Bug 858425 – dev-python/numpy: import issue when building dev-python/aesara-2.7.7 (RuntimeError: module compiled against API version 0x10 but this version of numpy is 0xf)

• Product: Gentoo Linux
• Status: RESOLVED CANTFIX

[Description Leonid Kopylov 2022-07-16 17:32:57 UTC]

# emerge -pqv '=dev-python/aesara-2.7.7::gentoo'
[ebuild  N    ] dev-python/aesara-2.7.7  USE="doc -test" PYTHON_TARGETS="python3_9 python3_10 -python3_8"

# emerge --info '=dev-python/aesara-2.7.7::gentoo'
Portage 3.0.32 (python 3.10.5-final-0, default/linux/arm64/17.0/desktop/gnome/systemd, gcc-12.1.1, glibc-2.35-r8, 5.18.12-gentoo-arm64 aarch64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.18.12-gentoo-arm64-aarch64-with-glibc2.35
KiB Mem:    16350184 total,  12528476 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Sat, 16 Jul 2022 17:00:01 +0000
Head commit of repository gentoo: a18255caa3529c0fbf9b18bd47f770189c99fb45
sh bash 5.1_p16
ld GNU ld (Gentoo 2.38 p4) 2.38
app-misc/pax-utils:        1.3.4::gentoo
app-shells/bash:           5.1_p16::gentoo
dev-java/java-config:      2.3.1::gentoo
dev-lang/perl:             5.36.0::gentoo
dev-lang/python:           3.9.13::gentoo, 3.10.5::gentoo, 3.11.0_beta4-r2::gentoo
dev-lang/rust-bin:         1.62.0::gentoo
dev-util/cmake:            3.23.2::gentoo
dev-util/meson:            0.63.0::gentoo
sys-apps/baselayout:       2.8-r1::gentoo
sys-apps/sandbox:          2.29::gentoo
sys-apps/systemd:          251.3::gentoo
sys-devel/autoconf:        2.13-r2::gentoo, 2.71-r1::gentoo
sys-devel/automake:        1.16.5::gentoo
sys-devel/binutils:        2.38-r2::gentoo
sys-devel/binutils-config: 5.4.1::gentoo
sys-devel/gcc:             12.1.1_p20220625::gentoo
sys-devel/gcc-config:      2.5-r1::gentoo
sys-devel/libtool:         2.4.7::gentoo
sys-devel/llvm:            14.0.6::gentoo
sys-devel/make:            4.3::gentoo
sys-kernel/linux-headers:  5.18-r1::gentoo (virtual/os-headers)
sys-libs/glibc:            2.35-r8::gentoo
Repositories:

gentoo
    location: /var/db/repos/gentoo
    sync-type: rsync
    sync-uri: rsync://rsync.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

brave-overlay
    location: /var/lib/layman/brave-overlay
    sync-type: laymansync
    sync-uri: https://gitlab.com/jason.oliveira/brave-overlay.git
    masters: gentoo
    priority: 50

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

ACCEPT_KEYWORDS="arm64 ~arm64"
ACCEPT_LICENSE="* -@EULA Microsoft-vscode Vivaldi"
CBUILD="aarch64-unknown-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="aarch64-unknown-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-php8.1/ext-active/ /etc/php/cgi-php8.1/ext-active/ /etc/php/cli-php8.1/ext-active/ /etc/php/fpm-php8.1/ext-active/ /etc/php/phpdbg-php8.1/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 -O2 -pipe"
DISTDIR="/var/cache/distfiles"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH 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="-march=native -O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live 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 strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="https://mirror.isoc.org.il/pub/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
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"
SHELL="/bin/bash"
USE="X a52 aac aalib accessibility acl acpi alsa ao archive arm64 audit bash-completion berkdb bidi bluetooth bluray boost branding brotli bzip2 cairo cdda cdr cgi cli colord cracklib crypt cryptsetup cups curl dbi dbus device-mapper djvu doc dri dts dvdr eds emacs enchant encode evo examples exif expat experimental extras fam fbcon fftw flac fontconfig fortran ftp fuse gamepad games gcrypt gd gdbm gdk-pixbuf geoip geolocation gif git glusterfs gmp gnome gnome-keyring gnome-online-accounts gnutls go gpg gphoto2 gpm graphite graphviz gssapi gstreamer gtk gtk-doc gtk3 gui guile harfbuzz hdf5 heif highlight html http http2 iconv icu idn imagemagick imlib introspection iodbc ipv6 iso jack java jbig jemalloc jpeg jpeg2k json kerberos latex lcms ldap libcaca libevent libglvnd libnotify libsecret libtirpc libxml2 lmdb lua lz4 lzip lzma lzo mad magic maildir man math matroska mbedtls mbox midi mng mongodb mp3 mp4 mpeg mtp mysql nas nautilus ncurses netlink nettle networkmanager nfs nls nptl nss ntlm odbc offensive ogg openal openexr opengl openmp openssl opus pam pango pcap pcre pdf perl pkcs11 plugins png policykit postgres postscript ppds pulseaudio python qdbm qrcode qt5 raw readline redis rss samba sasl screencast sctp sdl seccomp skey smtp snappy sndfile sndio snmp sound source spell split-usr sqlite ssh ssl startup-notification svg symlink syslog systemd tcl theora threads tiff tk tools tracker truetype udev udisks unicode unwind upower usb utils uuid v4l vala vim-syntax vorbis wayland webkit webp widgets wmf wxwidgets x264 x265 xattr xcb xface xinerama xml xpm xscreensaver xv xvid yaml zeroconf zeromq zip zlib zsh-completion zstd" ADA_TARGET="gnat_2020" 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_ARM="edsp thumb vfp vfpv3 vfpv4 vfp-d32 aes sha1 sha2 crc32 v4 v5 v6 v7 v8 thumb2" 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="evdev" KERNEL="linux" L10N="en en-US he ru" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_10" PYTHON_TARGETS="python3_10 python3_9" RUBY_TARGETS="ruby27 ruby30 ruby31" USERLAND="GNU" VIDEO_CARDS="virgl" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS

[Comment 1 Leonid Kopylov 2022-07-16 17:33:22 UTC]

Created attachment 791771 [details]
build.log

[Comment 2 Nowa Ammerlaan 2022-10-28 11:05:08 UTC]

This error occurs when you build scipy, then downgrade numpy, and then try to run the scipy that you built with the newer version of numpy.

Upgrading numpy or rebuilding scipy should fix your problem.

[Comment 3 Michał Górny 2022-10-28 12:22:07 UTC]

Unfortunately, rebuild-on-downgrade is not something we can cleanly support in Gentoo.