2 20:10:25 2021 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "[email protected]" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gemma_0.98.4+dfsg-1.dsc dpkg-source: info: extracting gemma in /<<PKGBUILDDIR>> dpkg-source: info: unpacking gemma_0.98.4+dfsg.orig.tar.xz dpkg-source: info: unpacking gemma_0.98.4+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Reproducible_builds.patch dpkg-source: info: applying no-lquadmath.patch dpkg-source: info: applying Makefile.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-1434b2eb-9477-4863-881a-09fc0a218636 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -sa -rfakeroot dpkg-buildpackage: info: source package gemma dpkg-buildpackage: info: source version 0.98.4+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra <[email protected]> dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean install -d /<<BUILDDIR>>/gemma-0.98.4\+dfsg/debian/.debhelper/generated/_source/home make -j4 clean make[1]: Entering directory '/<<PKGBUILDDIR>>' rm -vf ./src/*.o rm -vf ./src/*~ rm -vf ./test/src/*.o rm -vf ./bin/gemma rm -vf ./bin/unittests-gemma make[1]: Leaving directory '/<<PKGBUILDDIR>>' debian/rules override_dh_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/gemma.substvars debian/gemma-doc.substvars debian/files rm -fr -- debian/gemma/ debian/tmp/ debian/gemma-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *.log rm -rf test/output/ rm -f bin/gemma make[1]: Leaving directory '/<<PKGBUILDDIR>>' dpkg-source -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building gemma using existing ./gemma_0.98.4+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building gemma in gemma_0.98.4+dfsg-1.debian.tar.xz dpkg-source: info: building gemma in gemma_0.98.4+dfsg-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure install -d /<<BUILDDIR>>/gemma-0.98.4\+dfsg/debian/.debhelper/generated/_source/home dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[1]: 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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmm.o src/bslmm.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmmdap.o src/bslmmdap.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/debug.o src/debug.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/fastblas.o src/fastblas.cpp src/debug.cpp:61:44: warning: extra ‘;’ [-Wpedantic] 61 | bool is_debug_mode() { return debug_mode; }; | ^ src/debug.cpp:62:54: warning: extra ‘;’ [-Wpedantic] 62 | bool is_debug_data_mode() { return debug_data_mode; }; | ^ src/debug.cpp:63:49: warning: extra ‘;’ [-Wpedantic] 63 | bool is_no_check_mode() { return !debug_check; }; | ^ src/debug.cpp:64:45: warning: extra ‘;’ [-Wpedantic] 64 | bool is_check_mode() { return debug_check; }; | ^ src/debug.cpp:65:53: warning: extra ‘;’ [-Wpedantic] 65 | bool is_fpe_check_mode() { return debug_fpe_check; }; | ^ src/debug.cpp:66:47: warning: extra ‘;’ [-Wpedantic] 66 | bool is_strict_mode() { return debug_strict; }; | ^ src/debug.cpp:67:45: warning: extra ‘;’ [-Wpedantic] 67 | bool is_quiet_mode() { return debug_quiet; }; | ^ src/debug.cpp:68:59: warning: extra ‘;’ [-Wpedantic] 68 | bool is_issue(uint issue) { return issue == debug_issue; }; | ^ src/debug.cpp:69:47: warning: extra ‘;’ [-Wpedantic] 69 | bool is_legacy_mode() { return debug_legacy; }; | ^ 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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma.o src/gemma.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 -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++ -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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gzstream.o src/gzstream.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lapack.o src/lapack.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/ldr.o src/ldr.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lm.o src/lm.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lmm.o src/lmm.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/logistic.o src/logistic.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/main.o src/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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/mathfunc.o src/mathfunc.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/mvlmm.o src/mvlmm.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/param.o src/param.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/prdt.o src/prdt.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/varcov.o src/varcov.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 -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/vc.o src/vc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/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 make[1]: Leaving directory '/<<PKGBUILDDIR>>' debian/rules override_dh_auto_test make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_test --no-parallel make -j1 check 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 = 0.0556137 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 = 0.030633 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 = 0.0253045 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-DRVxrrgs dh_auto_test: error: make -j1 check returned exit code 2 make[1]: *** [debian/rules:22: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:12: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2021-02-19T14:48:05Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<<BUILDDIR>> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 254092 Build-Time: 60 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 14 Job: gemma_0.98.4+dfsg-1 Machine Architecture: amd64 Package: gemma Package-Time: 84 Source-Version: 0.98.4+dfsg-1 Space: 254092 Status: attempted Version: 0.98.4+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-02-19T14:48:05Z Build needed 00:01:24, 254092k disk space E: Build failure (dpkg-buildpackage died)
processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 85 model name : Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz stepping : 7 microcode : 0x5003005 cpu MHz : 3100.070 cache size : 36608 KB physical id : 0 siblings : 4 core id : 0 cpu cores : 2 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves ida arat pku ospke bugs : cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds swapgs itlb_multihit bogomips : 4999.99 clflush size : 64 cache_alignment : 64 address sizes : 46 bits physical, 48 bits virtual power management: processor : 1 vendor_id : GenuineIntel cpu family : 6 model : 85 model name : Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz stepping : 7 microcode : 0x5003005 cpu MHz : 3094.903 cache size : 36608 KB physical id : 0 siblings : 4 core id : 1 cpu cores : 2 apicid : 2 initial apicid : 2 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves ida arat pku ospke bugs : cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds swapgs itlb_multihit bogomips : 4999.99 clflush size : 64 cache_alignment : 64 address sizes : 46 bits physical, 48 bits virtual power management: processor : 2 vendor_id : GenuineIntel cpu family : 6 model : 85 model name : Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz stepping : 7 microcode : 0x5003005 cpu MHz : 3131.637 cache size : 36608 KB physical id : 0 siblings : 4 core id : 0 cpu cores : 2 apicid : 1 initial apicid : 1 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves ida arat pku ospke bugs : cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds swapgs itlb_multihit bogomips : 4999.99 clflush size : 64 cache_alignment : 64 address sizes : 46 bits physical, 48 bits virtual power management: processor : 3 vendor_id : GenuineIntel cpu family : 6 model : 85 model name : Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz stepping : 7 microcode : 0x5003005 cpu MHz : 3129.880 cache size : 36608 KB physical id : 0 siblings : 4 core id : 1 cpu cores : 2 apicid : 3 initial apicid : 3 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves ida arat pku ospke bugs : cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds swapgs itlb_multihit bogomips : 4999.99 clflush size : 64 cache_alignment : 64 address sizes : 46 bits physical, 48 bits virtual power management:
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