* Detected file collision(s): * * /usr/lib64/python3.4/site-packages/jupyter.py * /usr/lib64/python2.7/site-packages/jupyter.py * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * dev-python/jupyter_core-4.1.0:0::gentoo * /usr/lib64/python2.7/site-packages/jupyter.py * /usr/lib64/python3.4/site-packages/jupyter.py * * Package 'dev-python/jupyter-1.0.0' NOT merged due to file collisions. $ cat emerge-info.txt ----------------------------------------------------------------- This is an unstable amd64 chroot image (named amd64-gnome-systemd-unstable_20160707-230619) at a hardened host acting as a tinderbox. ----------------------------------------------------------------- make.conf: USE="pax_kernel xtpax -cdinstall -oci8 -bindist -aes-ni cdb -cdda cddb custom-optimization dec_av2 ecc -emacs evdev -extraengine fontconfig fortran ftp graphtft ibus -imap isag jadetex javaxml latex ldap lzma -mdnsresponder-compat melt -mp3 mpg123 networking nls ogg openmpi pdo png -printsupport qemu qt3support scripts -scrypt smpeg snmp -sqlite3 sslv2 system-cairo system-icu system-libevent system-libvpx v4l vala -x264 x265 xcb xkb xmp xscreensaver xslt xvmc zip" package specific USE flags: mail-mta/ssmtp ssl net-misc/wget ssl app-editors/emacs -dbus -svg -ssl -gtk -gtk3 ----------------------------------------------------------------- Portage 2.3.0 (python 3.4.5-final-0, default/linux/amd64/13.0/desktop/gnome/systemd, gcc-5.4.0, glibc-2.23-r2, 4.6.4-hardened-r2 x86_64) ================================================================= System uname: Linux-4.6.4-hardened-r2-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16156124 total, 6473508 free KiB Swap: 16777212 total, 16777212 free Timestamp of repository gentoo: Tue, 26 Jul 2016 10:05:30 +0000 sh bash 4.3_p46 ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1 distcc 3.2rc1 x86_64-pc-linux-gnu [disabled] ccache version 3.2.7 [disabled] app-shells/bash: 4.3_p46::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo dev-util/ccache: 3.2.7::gentoo dev-util/cmake: 3.6.1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.2-r1::gentoo sys-apps/openrc: 0.21.2::gentoo sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.9.6-r4::gentoo, 1.10.3-r2::gentoo, 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26.1::gentoo sys-devel/gcc: 5.4.0::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.6::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: 1 local location: /usr/local/portage masters: gentoo priority: 2 gentoo-mate location: /usr/local/gentoo-mate sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/gentoo-mate.git masters: gentoo priority: 3 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/entropy /etc/grs/systems.conf /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/qpsmtpd/plugins /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb /var/lib/i2pd/certificates /var/lib/redmine/config /var/yp/Makefile" 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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /var/lib/redmine/config/locales /var/lib/redmine/config/settings.yml" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/var/tmp/distfiles" EMERGE_DEFAULT_OPTS="--verbose --verbose-conflicts --color=n --nospinner --tree --quiet-build" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j1" 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" USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdb cddb cdr cli colord cracklib crypt cups custom-optimization cxx dbus dec_av2 dri dts dvd dvdr ecc eds emboss encode evdev evo exif fam firefox flac fontconfig fortran ftp gdbm gif glamor gnome gnome-keyring gnome-online-accounts gpm graphtft gstreamer gtk ibus iconv introspection ipv6 isag jadetex javaxml jpeg latex lcms ldap libnotify libsecret lzma mad melt mmx mmxext mng modules mp4 mpeg mpg123 multilib nautilus ncurses networking nls nptl ogg opengl openmp openmpi pam pango pax_kernel pcre pdf pdo png policykit ppds pulseaudio qemu qt3support qt4 readline scripts sdl seccomp session smpeg snmp spell sse sse2 ssl sslv2 startup-notification svg system-cairo system-icu system-libevent system-libvpx systemd tcpd tiff tracker truetype udev udisks unicode upower usb v4l vala vorbis wxwidgets x265 xattr xcb xkb xml xmp xscreensaver xslt xtpax xv xvid xvmc zip zlib" ABI_X86="64" 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="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev synaptics" 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="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 441630 [details] dev-python:jupyter-1.0.0:20160726-125756.log
Created attachment 441632 [details] emerge-history.txt
Seen on my system as well, emerge info below: Portage 2.2.28 (python 2.7.10-final-0, default/linux/amd64/13.0/desktop/gnome/systemd, gcc-4.9.3, glibc-2.22-r4, 4.4.6-gentoo x86_64) ================================================================= System uname: Linux-4.4.6-gentoo-x86_64-Intel-R-_Core-TM-_i7-4790_CPU_@_3.60GHz-with-gentoo-2.2 KiB Mem: 32829512 total, 15581224 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Thu, 18 Aug 2016 12:30:01 +0000 sh bash 4.3_p42-r1 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 app-shells/bash: 4.3_p42-r1::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.10-r1::gentoo, 3.4.3-r1::gentoo dev-util/cmake: 3.3.1-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.21.3::gentoo sys-apps/sandbox: 2.10-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers) sys-libs/glibc: 2.22-r4::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 x-portage location: /usr/local/portage masters: gentoo priority: 0 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="ftp://mirrors.rit.edu/gentoo/ http://mirrors.rit.edu/gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" 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" USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli colord cracklib crypt cups cxx dbus dri dts dvd dvdr eds emacs emboss encode evo exif fam firefox flac fortran gdbm gif glamor gnome gnome-keyring gnome-online-accounts gpm gstreamer gtk iconv introspection ipv6 jpeg lcms ldap libnotify libsecret mad mmx mmxext mng modules mp3 mp4 mpeg multilib nautilus ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio qt3support qt4 readline sdl seccomp session spell sse sse2 ssl startup-notification svg systemd tcpd tiff tracker truetype udev udisks unicode upower usb vorbis wxwidgets x264 xattr xcb xml xv xvid zlib zsh zsh-completion" ABI_X86="64" 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="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 fma3 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev" 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="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="nouveau" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
This is the jupyter.py that dev-python/jupyter is trying to install: """Launch the root jupyter command Alias to jupyter_core """ __version__ = '1.0.0' if __name__ == '__main__': from runpy import run_module run_module('jupyter_core') And this is what dev-python/jupyter_core installed: """Launch the root jupyter command""" if __name__ == '__main__': from jupyter_core.command import main main() Could we maybe just not install the jupyter.py from dev-python/jupyter, assuming that it's already there from dev-python/jupyter_core?
Hello folks, it looks to me as upstream jupyter moved the jupyter.py file from jupyter (“meta package“) to jupyter_core and just forgot to update jupyter-1.0.0 at pypy.python.org. I filed a bug report: https://github.com/jupyter/jupyter_core/issues/85
(In reply to Nils Freydank from comment #5) > Hello folks, > > it looks to me as upstream jupyter moved the jupyter.py file from jupyter > (“meta package“) to jupyter_core and just forgot to update jupyter-1.0.0 at > pypy.python.org. I filed a bug report: > > https://github.com/jupyter/jupyter_core/issues/85 Thanks for reporting to upstream, this was still on my too long todo list. I'll bump the jupyter metapackage as soon as a new version was released (hopefully fixing the file collision).
Created attachment 446496 [details, diff] Temporary patch to get around the issue In case it helps, this user patch is adapted from the fix upstream. I'm currently using it to run jupyter before 1.1.0 is posted on pypi. https://github.com/jupyter/jupyter/pull/198
*** Bug 598412 has been marked as a duplicate of this bug. ***
commit 1ba65cdc0162b073450fb4bcf30d1a3b8bd9d53b Author: Justin Lecher <jlec@gentoo.org> Date: Sat Nov 5 11:33:18 2016 +0100 dev-python/jupyter{,_core}: Backport patch to avoid File collision Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=589750 Package-Manager: portage-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org> https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1ba65cdc0162b073450fb4bcf30d1a3b8bd9d53b
