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Bug 717706 - dev-python/numpy-1.16.5 and dev-python/numpy-python2-1.16.5 failed emerging (install phase) - AttributeError: 'NoneType' object has no attribute 'endswith'
Summary: dev-python/numpy-1.16.5 and dev-python/numpy-python2-1.16.5 failed emerging (...
Status: RESOLVED FIXED
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:
: 717448 (view as bug list)
Depends on:
Blocks: 714384
  Show dependency tree
 
Reported: 2020-04-16 12:16 UTC by Sriram
Modified: 2020-04-16 21:16 UTC (History)
4 users (show)

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


Attachments
Build log. (build.log,504.00 KB, text/plain)
2020-04-16 12:25 UTC, Sriram
Details

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Description Sriram 2020-04-16 12:16:36 UTC
Numpy fails compiling and throws the aforementioned error. Please find the attached logs. Thanks.

Reproducible: Always

Steps to Reproduce:
1. Emerge dev-python/numpy.
2. Failure after the byte-compilation stage.
Actual Results:  
...
copying numpy/compat/tests/test_compat.py -> /var/tmp/portage/dev-python/numpy-1.16.5/image/_python2.7/usr/lib64/python2.7/site-packages/numpy/compat/tests/
copying numpy/compat/tests/__init__.py -> /var/tmp/portage/dev-python/numpy-1.16.5/image/_python2.7/usr/lib64/python2.7/site-packages/numpy/compat/tests/
running install_clib
customize UnixCCompiler
Traceback (most recent call last):
  File "setup.py", line 419, in <module>
    setup_package()
  File "setup.py", line 411, in setup_package
    setup(**metadata)
  File "/var/tmp/portage/dev-python/numpy-1.16.5/work/numpy-1.16.5/numpy/distutils/core.py", line 171, in setup
    return old_setup(**new_attr)
  File "/usr/lib64/python2.7/site-packages/setuptools/__init__.py", line 145, in setup
    return distutils.core.setup(**attrs)
  File "/usr/lib64/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/var/tmp/portage/dev-python/numpy-1.16.5/work/numpy-1.16.5/numpy/distutils/command/install.py", line 62, in run
    r = self.setuptools_run()
  File "/var/tmp/portage/dev-python/numpy-1.16.5/work/numpy-1.16.5/numpy/distutils/command/install.py", line 36, in setuptools_run
    return distutils_install.run(self)
  File "/usr/lib64/python2.7/distutils/command/install.py", line 575, in run
    self.run_command(cmd_name)
  File "/usr/lib64/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/var/tmp/portage/dev-python/numpy-1.16.5/work/numpy-1.16.5/numpy/distutils/command/install_data.py", line 19, in run
    self.run_command('install_clib')
  File "/usr/lib64/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/var/tmp/portage/dev-python/numpy-1.16.5/work/numpy-1.16.5/numpy/distutils/command/install_clib.py", line 34, in run
    source = os.path.join(build_dir, name)
  File "/usr/lib64/python2.7/posixpath.py", line 70, in join
    elif path == '' or path.endswith('/'):
AttributeError: 'NoneType' object has no attribute 'endswith'
 * ERROR: dev-python/numpy-1.16.5::gentoo failed (install phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  125:  Called src_install
 *   environment, line 3560:  Called distutils-r1_src_install
 *   environment, line 1511:  Called _distutils-r1_run_foreach_impl 'python_install'
 *   environment, line  462:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_install'
 *   environment, line 3049:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_install'
 *   environment, line 2488:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_install'
 *   environment, line 2486:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_install'
 *   environment, line 1046:  Called distutils-r1_run_phase 'python_install'
 *   environment, line 1481:  Called python_install
 *   environment, line 3203:  Called distutils-r1_python_install
 *   environment, line 1395:  Called esetup.py 'install' '--skip-build' '--root=/var/tmp/portage/dev-python/numpy-1.16.5/image/_python2.7'
 *   environment, line 1898:  Called die
 * The specific snippet of code:
 *       "${@}" || die "${die_args[@]}";
...

Expected Results:  
Emerged successfully.

`emerge --info` output:

Portage 2.3.89 (python 3.6.10-final-0, default/linux/amd64/17.1/desktop, gcc-9.2.0, glibc-2.29-r7, 5.4.28-gentoo-x86_64 x86_64)
=================================================================
System uname: Linux-5.4.28-gentoo-x86_64-x86_64-Intel-R-_Core-TM-_i5-7300HQ_CPU_@_2.50GHz-with-gentoo-2.6
KiB Mem:     7919060 total,   3090808 free
KiB Swap:    8151036 total,   8151036 free
Timestamp of repository gentoo: Thu, 16 Apr 2020 05:00:01 +0000
Head commit of repository gentoo: 7ffd39f547c65e3ff9a409ec1b205089fdbf474a
sh bash 4.4_p23-r1
ld GNU ld (Gentoo 2.33.1 p2) 2.33.1
app-shells/bash:          4.4_p23-r1::gentoo
dev-lang/perl:            5.30.1::gentoo
dev-lang/python:          2.7.17-r2::gentoo, 3.6.10-r1::gentoo, 3.7.7-r1::gentoo
dev-util/cmake:           3.16.5::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.16.1-r1::gentoo
sys-devel/binutils:       2.33.1-r1::gentoo
sys-devel/gcc:            9.2.0-r2::gentoo
sys-devel/gcc-config:     2.2.1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 5.4::gentoo (virtual/os-headers)
sys-libs/glibc:           2.29-r7::gentoo
Repositories:

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

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0"
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="-march=native -O2 -pipe"
DISTDIR="/var/cache/distfiles"
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="-march=native -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="-march=native -O2 -pipe"
GENTOO_MIRRORS="https://mirror.bytemark.co.uk/gentoo/ http://mirror.bytemark.co.uk/gentoo/ rsync://mirror.bytemark.co.uk/gentoo/ http://mirrors.evowise.com/gentoo/ https://mirrors.evowise.com/gentoo/ ftp://mirror.bytemark.co.uk/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
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"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli connman corefonts crypt cuda cups dbus djvu dri dts dvd dvdr elogind emboss encode exif flac fontconfig fortran gdbm gif gpm gtk iconv icu ipv6 jpeg lcms ldap libnotify libtirpc lm-sensors mad mng mp3 mp4 mpeg multilib ncurses nls nptl offensive ogg opengl openmp pam pango pcre pdf png policykit ppds qt5 readline sdl seccomp spell split-usr ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wifi wxwidgets x264 xattr xcb xml xv xvid zlib" 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="mmx mmxext sse sse2 aes avx avx2 f16c fma3 pclmul popcnt sse3 sse4_1 sse4_2 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="intel i965 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, MAKEOPTS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Sriram 2020-04-16 12:25:21 UTC
Created attachment 633236 [details]
Build log.
Comment 2 Pacho Ramos gentoo-dev 2020-04-16 16:42:42 UTC
I also get this breakage now :/
Comment 3 Mike Gilbert gentoo-dev 2020-04-16 16:43:18 UTC
I can reproduce the issue on an ~amd64 system with python3.7.
Comment 4 Mike Gilbert gentoo-dev 2020-04-16 16:47:45 UTC
Issue does not occur with dev-python/numpy-1.17.4-r2.
Comment 5 Pacho Ramos gentoo-dev 2020-04-16 16:58:20 UTC
the same failure bumping locally to 1.16.6 :/
Comment 7 Pacho Ramos gentoo-dev 2020-04-16 17:14:33 UTC
without "--skip-build" it compiles fine
Comment 8 Pacho Ramos gentoo-dev 2020-04-16 17:24:55 UTC
OK, this is:
https://github.com/numpy/numpy/issues/13265

Fixed by upstream:
https://github.com/numpy/numpy/commit/9839f301d21c7dc6e9c64ca635e702c0943367f2 

just tested and it works
Comment 9 Larry the Git Cow gentoo-dev 2020-04-16 17:44:18 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ec5de2845d7ccd00188c7a46a32e5a992d7ef03d

commit ec5de2845d7ccd00188c7a46a32e5a992d7ef03d
Author:     Mike Gilbert <floppym@gentoo.org>
AuthorDate: 2020-04-16 17:43:42 +0000
Commit:     Mike Gilbert <floppym@gentoo.org>
CommitDate: 2020-04-16 17:43:42 +0000

    dev-python/numpy: fix build with recent distutils-r1 change
    
    Closes: https://bugs.gentoo.org/717706
    Signed-off-by: Mike Gilbert <floppym@gentoo.org>

 ...-1.16.5-setup.py-install-skip-build-fails.patch | 23 ++++++++++++++++++++++
 dev-python/numpy/numpy-1.16.5.ebuild               |  1 +
 2 files changed, 24 insertions(+)
Comment 10 Larry the Git Cow gentoo-dev 2020-04-16 17:46:56 UTC
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=81bcae35ca3f42bc92c1cbf977f5d08d4ea4409c

commit 81bcae35ca3f42bc92c1cbf977f5d08d4ea4409c
Author:     Mike Gilbert <floppym@gentoo.org>
AuthorDate: 2020-04-16 17:46:30 +0000
Commit:     Mike Gilbert <floppym@gentoo.org>
CommitDate: 2020-04-16 17:46:30 +0000

    dev-python/numpy-python2: fix install with recent distutils-r1 change
    
    Bug: https://bugs.gentoo.org/717706
    Signed-off-by: Mike Gilbert <floppym@gentoo.org>

 ...-1.16.5-setup.py-install-skip-build-fails.patch | 23 ++++++++++++++++++++++
 .../numpy-python2/numpy-python2-1.16.5.ebuild      |  1 +
 2 files changed, 24 insertions(+)
Comment 11 Mike Gilbert gentoo-dev 2020-04-16 19:29:11 UTC
*** Bug 717448 has been marked as a duplicate of this bug. ***