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Bug 661836 - =dev-python/numpy-1.14.5 build failure: missing <math.h> include, other libraries
Summary: =dev-python/numpy-1.14.5 build failure: missing <math.h> include, other libra...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2018-07-22 21:19 UTC by zlg
Modified: 2018-09-04 11:22 UTC (History)
6 users (show)

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


Attachments
dev-python_numpy-1.14.5-build.log (dev-python:numpy-1.14.5:20180722-114410.log.gz,90.21 KB, application/gzip)
2018-07-22 21:21 UTC, zlg
Details

Note You need to log in before you can comment on or make changes to this bug.
Description zlg 2018-07-22 21:19:10 UTC
dev-python/numpy-1.14.5 fails to build. The log indicates a possible missing <math.h> include and missing "blas", "atlas", and "lapack" libraries.

emerge --info:

Portage 2.3.43 (python 3.5.5-final-0, default/linux/amd64/17.0/developer, gcc-7.3.0, glibc-2.27-r5, 4.15.18-gentoo x86_64)
=================================================================
System uname: Linux-4.15.18-gentoo-x86_64-AMD_Phenom-tm-_II_X6_1090T_Processor-with-gentoo-2.6
KiB Mem:    16425600 total,   1067456 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Sun, 22 Jul 2018 20:15:01 +0000
Head commit of repository gentoo: 1c5131e82ea9708d7c627c5aa4aae3baade70c9b
sh bash 4.4_p23
ld GNU ld (Gentoo 2.30 p3) 2.30.0
app-shells/bash:          4.4_p23::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.26.2::gentoo
dev-lang/python:          2.7.15::gentoo, 3.4.8-r1::gentoo, 3.5.5-r1::gentoo, 3.6.6::gentoo, 3.7.0::gentoo
dev-util/cmake:           3.11.4::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6::gentoo
sys-apps/openrc:          0.38.1::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.11.6-r3::gentoo, 1.13.4-r2::gentoo, 1.16.1-r1::gentoo
sys-devel/binutils:       2.30-r3::gentoo
sys-devel/gcc:            7.3.0-r3::gentoo
sys-devel/gcc-config:     1.9.1::gentoo
sys-devel/libtool:        2.4.6-r5::gentoo
sys-devel/make:           4.2.1-r3::gentoo
sys-kernel/linux-headers: 4.17::gentoo (virtual/os-headers)
sys-libs/glibc:           2.27-r5::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.us.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-extra-opts: 
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-metamanifest: yes

zlg-overlay
    location: /home/zlg/projects/overlay
    masters: gentoo

0x4d4c
    location: /var/lib/layman/0x4d4c
    sync-type: laymansync
    sync-uri: https://github.com/0x4d4c/gentoo-overlay.git
    masters: gentoo
    priority: 50

fusion809
    location: /var/lib/layman/fusion809
    sync-type: laymansync
    sync-uri: https://github.com/fusion809/fusion809-overlay.git
    masters: gentoo
    priority: 50

gamerlay
    location: /var/lib/layman/gamerlay
    sync-type: laymansync
    sync-uri: git://anongit.gentoo.org/proj/gamerlay.git
    masters: gentoo
    priority: 50

games-overlay
    location: /var/lib/layman/games-overlay
    sync-type: laymansync
    sync-uri: https://github.com/hasufell/games-overlay.git
    masters: gentoo
    priority: 50

steam-overlay
    location: /var/lib/layman/steam-overlay
    sync-type: laymansync
    sync-uri: git://github.com/anyc/steam-overlay.git
    masters: gentoo
    priority: 50

Installed sets: @base, @cli, @desktop, @dev, @esteam, @fonts, @games, @gui
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /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"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--ask-enter-invalid --binpkg-respect-use=y"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs collision-protect compress-build-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms sign splitdebug strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirrors.evowise.com/gentoo/ http://gentoo.gossamerhost.com http://mirror.leaseweb.com/gentoo/ http://gentoo.mirrors.tds.net/gentoo http://cosmos.illinois.edu/pub/gentoo/"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j6"
PKGDIR="/usr/portage/packages"
PORTAGE_BINHOST="file:///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 alsa amd64 bash-completion branding bzip2 cairo cdda cdr cli consolekit crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam flac fortran gdbm gif glamor gtk iconv ipv6 jpeg lcms ldap libnotify libtirpc mad mng modules mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio qt5 readline sdl seccomp snmp spell ssl startup-notification svg tcpd tiff truetype udev unicode usb vim-syntax vorbis wxwidgets x264 xattr xcb xft xml xv 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="karbon plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext popcnt sse sse2 sse3 sse4a" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev joystick wacom" 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="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_4 python3_5 python3_6 python3_7" RUBY_TARGETS="ruby23 ruby23 ruby24 ruby25" 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, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS


emerge -pqv '=dev-python/numpy-1.14.5::gentoo'
[ebuild     U ] dev-python/numpy-1.14.5 [1.13.3] USE="-doc -lapack {-test}" PYTHON_TARGETS="python2_7 python3_4 python3_5 python3_6 python3_7%*"
Comment 1 zlg 2018-07-22 21:21:07 UTC
Created attachment 540542 [details]
dev-python_numpy-1.14.5-build.log

build log
Comment 2 Thomas Deutschmann gentoo-dev Security 2018-08-05 14:05:53 UTC
Same here, looks like enabling USE=lapack 'fixes' the problem, i.e. USE=-lapack is broken.
Comment 3 Mark Nowiasz 2018-08-06 06:02:38 UTC
(In reply to Thomas Deutschmann from comment #2)
> Same here, looks like enabling USE=lapack 'fixes' the problem, i.e.
> USE=-lapack is broken.

This problem is a little bit odd: I've got one machine where the problem reliably occurs (i.e. numpy fails to compile), on another one numpy compiled just fine. Both have the same useflags (including -lapack), the same default python version (3.7), and so on.

The only difference: make -j8 -l8 on the one failing to compile (the faster one) , and make -j4 -l4 on the one emerging it just fine
Comment 4 Thomas Deutschmann gentoo-dev Security 2018-08-08 11:42:29 UTC
@Mark: On the system where building with USE=-lapack is passing, do you still have required lapack dependency installed?
Comment 5 Sander Sweers 2018-08-08 15:47:45 UTC
Setting MAKEOPTS="-j1" makes the previously failing numpy build with no changes in flags. This suggest some sort of linking order problem

$ emerge --info numpy
Portage 2.3.44 (python 3.6.6-final-0, default/linux/amd64/17.0/desktop, gcc-7.3.0, glibc-2.27-r5, 4.17.8-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.17.8-gentoo-x86_64-AMD_Ryzen_5_2600_Six-Core_Processor-with-gentoo-2.6
KiB Mem:    16402420 total,  13620116 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Fri, 03 Aug 2018 17:15:01 +0000
Head commit of repository gentoo: 3cdd2929e47d1f2d9e90d20e7273dab82c433b33
sh bash 4.4_p23
ld GNU ld (Gentoo 2.30 p3) 2.30.0
app-shells/bash:          4.4_p23::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.26.2::gentoo
dev-lang/python:          2.7.15::gentoo, 3.5.5-r1::gentoo, 3.6.6::gentoo, 3.7.0::gentoo
dev-util/cmake:           3.12.0::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/openrc:          0.38.1::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.13.4-r2::gentoo, 1.16.1-r1::gentoo
sys-devel/binutils:       2.30-r3::gentoo
sys-devel/gcc:            7.3.0-r3::gentoo
sys-devel/gcc-config:     1.9.1::gentoo
sys-devel/libtool:        2.4.6-r5::gentoo
sys-devel/make:           4.2.1-r3::gentoo
sys-kernel/linux-headers: 4.17::gentoo (virtual/os-headers)
sys-libs/glibc:           2.27-r5::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.nl.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-extra-opts: 
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-metamanifest: no
    sync-rsync-verify-max-age: 24

infirit
    location: /home/sander/repos/infirit
    masters: gentoo
    priority: 0

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=znver1"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /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"
CXXFLAGS="-O2 -pipe -march=znver1"
DISTDIR="/usr/portage/distfiles"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="ftp://ftp.snt.utwente.nl/pub/os/linux/gentoo"
LANG="nl_NL.utf8"
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="/var/tmp"
USE="X a52 aac acl acpi alsa amd64 appindicator archive ayatana berkdb bluetooth bluray branding bzip2 cairo cdda cdr cli crypt cups cxx dbus dri dts dvd dvdr elogind emboss encode exif fam ffmpeg flac fontconfig fortran fuse gdbm gif glamor gnome-keyring gpm gstreamer gtk iconv icu introspection ipv6 jpeg lcms ldap libnotify libtirpc logrotate lzma mad matroska mng modules mp3 mp4 mpeg mtp multilib ncurses networkmanager nls nptl ogg opengl openmp opus pam pango pcre pdf png policykit ppds pulseaudio qt5 readline sdl seccomp snappy speex spell ssl startup-notification svg tcpd theora threads tiff tk truetype udev udisks unicode upower usb vaapi vdpau vorbis vpx vulkan wxwidgets x264 x265 xattr xcb xml xv xvid xvmc 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="karbon plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard libinput mouse evdev" KERNEL="linux" L10N="en en-GB en-US nl it fr es ru" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_5 python3_6 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu radeon radeonsi" 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, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

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

dev-python/numpy-1.14.5::gentoo was built with the following:
USE="-doc -lapack -test" ABI_X86="(64)" PYTHON_TARGETS="python2_7 python3_5 python3_6 python3_7 -python3_4"
CFLAGS="-O2 -pipe -march=znver1 -fno-strict-aliasing"
CXXFLAGS="-O2 -pipe -march=znver1 -fno-strict-aliasing"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -shared"
Comment 6 Mark Nowiasz 2018-08-08 15:52:50 UTC
(In reply to Thomas Deutschmann from comment #4)
> @Mark: On the system where building with USE=-lapack is passing, do you
> still have required lapack dependency installed?

No, there's no lapack installed.

But since according to comment #5, make -j1 seems to work, there might be a race condition - the -j4 machine is rather slow (Celeron N3150), the -j8 machine is reasonable fast (i5-8250U)

Regards,
Mark
Comment 7 abnd 2018-08-11 11:27:17 UTC
the missing libraries don't seem to be an issue, blas, atlas, and lapack. when numpy is compiled with the lapack useflag, it pulls them in.

i compiled numpy successfully on my laptop, without lapack or its required dependencies, so those warnings seem to be normal.

however, on my desktop the compile is still failing. with and without lapack. and using makeopts -j1 doesn't help either.

the only real difference i'm seeing between my two environments, which i just setup, is hardware.

the specific line of code executed doesn't seem to be related to any math library, it's just a test to compile a c function that returns 0. 

numpy is the only package failing for me like this though. 

is it possible a race condition was introduced for reason other than makeopts?
Comment 8 Joonas Niilola gentoo-dev 2018-08-17 08:10:50 UTC
Hit this error while doing PYTHON_TARGETS rebuilds. I had the build complete after lowering MAKEOPTS to -j1. I don't understand how initially I've been able to build this with -j9, but this rebuild required changes...

[ebuild   R    ] dev-python/numpy-1.14.5::gentoo  USE="-doc -lapack -test" PYTHON_TARGETS="python2_7 python3_4 python3_5 python3_6 python3_7"
Comment 9 Mark Nowiasz 2018-08-17 18:22:50 UTC
(In reply to Joonas Niilola from comment #8)
> Hit this error while doing PYTHON_TARGETS rebuilds. I had the build complete
> after lowering MAKEOPTS to -j1. I don't understand how initially I've been
> able to build this with -j9, but this rebuild required changes...

Same here. I was fed up whith numpy failing every emerge -uDN @world @system, so I used MAKEOPTS="-j1" and numpy compiled/installed just fine.
Comment 10 Chris Faulkner 2018-09-04 11:22:05 UTC
Can confirm, I have a 4 core processor, running emerge with -j1 was able to compile without a flaw.