Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!

Bug 597288

Summary: sci-libs/scipy-{0.16.1,0.17.0,0.18.1}: Build failure
Product: Gentoo Linux Reporter: Alexander Bezrukov <phmagic>
Component: Current packagesAssignee: Gentoo Science Related Packages <sci>
Status: RESOLVED WORKSFORME    
Severity: normal CC: jstein, sci
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Attachments: The complete build log

Description Alexander Bezrukov 2016-10-16 15:03:19 UTC 
Created attachment 450398 [details]
The complete build log

The said package is failing to build. Please see the build log (for 0.16.1, which is the latest stable) in the attachment.

# emerge --info '=sci-libs/scipy-0.16.1::gentoo'
Portage 2.3.0 (python 3.4.3-final-0, default/linux/amd64/13.0, gcc-4.9.3, glibc-2.22-r4, 4.4.24-alb x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.4.24-alb-x86_64-Dual_Core_AMD_Opteron-tm-_Processor_285-with-gentoo-2.2
KiB Mem:    16504624 total,   1929276 free
KiB Swap:   50331636 total,  49474412 free
Timestamp of repository gentoo: Sun, 16 Oct 2016 11:15:01 +0000
Timestamp of repository xwing: Sun, 16 Oct 2016 11:00:12 +0000
sh bash 4.3_p48
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p48::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.22.2::gentoo
dev-lang/python:          2.7.10-r1::gentoo, 3.4.3-r1::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, 5.4.0::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.6::gentoo (virtual/os-headers)
sys-libs/glibc:           2.22-r4::gentoo
Repositories:

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

xwing
    location: /var/lib/layman/xwing
    masters: gentoo
    priority: 0

science
    location: /var/lib/layman/science
    masters: gentoo
    priority: 1

vmware
    location: /var/lib/layman/vmware
    masters: gentoo
    priority: 2

x-portage
    location: /usr/local/portage
    masters: gentoo
    priority: 3

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA sun-bcla-java-vm Oracle-BCLA-JavaSE dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x Intel-SDP TeamViewer NVIDIA-CUDA NVIDIA-gdk ACML-EULA OPERA-12"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -mtune=native -O2 -pipe -fomit-frame-pointer -finline-functions-called-once -ftree-vectorize -fno-stack-protector"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf"
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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -mtune=native -O2 -pipe -fomit-frame-pointer -finline-functions-called-once -ftree-vectorize -fno-stack-protector"
DISTDIR="/scratch/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified 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="-march=native -mtune=native -O2 -pipe -fomit-frame-pointer -finline-functions-called-once -ftree-vectorize -fprefetch-loop-arrays -funroll-loops -fno-stack-protector"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LC_ALL=""
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j8"
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="/tmp"
USE="X a52 aac acl acpi alsa amd64 amr apng bash-completion berkdb bidi bundled-libs bzip2 caps cdda cdr celt cjk cli cracklib crypt cryptsetup cscope cups cxx dbus dirac djvu dri dv dvb dvd dvdr dvdread eselect exif faac ffmpeg flac fontconfig fortran g726 g729 gdbm gif gimp gmp gpm gsm gsm-nonstandard gtk http iconv icu idn ieee1394 ilbc java jpeg jpeg2k lame lcms ldap ldapsam libnotify lm_sensors lock logrotate mad matroska mmap mms mmx mmxext mng modules mp3 mpeg multilib musepack ncurses nls nodrm nptl nsplugin numa ogg opencl opengl openmp opus pam pcre pkcs11 png qt5 readline samba seccomp session silk srtp sse sse2 ssl startup-notification taglib tcpd theora threads thunar tiff timidity truetype udev unicode usb vcd vdpau vim-syntax visio vorbis vpx wavpack winbind wmf wpg x264 xattr xcomposite xinerama xmp xv xvid xvmc zlib" 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="alias auth_basic auth_digest authn_alias authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_user autoindex dir env expires filter headers deflate info log_config logio mime mime_magic negotiation status unique_id userdir rewrite reqtimeout proxy proxy_connect proxy_http authn_core authz_core unixd socache_shmcb" 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="3dnow 3dnowext mmx mmxext sse sse2 sse3" 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="evdev wacom" KERNEL="linux" L10N="en fa ru" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en fa ru" NGINX_MODULES_HTTP="auth_pam access auth_basic autoindex browser charset fastcgi fancyindex geoip gzip headers_more limit_conn limit_req proxy referer rewrite scgi spdy stub_status" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 Jouni Kosonen 2016-10-16 15:22:26 UTC 
  File "/usr/lib64/python2.7/site-packages/numpy/lib/__init__.py", line 17, in <module>
    from . import scimath as emath
ImportError: cannot import name scimath

Bug 555228 suggests rebuilding dev-python/numpy and trying again.
Comment 2 Alexander Bezrukov 2016-10-16 23:07:44 UTC 
(In reply to Jouni Kosonen from comment #1)

> Bug 555228 suggests rebuilding dev-python/numpy and trying again.

This didn't help in my case. I tried that just before reporting and I repeated this experiment just to be double sure.
Comment 3 Alexander Bezrukov 2016-10-30 02:27:45 UTC 
I am not sure why this has happened, but the issue has gone when I switched from gotoblas2::science (which was used for a reason) to plain blas-reference::gentoo.
Before doing that, I rebuilt gotoblas2 and numpy (in this order) -- to no avail.
Comment 4 Alexander Bezrukov 2016-10-30 03:14:44 UTC 
*** Bug 597290 has been marked as a duplicate of this bug. ***