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Bug 593616

Summary: dev-python/numpy-1.11.1 + distcc: ValueError: Could not lock sequences (None)
Product: Gentoo Linux Reporter: Maciej Piechotka <uzytkownik2>
Component: Current packagesAssignee: Gentoo Science Related Packages <sci>
Status: CONFIRMED ---    
Severity: normal CC: bkohler, herb, mgorny, python
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Attachments: dev-python:numpy-1.11.1:20160921-035245.log.gz
Package: dev-python/numpy-1.10.4

Description Maciej Piechotka 2016-09-12 20:30:14 UTC
compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/mult
iarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python2.7 -c'
x86_64-pc-linux-gnu-gcc-5.4.0: _configtest.c
x86_64-pc-linux-gnu-gcc-5.4.0 -O2 -pipe -fomit-frame-pointer -g -march=core2 -mcx16 -msahf -maes -mpclmul -mpopcnt -mav
x --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=256 -mtune=core2 _configtest.o -o _confi
gtest
removing: _configtest.c _configtest.o _configtest.c _configtest.o _configtest
Traceback (most recent call last):
  File "setup.py", line 386, in <module>
    setup_package()
  File "setup.py", line 378, in setup_package
    setup(**metadata)
  File "/var/tmp/portage/dev-python/numpy-1.11.1/work/numpy-1.11.1/numpy/distutils/core.py", line 169, in setup
    return old_setup(**new_attr)
  File "/usr/lib64/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/var/tmp/portage/dev-python/numpy-1.11.1/work/numpy-1.11.1/numpy/distutils/command/build.py", line 47, in run
    old_build.run(self)
  File "/usr/lib64/python2.7/distutils/command/build.py", line 127, in run
    self.run_command(cmd_name)
  File "/usr/lib64/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/var/tmp/portage/dev-python/numpy-1.11.1/work/numpy-1.11.1/numpy/distutils/command/build_src.py", line 147, in run
    self.build_sources()
  File "/var/tmp/portage/dev-python/numpy-1.11.1/work/numpy-1.11.1/numpy/distutils/command/build_src.py", line 164, in build_sources
    self.build_extension_sources(ext)
  File "/var/tmp/portage/dev-python/numpy-1.11.1/work/numpy-1.11.1/numpy/distutils/command/build_src.py", line 323, in build_extension_sources
    sources = self.generate_sources(sources, ext)
  File "/var/tmp/portage/dev-python/numpy-1.11.1/work/numpy-1.11.1/numpy/distutils/command/build_src.py", line 376, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/setup.py", line 443, in generate_config_h
    rep = check_long_double_representation(config_cmd)
  File "numpy/core/setup_common.py", line 212, in check_long_double_representation
    ltype = long_double_representation(pyod("_configtest"))
  File "numpy/core/setup_common.py", line 356, in long_double_representation
    raise ValueError("Could not lock sequences (%s)" % saw)
ValueError: Could not lock sequences (None)


!!! Invalid PORTDIR_OVERLAY (not a dir): '/var/lib/layman/vmware'
Portage 2.3.0 (python 2.7.12-final-0, default/linux/amd64/13.0/desktop, gcc-5.3.0, glibc-2.23-r2, 4.7.2-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.7.2-gentoo-x86_64-Intel-R-_Core-TM-_i7-3740QM_CPU_@_2.70GHz-with-gentoo-2.3
KiB Mem:    32832884 total,   3160636 free
KiB Swap:   20971512 total,  20971512 free
Timestamp of repository gentoo: Mon, 12 Sep 2016 19:30:01 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
distcc 3.2rc1 x86_64-pc-linux-gnu [enabled]
app-shells/bash:          4.3_p46::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo
dev-util/cmake:           3.6.2::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.21.7::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo, 2.26.1::gentoo
sys-devel/gcc:            5.3.0::gentoo, 5.4.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:
(...)
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CC="x86_64-pc-linux-gnu-gcc-5.4.0"
CFLAGS="-O2 -pipe -fomit-frame-pointer -g -march=core2 -mcx16 -msahf -maes -mpclmul -mpopcnt -mavx --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=256 -mtune=core2"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
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"
CXX="x86_64-pc-linux-gnu-g++-5.4.0"
CXXFLAGS="-O2 -pipe -fomit-frame-pointer -g -march=core2 -mcx16 -msahf -maes -mpclmul -mpopcnt -mavx --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=256 -mtune=core2"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="-j12 --load-average=7"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs clean-logs compress-build-logs compressdebug config-protect-if-modified distcc distcc-pump distlocks ebuild-locks fail-clean fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms split-elog splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LC_ALL="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=both -Wl,--sort-common"
MAKEOPTS="-j12 -l7"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi aes alsa amd64 avahi avx berkdb bindist bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cryptsetup cups cxx dbus device-mapper dmenu dri dts dvd dvdr emacs emboss encode exif fam firefox flac fontconfig fortran gdbm gif glamor gles2 gpm gssapi gtk iconv icu ipv6 jpeg kerberos lcms ldap libkms libnotify lvm lzma mad mmx mmxext mng modules mp3 mp4 mpeg multilib ncurses networkmanager nls nptl ntlm ogg opengl openldap openmp pam pango pcre pdf png policykit popcnt ppds qt3support qt4 readline samba sasl sctp sdl seccomp session spell sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 startup-notification svg systemd tcpd tiff truetype udev udisks unicode upower usb vim-syntax vorbis wxwidgets x264 xattr xcb xcomposite xinerama xml xv xvid zeroconf zlib zsh-completion" ABI_X86="32 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" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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" GRUB_PLATFORMS="efi-64" 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" LINGUAS="en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="intel nouveau" 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, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

=================================================================
                        Package Settings
=================================================================

dev-python/numpy-1.11.0::gentoo was built with the following:
USE="-doc -lapack -test" ABI_X86="64" PYTHON_TARGETS="python2_7 python3_4 -python3_5"
CFLAGS="-O2 -pipe -fomit-frame-pointer -g -march=core2 -mcx16 -msahf -maes -mpclmul -mpopcnt -mavx --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=256 -mtune=core2 -fno-strict-aliasing"
CXXFLAGS="-O2 -pipe -fomit-frame-pointer -g -march=core2 -mcx16 -msahf -maes -mpclmul -mpopcnt -mavx --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=256 -mtune=core2 -fno-strict-aliasing"
Comment 1 Mike Gilbert gentoo-dev 2016-09-17 14:02:17 UTC
Please attach a full build log.
Comment 2 Maciej Piechotka 2016-09-21 04:12:00 UTC
Created attachment 447004 [details]
dev-python:numpy-1.11.1:20160921-035245.log.gz
Comment 3 matt 2016-12-14 09:53:05 UTC
Created attachment 456166 [details]
Package:    dev-python/numpy-1.10.4

Portage 2.3.0 (python 2.7.12-final-0, !../../var/lib/layman/dantrell-gnome/profiles/default/amd64/3.18, gcc-4.9.3, glibc-2.22-r4, 4.4.21-gentoo x86_64)
=================================================================
System uname: Linux-4.4.21-gentoo-x86_64-Pentium-R-_Dual-Core_CPU_E5800_@_3.20GHz-with-gentoo-2.2
KiB Mem:     2007620 total,    411180 free
KiB Swap:    4194300 total,   3279076 free
Timestamp of repository gentoo: Mon, 12 Dec 2016 05:00:01 +0000
sh bash 4.3_p48-r1
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
distcc 3.2rc1 x86_64-pc-linux-gnu [enabled]
ccache version 3.2.4 [disabled]
app-shells/bash:          4.3_p48-r1::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.22.2::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo
dev-util/ccache:          3.2.4::gentoo
dev-util/cmake:           3.5.2-r1::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.21.7::gentoo
sys-apps/sandbox:         2.10-r1::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.11.6-r1::gentoo, 1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc:           2.22-r4::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

dantrell-gnome-3-18
    location: /var/lib/layman/dantrell-gnome-3-18
    masters: gentoo
    priority: 0

dantrell-gnome
    location: /var/lib/layman/dantrell-gnome
    masters: gentoo
    priority: 1

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=core2"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -march=core2"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distcc distcc-pump distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j17 -l3"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 ac3 acl alsa amd64 ao asound berkdb bluetooth bzip2 cdda cdr cifs cli colord consolekit cracklib crypt cxx dbus dri egl evdev fortran gdbm gnome gnome-keyring gnome-online-accounts gtk gtk3 gtkstyle iconv introspection ipv6 libnotify llvm minizip mmx mmxext modules nautilus ncurses networkmanager nls nptl openal opencl opengl openmp openrc pam pch pcre policykit pulseaudio qt5 readline samba sdl seccomp session spell sse sse2 ssl ssse3 tcpd tracker udev unicode upnp webserver wxwidgets xattr zeroconf 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" CPU_FLAGS_X86="mmx sse sse2 mmxext sse3 ssse3" 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" LINGUAS="en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21" USERLAND="GNU" VIDEO_CARDS="nvidia" 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:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 4 Ben Kohler gentoo-dev 2016-12-20 20:13:25 UTC
I believe this is distcc-related, try without distcc.  Another user came across this very problem and FEATURES="-distcc" worked around it.
Comment 5 Matt Turner gentoo-dev 2018-03-21 19:56:14 UTC
Indeed, this is a result of distcc I can confirm.
Comment 6 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2018-03-22 03:56:37 UTC
Try disabling distcc-pump. It breaks a lot of packages (some of them silently).