[Debian-med-packaging] Bug#982692: Bug#982692: gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2
Lucas Nussbaum
lucas at debian.org
Fri Feb 19 14:52:34 GMT 2021
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
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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
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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
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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
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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
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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
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Selecting previously unselected package libopenblas0-pthread:amd64.
Preparing to unpack .../42-libopenblas0-pthread_0.3.13+ds-2_amd64.deb ...
Unpacking libopenblas0-pthread:amd64 (0.3.13+ds-2) ...
Selecting previously unselected package libopenblas0:amd64.
Preparing to unpack .../43-libopenblas0_0.3.13+ds-2_amd64.deb ...
Unpacking libopenblas0:amd64 (0.3.13+ds-2) ...
Selecting previously unselected package libopenblas-pthread-dev:amd64.
Preparing to unpack .../44-libopenblas-pthread-dev_0.3.13+ds-2_amd64.deb ...
Unpacking libopenblas-pthread-dev:amd64 (0.3.13+ds-2) ...
Selecting previously unselected package libopenblas-dev:amd64.
Preparing to unpack .../45-libopenblas-dev_0.3.13+ds-2_amd64.deb ...
Unpacking libopenblas-dev:amd64 (0.3.13+ds-2) ...
Selecting previously unselected package shunit2.
Preparing to unpack .../46-shunit2_2.1.6-1.2_all.deb ...
Unpacking shunit2 (2.1.6-1.2) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../47-zlib1g-dev_1%3a1.2.11.dfsg-2_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../48-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ...
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 <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller at debian.org>
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:
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73457690c96895a5444690b21a835bdf9dfae5d6 5152 gemma_0.98.4+dfsg-1.debian.tar.xz
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Files:
81a168398df11339385afb0643057463 42535920 gemma_0.98.4+dfsg.orig.tar.xz
0f1db7a9d2829256ac137b377ad66d8e 5152 gemma_0.98.4+dfsg-1.debian.tar.xz
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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 "npatra974 at gmail.com"
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 <npatra974 at gmail.com>
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)
-------------- next part --------------
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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