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Bug 698122 - dev-python/pbkdf2-1.3-r1 with dev-python/pypy3-7.2.0 - OSError: Cannot load native module 'Crypto.Hash._MD5': Trying '_MD5.pypy3-72-x86_64-linux-gnu.so': Cannot load library .../_MD5.pypy3-72-x86_64-linux-gnu.so
Summary: dev-python/pbkdf2-1.3-r1 with dev-python/pypy3-7.2.0 - OSError: Cannot load n...
Status: UNCONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Anthony Basile
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2019-10-20 16:20 UTC by Dennis Schridde
Modified: 2019-10-21 19:10 UTC (History)
3 users (show)

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


Attachments
build.log (build.log,4.39 KB, text/plain)
2019-10-20 16:20 UTC, Dennis Schridde
Details

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Description Dennis Schridde 2019-10-20 16:20:54 UTC
Created attachment 593422 [details]
build.log

* pypy3: running distutils-r1_run_phase distutils-r1_python_compile
pypy3 setup.py build -j 6
Traceback (most recent call last):
  File "setup.py", line 11, in <module>
    from pbkdf2 import __version__
  File "/tmp/portage/dev-python/pbkdf2-1.3-r1/work/pbkdf2-1.3/pbkdf2.py", line 62, in <module>
    from Crypto.Hash import HMAC, SHA as SHA1
  File "/usr/lib/pypy3.6/site-packages/Crypto/Hash/HMAC.py", line 38, in <module>
    from Crypto.Hash import MD5
  File "/usr/lib/pypy3.6/site-packages/Crypto/Hash/MD5.py", line 30, in <module>
    """
  File "/usr/lib/pypy3.6/site-packages/Crypto/Util/_raw_api.py", line 300, in load_pycryptodome_raw_lib
    raise OSError("Cannot load native module '%s': %s" % (name, ", ".join(attempts)))
OSError: Cannot load native module 'Crypto.Hash._MD5': Trying '_MD5.pypy3-72-x86_64-linux-gnu.so': Cannot load library /usr/lib/pypy3.6/site-packages/Crypto/Util/../Hash/_MD5.pypy3-72-x86_64-linux-gnu.so: /usr/lib/pypy3.6/site-packages/Crypto/Util/../Hash/_MD5.pypy3-72-x86_64-linux-gnu.so: cannot open shared object file: No such file or directory.  Additionally, ctypes.util.find_library() did not manage to locate a library called '/usr/lib/pypy3.6/site-packages/Crypto/Util/../Hash/_MD5.pypy3-72-x86_64-linux-gnu.so'
Comment 1 Dennis Schridde 2019-10-20 16:21:53 UTC
Portage 2.3.77 (python 2.7.13-final-42, default/linux/amd64/17.1/desktop/plasma/systemd, gcc-9.2.0, glibc-2.29-r5, 5.3.6-gentoo-r1 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.3.6-gentoo-r1-x86_64-AMD_Ryzen_5_2400G_with_Radeon_Vega_Graphics-with-gentoo-2.6
KiB Mem:    14134992 total,    597004 free
KiB Swap:   16776188 total,  16661500 free
Timestamp of repository gentoo: Sun, 20 Oct 2019 11:15:01 +0000
Head commit of repository gentoo: 60dc0eef8abecdbd8b5beb0337a9c4c2db0b5545
Head commit of repository flatpak-overlay: dba2292fa92fbe7f51a437ff89d27cbab6105b67

Head commit of repository local: a67ba6c09db53453a0aace44e2f487ff5bce5f5c

sh bash 5.0_p11
ld GNU gold (Gentoo 2.32 p2 2.32.0) 1.16
ccache version 3.7.4 [disabled]
app-shells/bash:          5.0_p11::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.30.0::gentoo
dev-lang/python:          2.7.16::gentoo, 3.5.7::gentoo, 3.6.9::gentoo, 3.7.5::gentoo
dev-util/ccache:          3.7.4::gentoo
dev-util/cmake:           3.16.0_rc2::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/sandbox:         2.18::gentoo
sys-devel/autoconf:       2.13-r1::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:       2.32-r1::gentoo
sys-devel/gcc:            9.1.0::gentoo, 9.2.0-r1::gentoo
sys-devel/gcc-config:     2.1::gentoo
sys-devel/libtool:        2.4.6-r5::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 5.3::gentoo (virtual/os-headers)
sys-libs/glibc:           2.29-r5::gentoo
Repositories:

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

flatpak-overlay
    location: /var/db/repos/flatpak-overlay
    sync-type: git
    sync-uri: https://github.com/fosero/flatpak-overlay.git
    masters: gentoo

local
    location: /var/cache/portage/local
    sync-type: git
    sync-uri: https://github.com/devurandom/gentoo-overlay.git
    masters: gentoo
    priority: 1000

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-pipe -O2 -march=znver1"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/grs/systems.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.6/conf"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.3/ext-active/ /etc/php/cgi-php7.3/ext-active/ /etc/php/cli-php7.3/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="-pipe -O2 -march=znver1"
DISTDIR="/var/cache/portage/distfiles"
EMERGE_DEFAULT_OPTS="--keep-going --nospinner --verbose-conflicts"
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 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildsyspkg cgroup compressdebug config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch parallel-install pid-sandbox preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.spline.inf.fu-berlin.de/mirrors/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://distfiles.gentoo.org"
LANG="en_GB.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
MAKEOPTS="-j6 -l4"
PKGDIR="/var/cache/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="/tmp"
USE="7z 7zip X a52 aac aacplus aacs acl acpi activities aio alsa amd64 appindicator appstream archive audit avahi ayatana bash-completion bdplus berkdb bluetooth bluray branding brotli bs2b btrfs bzip2 cairo caps cdda cddb cdio cdr celt chromaprint cjk clang cli clipboard color-management colord conntrack crypt cups cxx d3d9 dav1d dbus declarative device-mapper dirac djvu dri drm dts dvb dvd dvdr ed25519 editorconfig egl elf emboss encode epub exif fam faudio fax fbcon ffmpeg fftw filecaps firefox firewalld fish-completion fits flac fontconfig fontforge fortran fribidi gbm gdal gdbm geoclue geolocation gif git glamor gles gmp gnupg google googledrive gpg gps graphicsmagick gstreamer gtk gtk3 gzip harfbuzz hdf5 heif http2 ibus iconv icu idn imlib inotify introspection ipv6 jemalloc jpeg jpeg2k json kde kipi kms kwallet ladspa latex lcms ldap libatomic libglvnd libidn2 libinput libnotify libproxy libsecret libsoxr libtirpc libvirt lm-sensors lrz lv2 lvm lz4 lzma lzo mad mariadb markdown mbim mercurial mjpeg mng mobi modemmanager modplug mp3 mp4 mpeg mplayer mpris mtp multilib mysql ncurses netlink networkmanager nls nptl office ofx ogg openal opencl opencv openexr opengl openh264 openmax openmp opus pam pango pcap pch pcre pcre2 pdf pgo phonon pixman plasma pm-utils png policykit postscript ppds prison pulseaudio python qml qrcode qt5 raw readline redfish samba sasl scanner schroedinger screencast sctp sdl sdl2 seccomp semantic-desktop share smartcard snappy sparse speech speex spell ssl startup-notification steamruntime stemmer svg systemd systemtap tbb tcpd teamd telepathy tga theora threads tiff timezone tmux truetype tslib udev udisks unicode unwind upnp upnp-av upower usb utempter v4l v4l2 vaapi vdpau vkd3d vorbis vpx vulkan wasm wavpack wayland webchannel webengine webkit webp widgets wmf wps x264 x265 xattr xcb xcomposite xinerama xkb xml xmp xrandr xscreensaver xv xvid xwayland xz yaml zeroconf zeromq zlib zstd" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="hda-intel" 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" CAMERAS="ptp2" 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" ENLIGHTENMENT_MODULES="*" 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="joystick libinput" KERNEL="linux" L10N="de de-DE en en-GB ar fa tr ja ko zh zh-CN zh-TW" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver scripting-javascript wiki-publisher" LIRC_DEVICES="devinput" LLVM_TARGETS="AMDGPU BPF RISCV WebAssembly" LUA_TARGET="lua5-2" NETBEANS_MODULES="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6 pypy pypy3" QEMU_SOFTMMU_TARGETS="riscv32 riscv64 x86_64" QEMU_USER_TARGETS="riscv32 riscv64" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu virgl" 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

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

dev-python/pbkdf2-1.3-r1::gentoo was built with the following:
USE="" ABI_X86="(64)" PYTHON_TARGETS="pypy pypy3 python2_7 python3_6 -python3_5 -python3_7"


dev-python/pypy3-7.2.0::gentoo was built with the following:
USE="bzip2 gdbm jit ncurses sqlite -libressl -low-memory (-sandbox) -tk" ABI_X86="(64)" CPU_FLAGS_X86="(-sse2)"
Comment 2 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2019-10-20 16:45:30 UTC
Please try rebuilding pycrypto[dome].
Comment 3 Dennis Schridde 2019-10-21 19:10:39 UTC
(In reply to Michał Górny from comment #2)
> Please try rebuilding pycrypto[dome].

That solved the issue!  Thanks!

Should a dependency be added, or how can this be handled more gracefully for other users?