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Bug 832517 - dev-python/pandas-1.3.4 - missing build dependency on cython
Summary: dev-python/pandas-1.3.4 - missing build dependency on cython
Status: UNCONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2022-02-01 18:04 UTC by Frédéric Lochon
Modified: 2022-02-01 22:45 UTC (History)
2 users (show)

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


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Description Frédéric Lochon 2022-02-01 18:04:22 UTC
I have dev-python/cython-0.29.23 installed and I want to emerge pandas.
But emerge fails because it requires cython >= 0.29.24.
The dependency upton the cython version is not OK.


Reproducible: Always

Steps to Reproduce:
emerge dev-python/pandas
Actual Results:  
>>> Emerging (5 of 5) dev-python/pandas-1.3.4::gentoo
 * pandas-1.3.4.tar.gz BLAKE2B SHA512 size ;-) ...                                                                                                  [ ok ]
>>> Unpacking source...
>>> Unpacking pandas-1.3.4.tar.gz to /var/tmp/portage/dev-python/pandas-1.3.4/work
>>> Source unpacked in /var/tmp/portage/dev-python/pandas-1.3.4/work
>>> Preparing source in /var/tmp/portage/dev-python/pandas-1.3.4/work/pandas-1.3.4 ...
 * Applying pandas-1.3.4-arm-tests.patch ...                                                                                                        [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/dev-python/pandas-1.3.4/work/pandas-1.3.4 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/dev-python/pandas-1.3.4/work/pandas-1.3.4 ...
 * python3_9: running distutils-r1_run_phase python_compile
python3.9 setup.py build -j 9 -j1
Traceback (most recent call last):
  File "/var/tmp/portage/dev-python/pandas-1.3.4/work/pandas-1.3.4/setup.py", line 650, in <module>
    ext_modules=maybe_cythonize(extensions, compiler_directives=directives),
  File "/var/tmp/portage/dev-python/pandas-1.3.4/work/pandas-1.3.4/setup.py", line 410, in maybe_cythonize
    raise RuntimeError(
RuntimeError: Cannot cythonize with old Cython version (0.29.23 installed, needs 0.29.24)



# emerge --info
Portage 3.0.20 (python 3.9.9-final-0, default/linux/amd64/17.1, gcc-10.3.0, glibc-2.33-r1, 5.4.72-gentoo x86_64)
=================================================================
System uname: Linux-5.4.72-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-1620_v3_@_3.50GHz-with-glibc2.33
KiB Mem:     7971384 total,   4491148 free
KiB Swap:    8191996 total,   8191996 free
Timestamp of repository gentoo: Tue, 01 Feb 2022 00:45:01 +0000
Head commit of repository gentoo: 9d673238b37622d80ea52de2aa512c6c50e7fa16
sh bash 5.1_p8
ld GNU ld (Gentoo 2.35.2 p1) 2.35.2
app-misc/pax-utils:        1.3.2::gentoo
app-shells/bash:           5.1_p8::gentoo
dev-java/java-config:      2.3.1::gentoo
dev-lang/perl:             5.34.0::gentoo
dev-lang/python:           3.7.11::gentoo, 3.9.9-r1::gentoo
dev-lang/rust-bin:         1.53.0::gentoo
dev-util/cmake:            3.20.5::gentoo
dev-util/meson:            0.58.1::gentoo
sys-apps/baselayout:       2.7::gentoo
sys-apps/openrc:           0.42.1-r1::gentoo
sys-apps/sandbox:          2.24::gentoo
sys-devel/autoconf:        2.13-r1::gentoo, 2.69-r5::gentoo, 2.71-r1::gentoo
sys-devel/automake:        1.16.4::gentoo
sys-devel/binutils:        2.35.2::gentoo
sys-devel/binutils-config: 5.4::gentoo
sys-devel/gcc:             10.3.0-r2::gentoo
sys-devel/gcc-config:      2.4::gentoo
sys-devel/libtool:         2.4.6-r6::gentoo
sys-devel/llvm:            12.0.1::gentoo
sys-devel/make:            4.3::gentoo
sys-kernel/linux-headers:  5.10::gentoo (virtual/os-headers)
sys-libs/glibc:            2.33-r1::gentoo
Repositories:

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

crossdev
    location: /usr/local/portage
    masters: gentoo
    priority: 0

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native"
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 -pipe -march=native"
DISTDIR="/share/portage/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="-O2 -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 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="fr_FR.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="fr en"
MAKEOPTS="-j9"
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"
SHELL="/bin/bash"
USE="X acl alsa amd64 bash-completion btrfs bzip2 caps cli crypt dbus dri elogind fortran gdbm glib iconv ipv6 libglvnd libtirpc mmx multilib ncurse ncurses nls nptl openmp orc pam pcre pulseaudio qt3support qt5 readline samba seccomp split-usr sse sse2 ssl udev unicode xattr zlib" ABI_X86="64" 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_X86="mmx sse sse2 ssse3 sse3 mmxext" 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="libinput" KERNEL="linux" L10N="fr en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" 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_9" PYTHON_TARGETS="python3_9" QEMU_USER_TARGETS="x86_64" RUBY_TARGETS="ruby26 ruby27" USERLAND="GNU" VIDEO_CARDS="nouveau fbdev" 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, 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