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Bug 492484 - sci-libs/spqr-1.3.1 fails tests
Summary: sci-libs/spqr-1.3.1 fails tests
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords: TESTFAILURE
Depends on:
Blocks: 575366 627094
  Show dependency tree
 
Reported: 2013-11-25 07:39 UTC by Patrick Lauer
Modified: 2019-03-21 22:39 UTC (History)
5 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments

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Description Patrick Lauer gentoo-dev 2013-11-25 07:39:18 UTC
./qrdemo < /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1/Matrix/west0067.mtx || exit 1
Matrix     67-by-67     nnz:    294
residual:  8.2e+00 rank:     67
*** Error in `/var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Demo/.libs/qrdemo': free(): invalid next size (fast): 0x0000000002608040 ***
residual:  8.2e+00 rank:      0
======= Backtrace: =========
/lib64/libc.so.6(+0x7c83e)[0x7f09712fa83e]
/lib64/libc.so.6(+0x7d527)[0x7f09712fb527]
/usr/lib64/libcholmod.so.0(cholmod_l_free+0x3f)[0x7f09716daa7f]
/var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Source/.libs/libspqr.so.0(_Z19SuiteSparseQR_qmultIdEP20cholmod_dense_structiP27SuiteSparseQR_factorizationIT_ES1_P21cholmod_common_struct+0x427)[0x7f09718f70a7]
/var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Demo/.libs/qrdemo[0x401234]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f09712a2c05]
/var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Demo/.libs/qrdemo[0x4012dd]
======= Memory map: ========
00400000-00402000 r-xp 00000000 fd:03 2952850701                         /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Demo/.libs/qrdemo
00601000-00602000 r--p 00001000 fd:03 2952850701                         /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Demo/.libs/qrdemo
00602000-00603000 rw-p 00002000 fd:03 2952850701                         /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Demo/.libs/qrdemo
02601000-02622000 rw-p 00000000 00:00 0                                  [heap]
7f096f18e000-7f096f1c9000 r-xp 00000000 fd:03 1350541925                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libquadmath.so.0.0.0
7f096f1c9000-7f096f3c8000 ---p 0003b000 fd:03 1350541925                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libquadmath.so.0.0.0
7f096f3c8000-7f096f3c9000 r--p 0003a000 fd:03 1350541925                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libquadmath.so.0.0.0
7f096f3c9000-7f096f3ca000 rw-p 0003b000 fd:03 1350541925                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libquadmath.so.0.0.0
7f096f3ca000-7f096f3e2000 r-xp 00000000 fd:03 1885042221                 /lib64/libpthread-2.17.so
7f096f3e2000-7f096f5e1000 ---p 00018000 fd:03 1885042221                 /lib64/libpthread-2.17.so
7f096f5e1000-7f096f5e2000 r--p 00017000 fd:03 1885042221                 /lib64/libpthread-2.17.so
7f096f5e2000-7f096f5e3000 rw-p 00018000 fd:03 1885042221                 /lib64/libpthread-2.17.so
7f096f5e3000-7f096f5e7000 rw-p 00000000 00:00 0 
7f096f5e7000-7f096f6ff000 r-xp 00000000 fd:03 1350541929                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libgfortran.so.3.0.0
7f096f6ff000-7f096f8fe000 ---p 00118000 fd:03 1350541929                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libgfortran.so.3.0.0
7f096f8fe000-7f096f8ff000 r--p 00117000 fd:03 1350541929                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libgfortran.so.3.0.0
7f096f8ff000-7f096f901000 rw-p 00118000 fd:03 1350541929                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libgfortran.so.3.0.0
7f096f901000-7f096f908000 r-xp 00000000 fd:03 1885042230                 /lib64/librt-2.17.so
7f096f908000-7f096fb07000 ---p 00007000 fd:03 1885042230                 /lib64/librt-2.17.so
7f096fb07000-7f096fb08000 r--p 00006000 fd:03 1885042230                 /lib64/librt-2.17.so
7f096fb08000-7f096fb09000 rw-p 00007000 fd:03 1885042230                 /lib64/librt-2.17.so
7f096fb09000-7f096fb0f000 r-xp 00000000 fd:03 1113259405                 /usr/lib64/libcolamd.so.0.0.0
7f096fb0f000-7f096fd0e000 ---p 00006000 fd:03 1113259405                 /usr/lib64/libcolamd.so.0.0.0
7f096fd0e000-7f096fd0f000 r--p 00005000 fd:03 1113259405                 /usr/lib64/libcolamd.so.0.0.0
7f096fd0f000-7f096fd10000 rw-p 00006000 fd:03 1113259405                 /usr/lib64/libcolamd.so.0.0.0
7f096fd10000-7f096fd18000 r-xp 00000000 fd:03 32186911                   /usr/lib64/libamd.so.0.0.0
7f096fd18000-7f096ff17000 ---p 00008000 fd:03 32186911                   /usr/lib64/libamd.so.0.0.0
7f096ff17000-7f096ff18000 r--p 00007000 fd:03 32186911                   /usr/lib64/libamd.so.0.0.0
7f096ff18000-7f096ff19000 rw-p 00008000 fd:03 32186911                   /usr/lib64/libamd.so.0.0.0
7f096ff19000-7f096ff2f000 r-xp 00000000 fd:03 1350460951                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libgcc_s.so.1
7f096ff2f000-7f097012e000 ---p 00016000 fd:03 1350460951                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libgcc_s.so.1
7f097012e000-7f097012f000 r--p 00015000 fd:03 1350460951                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libgcc_s.so.1
7f097012f000-7f0970130000 rw-p 00016000 fd:03 1350460951                 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.8.2/libgcc_s.so.1
7f0970130000-7f097022d000 r-xp 00000000 fd:03 1880950226                 /lib64/libm-2.17.so
7f097022d000-7f097042c000 ---p 000fd000 fd:03 1880950226                 /lib64/libm-2.17.so
7f097042c000-7f097042d000 r--p 000fc000 fd:03 1880950226                 /lib64/libm-2.17.so
7f097042d000-7f097042e000 rw-p 000fd000 fd:03 1880950226                 /lib64/libm-2.17.so
7f097042e000-7f097042f000 r-xp 00000000 fd:03 2958108593                 /usr/lib64/libsuitesparseconfig.so.0.0.0
7f097042f000-7f097062e000 ---p 00001000 fd:03 2958108593                 /usr/lib64/libsuitesparseconfig.so.0.0.0
7f097062e000-7f097062f000 r--p 00000000 fd:03 2958108593                 /usr/lib64/libsuitesparseconfig.so.0.0.0
7f097062f000-7f0970630000 rw-p 00001000 fd:03 2958108593                 /usr/lib64/libsuitesparseconfig.so.0.0.0
7f0970630000-7f0970686000 r-xp 00000000 fd:03 1627204943                 /usr/lib64/blas/reference/libblas.so.0.0.0
7f0970686000-7f0970885000 ---p 00056000 fd:03 1627204943                 /usr/lib64/blas/reference/libblas.so.0.0.0
7f0970885000-7f0970886000 r--p 00055000 fd:03 1627204943                 /usr/lib64/blas/reference/libblas.so.0.0.0
7f0970886000-7f0970887000 rw-p 00056000 fd:03 1627204943                 /usr/lib64/blas/reference/libblas.so.0.0.0
7f0970887000-7f0970d69000 r-xp 00000000 fd:03 1627986175                 /usr/lib64/lapack/reference/liblapack.so.0.0.0
7f0970d69000-7f0970f68000 ---p 004e2000 fd:03 1627986175                 /usr/lib64/lapack/reference/liblapack.so.0.0.0
7f0970f68000-7f0970f69000 r--p 004e1000 fd:03 1627986175                 /usr/lib64/lapack/reference/liblapack.so.0.0.0
7f0970f69000-7f0970f6d000 rw-p 004e2000 fd:03 1627986175                 /usr/lib64/lapack/reference/liblapack.so.0.0.0
7f0970f6d000-7f097107a000 rw-p 00000000 00:00 0 
7f097107a000-7f097107c000 r-xp 00000000 fd:03 1885042222                 /lib64/libdl-2.17.so
7f097107c000-7f097127c000 ---p 00002000 fd:03 1885042222                 /lib64/libdl-2.17.so
7f097127c000-7f097127d000 r--p 00002000 fd:03 1885042222                 /lib64/libdl-2.17.so
7f097127d000-7f097127e000 rw-p 00003000 fd:03 1885042222                 /lib64/libdl-2.17.so
7f097127e000-7f097141f000 r-xp 00000000 fd:03 1885924040                 /lib64/libc-2.17.so
7f097141f000-7f097161f000 ---p 001a1000 fd:03 1885924040                 /lib64/libc-2.17.so
7f097161f000-7f0971623000 r--p 001a1000 fd:03 1885924040                 /lib64/libc-2.17.so
7f0971623000-7f0971625000 rw-p 001a5000 fd:03 1885924040                 /lib64/libc-2.17.so
7f0971625000-7f0971629000 rw-p 00000000 00:00 0 
7f0971629000-7f09716ec000 r-xp 00000000 fd:03 2958127766                 /usr/lib64/libcholmod.so.0.0.0
7f09716ec000-7f09718eb000 ---p 000c3000 fd:03 2958127766                 /usr/lib64/libcholmod.so.0.0.0
7f09718eb000-7f09718ec000 r--p 000c2000 fd:03 2958127766                 /usr/lib64/libcholmod.so.0.0.0
7f09718ec000-7f09718ed000 rw-p 000c3000 fd:03 2958127766                 /usr/lib64/libcholmod.so.0.0.0
7f09718ed000-7f0971919000 r-xp 00000000 fd:03 2689577398                 /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Source/.libs/libspqr.so.0.0.0
7f0971919000-7f0971b18000 ---p 0002c000 fd:03 2689577398                 /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Source/.libs/libspqr.so.0.0.0
7f0971b18000-7f0971b19000 r--p 0002b000 fd:03 2689577398                 /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Source/.libs/libspqr.so.0.0.0
7f0971b19000-7f0971b1a000 rw-p 0002c000 fd:03 2689577398                 /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Source/.libs/libspqr.so.0.0.0
7f0971b1a000-7f0971b2a000 r-xp 00000000 fd:03 1108188910                 /usr/lib64/libsandbox.so
7f0971b2a000-7f0971d2a000 ---p 00010000 fd:03 1108188910                 /usr/lib64/libsandbox.so
7f0971d2a000-7f0971d2b000 r--p 00010000 fd:03 1108188910                 /usr/lib64/libsandbox.so
7f0971d2b000-7f0971d2c000 rw-p 00011000 fd:03 1108188910                 /usr/lib64/libsandbox.so
7f0971d2c000-7f0971d32000 rw-p 00000000 00:00 0 
7f0971d32000-7f0971d54000 r-xp 00000000 fd:03 1880776186                 /lib64/ld-2.17.so
7f0971f33000-7f0971f3c000 rw-p 00000000 00:00 0 
7f0971f4f000-7f0971f53000 rw-p 00000000 00:00 0 
7f0971f53000-7f0971f54000 r--p 00021000 fd:03 1880776186                 /lib64/ld-2.17.so
7f0971f54000-7f0971f55000 rw-p 00022000 fd:03 1880776186                 /lib64/ld-2.17.so
7f0971f55000-7f0971f56000 rw-p 00000000 00:00 0 
7fff62a22000-7fff62a47000 rw-p 00000000 00:00 0                          [stack]
7fff62b34000-7fff62b35000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
/bin/sh: line 1:  3166 Aborted                 ./qrdemo < /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1/Matrix/west0067.mtx
make[2]: *** [check-local] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Demo'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1_build/Demo'
make: *** [check-recursive] Error 1
 * ERROR: sci-libs/spqr-1.3.1::gentoo failed (test phase):
 *   emake failed


Portage 2.2.7 (default/linux/amd64/13.0/desktop/kde, gcc-4.8.2, glibc-2.17, 3.11.6-gentoo x86_64)
=================================================================
System uname: Linux-3.11.6-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2
KiB Mem:     7920588 total,   3132428 free
KiB Swap:   25165812 total,  25165812 free
Timestamp of tree: Unknown
ld GNU ld (GNU Binutils) 2.23.2
app-shells/bash:          4.2_p45
dev-lang/python:          2.7.5-r4, 3.3.2-r2
dev-util/cmake:           2.8.12.1-r1
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.12.6, 1.13.4, 1.14
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.8.2
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.11 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo x-overlay
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms split-elog strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/overlay"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr egl emboss encode exif fam firefox flac fortran gdbm gif gpm gtk iconv ipv6 jpeg kde kipi lcms ldap libnotify mad mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl ogg opengl openmp openvg pam pango pcre pdf phonon plasma png policykit ppds qt3support qt4 readline sdl semantic-desktop session spell sqlite sse sse2 ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xa xcb xcomposite xinerama xml xscreensaver xv xvfb xvid zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19" USERLAND="GNU" VIDEO_CARDS="vesa" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON
Comment 1 Tobias Klausmann gentoo-dev 2016-06-07 16:37:51 UTC
Similar on alpha:

Matrix      2-by-2      nnz:      3
residual:  0.0e+00 rank:      2
residual:  0.0e+00 rank:      2
residual:  0.0e+00 rank:      2
./qrdemo < /var/tmp/portage/sci-libs/spqr-1.3.1/work/spqr-1.3.1/Matrix/west0067.
mtx || exit 1
Matrix     67-by-67     nnz:    294
residual:  8.2e+00 rank:     67
/bin/sh: line 1: 17479 Segmentation fault      ./qrdemo < /var/tmp/portage/sci-l
ibs/spqr-1.3.1/work/spqr-1.3.1/Matrix/west0067.mtx
make[2]: *** [Makefile:649: check-local] Error 1
Comment 2 Sergei Trofimovich gentoo-dev 2017-09-23 10:26:03 UTC
similar on ppc
Comment 3 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2019-03-13 09:50:46 UTC
Hmm, this isn't masked.  And it has revdeps:

==rdep of sci-libs/spqr==
dev-lang/julia-1.1.0
dev-lang/julia-9999
sci-libs/ceres-solver-1.11.0:sparse
sci-libs/ceres-solver-1.12.0:sparse
sci-libs/suitesparse-4.0.2
sci-libs/suitesparse-4.2.1
==bdep of sci-libs/spqr==
dev-cpp/eigen-3.3.7:test
dev-lang/julia-1.1.0
dev-lang/julia-9999
sci-libs/ceres-solver-1.11.0:sparse
sci-libs/ceres-solver-1.12.0:sparse

Being hard-dep of julia, we can't really treeclean it.
Comment 4 Pacho Ramos gentoo-dev 2019-03-13 21:25:57 UTC
it is not masked because, after masking, maintainers remove the mask but didn't fix any bugs, then, current stable is still not buildable but we cannot stabilize newer one due to this test failures -> https://bugs.gentoo.org/627094#c3
Comment 5 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2019-03-14 04:25:54 UTC
Hmm, maybe we could start by moving it to ~arch.
Comment 6 Pacho Ramos gentoo-dev 2019-03-15 09:47:48 UTC
yes, but I am unsure about how this is really working taking into account the test failures:
- If tests are broken due to a real bug, the issue is major (even if it's in testing it is still broken)
- If tests are broken because of the tests doing something wrong, probably they could be skipped and we could simply stabilize the new version
Comment 7 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2019-03-15 09:49:34 UTC
...which brings us to the essential problem of lack of dedicated maintainer who would look into this.
Comment 8 François Bissey 2019-03-21 22:39:07 UTC
I am willing to proxy maintain suitesparse for a while. I have recovered bicatali github repo to convert the suitesparse meta package into some of its components and updated it to the latest available version (5.4.0) at 
https://github.com/kiwifb/suitesparse

I have updated ebuilds for all the packages currently in Gentoo in the sage-on-gentoo overlay for a test run.

I don't have cuda enabled hardware to test cuda in cholmod. I updated that to the best of my abilities but someone with a cuda install needs to test it.

Ideally I'll aim for package parity with debian which means packaging the last three packages not currently in Gentoo (rbio, graphblas and moongoose). But priority should be for the existing packages.

I cannot reproduce this test failure with the new spqr (2.0.9).