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Bug 717594 - dev-python/numpy-1.17.4: does not include _numpyconfig.h header causing sci-libs/gdal-3.0.4-r1[python] build failure
Summary: dev-python/numpy-1.17.4: does not include _numpyconfig.h header causing sci-l...
Status: RESOLVED DUPLICATE of bug 717502
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
: 717600 717644 717656 717672 (view as bug list)
Depends on:
Blocks: 714384
  Show dependency tree
Reported: 2020-04-15 15:22 UTC by Candy Gumdrop
Modified: 2020-04-17 11:15 UTC (History)
15 users (show)

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

numpy build log, built without error (dev-python_numpy-1.17.4-r2_20200415-150322.log,525.90 KB, text/plain)
2020-04-15 15:25 UTC, Candy Gumdrop
gdal build log, with error (sci-libs:gdal-3.0.4-r1:20200415-151010.log.gz,47.65 KB, application/gzip)
2020-04-15 15:27 UTC, Candy Gumdrop
numpy install log, showing files that were removed (3AA205H.txt,172.65 KB, text/plain)
2020-04-15 15:44 UTC, Candy Gumdrop
Fix to compile numpy with a correct installation (numpy-1.17.4.ebuild.patch,351 bytes, patch)
2020-04-17 00:28 UTC, Alexandre Ferreira
Details | Diff

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Description Candy Gumdrop 2020-04-15 15:22:03 UTC
sci-libs/gdal fails to build due to the missing header _numpyconfig.h from numpy.  This header is referenced by the header numpyconfig.h (without the underscore), which is installed from dev-python/numpy.  Another user on IRC had the missing header installed on their system and was able to reproduce having it disappear after rebuilding dev-python/numpy.  We both have dev-python/setuptools-44.1.0 installed if that helps.

Reproducible: Always

Steps to Reproduce:
1. Use ACCEPT_KEYWORDS="~amd64"
2. Have PYTHON_TARGETS="python3_6"
3. Install sci-libs/gdal-3.0.4-r1 with USE="python"
Actual Results:  
In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/npy_common.h:5,
                 from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:4,
                 from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from extensions/gdal_array_wrap.cpp:3196:
/usr/lib64/python3.6/site-packages/numpy/core/include/numpy/numpyconfig.h:4:10: fatal error: _numpyconfig.h: No such file or directory
    4 | #include "_numpyconfig.h"
      |          ^~~~~~~~~~~~~~~~
compilation terminated.

Expected Results:  
GDAL installed without error.

Portage 2.3.99 (python 3.6.10-final-0, default/linux/amd64/17.1, gcc-9.3.0, glibc-2.30-r8, 5.4.32-gentoo x86_64)
System uname: Linux-5.4.32-gentoo-x86_64-AMD_Ryzen_9_3900X_12-Core_Processor-with-gentoo-2.7
KiB Mem:    32793152 total,  22515524 free
KiB Swap:   33554428 total,  33554428 free
Timestamp of repository gentoo: Wed, 15 Apr 2020 11:38:15 +0000
Head commit of repository gentoo: 9701327ebf4a428d8d9da5a532eb0e0583a3e97f

sh bash 5.0_p16
ld GNU ld (Gentoo 2.34 p1) 2.34.0
app-shells/bash:          5.0_p16::gentoo
dev-lang/perl:            5.30.2::gentoo
dev-lang/python:          2.7.17-r2::gentoo, 3.6.10-r1::gentoo, 3.7.7-r1::gentoo, 3.8.2-r1::gentoo
dev-util/cmake:           3.17.1::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.18::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.16.2::gentoo
sys-devel/binutils:       2.34::gentoo
sys-devel/gcc:            9.3.0::gentoo
sys-devel/gcc-config:     2.2.1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers)
sys-libs/glibc:           2.30-r8::gentoo

    location: /var/db/repos/gentoo
    sync-type: git
    priority: -1000

ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-O2 -march=native -pipe"
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"
CXXFLAGS="-O2 -march=native -pipe"
EMERGE_DEFAULT_OPTS="--jobs 3 --quiet-build"
FCFLAGS="-O2 -march=native -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -march=native -pipe"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
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"
USE="X acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre pulseaudio readline seccomp split-usr ssl tcpd unicode xattr zlib zsh-completion" ABI_X86="64" ADA_TARGET="gnat_2018" 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 sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt sha sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev" KERNEL="linux" L10N="en-GB" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="NVPTX WebAssembly AVR BPF" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby27" 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"
Comment 1 Candy Gumdrop 2020-04-15 15:25:01 UTC
Created attachment 633078 [details]
numpy build log, built without error
Comment 2 Candy Gumdrop 2020-04-15 15:27:01 UTC
Created attachment 633080 [details]
gdal build log, with error
Comment 3 Candy Gumdrop 2020-04-15 15:44:10 UTC
Created attachment 633086 [details]
numpy install log, showing files that were removed

This shows the files which were suddenly removed after a rebuild, including various missing files required to build GDAL.
Comment 4 Alexandre Ferreira 2020-04-15 16:49:23 UTC
*** Bug 717600 has been marked as a duplicate of this bug. ***
Comment 5 Alexandre Ferreira 2020-04-15 16:51:08 UTC
matplotlib, opencv are other applications that also fail with numpy-1.17.4. The file __multiarray_api.h is also missing from the installation.
Comment 6 Candy Gumdrop 2020-04-16 13:56:01 UTC
This bug appears to have been introduced by the following recent commit:

distutils-r1.eclass: Pass --skip-build when installing

After temporarily removing the --skip-build flag in distutils-r1.eclass, I am able to successfully install sci-libs/gdal after rebuilding dev-python/numpy.  All missing headers are back.
Comment 7 Toralf Förster gentoo-dev 2020-04-16 14:18:12 UTC
*** Bug 717656 has been marked as a duplicate of this bug. ***
Comment 8 Pacho Ramos gentoo-dev 2020-04-16 15:56:26 UTC
*** Bug 717644 has been marked as a duplicate of this bug. ***
Comment 9 Andrés Becerra Sandoval 2020-04-16 20:44:55 UTC
It also causes build failure on dev-python/numexpr-2.6.9
Comment 10 Alexandre Ferreira 2020-04-17 00:28:09 UTC
Created attachment 633292 [details, diff]
Fix to compile numpy with a correct installation

This patch allows numpy to install all the missing files. It is very kludge since it is installing twice. I tried to install only once but it fails.
Comment 11 David Seifert gentoo-dev 2020-04-17 09:44:51 UTC
*** Bug 717672 has been marked as a duplicate of this bug. ***
Comment 12 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-04-17 11:15:46 UTC

*** This bug has been marked as a duplicate of bug 717502 ***