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 Repositories: gentoo location: /var/db/repos/gentoo sync-type: git sync-uri: https://github.com/gentoo-mirror/gentoo.git priority: -1000 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=native -pipe" 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" CXXFLAGS="-O2 -march=native -pipe" DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--jobs 3 --quiet-build" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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 -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" GENTOO_MIRRORS="https://mirror.bytemark.co.uk/gentoo http://distfiles.gentoo.org" LANG="en_GB.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j24" PKGDIR="/var/cache/binpkgs" 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/portage_tmp" 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" Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 633078 [details] numpy build log, built without error
Created attachment 633080 [details] gdal build log, with error
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.
*** Bug 717600 has been marked as a duplicate of this bug. ***
matplotlib, opencv are other applications that also fail with numpy-1.17.4. The file __multiarray_api.h is also missing from the installation.
This bug appears to have been introduced by the following recent commit: distutils-r1.eclass: Pass --skip-build when installing https://gitweb.gentoo.org/repo/gentoo.git/commit/eclass/distutils-r1.eclass?id=180fa85d7d00aea463c399f70348beaad9166eb7 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.
*** Bug 717656 has been marked as a duplicate of this bug. ***
*** Bug 717644 has been marked as a duplicate of this bug. ***
It also causes build failure on dev-python/numexpr-2.6.9
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.
*** Bug 717672 has been marked as a duplicate of this bug. ***
*** This bug has been marked as a duplicate of bug 717502 ***
