Created attachment 483350 [details] build.log.gz [84/320] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++ -DBOOST_TEST_DYN_LINK -DEIGEN_MPL2_ONLY -DENABLE_HPMC_MIXED_PRECISION -DENABLE_SQLITE -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -DPY_ARRAY_UNIQUE_SYMBOL=PyArrayHandle -D_REENTRANT -DNO_IMPORT_ARRAY -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/var/tmp/portage/sci-physics/hoomd-blue-2.0.2/work/hoomd-blue-2.0.2 -Iinclude -DNDEBUG -O2 -pipe -march=native -fno-stack-protector -std=c++11 -MD -MT hoomd/test/CMakeFiles/test_vec2.dir/test_vec2.cc.o -MF hoomd/test/CMakeFiles/test_vec2.dir/test_vec2.cc.o.d -o hoomd/test/CMakeFiles/test_vec2.dir/test_vec2.cc.o -c /var/tmp/portage/sci-physics/hoomd-blue-2.0.2/work/hoomd-blue-2.0.2/hoomd/test/test_vec2.cc [85/320] : && /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-stack-protector -std=c++11 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu hoomd/test/CMakeFiles/test_vec3.dir/test_vec3.cc.o -o hoomd/test/test_vec3 -Wl,-rpath,/var/tmp/portage/sci-physics/hoomd-blue-2.0.2/work/hoomd-blue-2.0.2-python2_7/hoomd -rdynamic hoomd/_hoomd.so -lboost_unit_test_framework-mt -lboost_timer-mt -lboost_chrono-mt -lboost_system-mt -lpython2.7 -lboost_signals-mt -lboost_python-2.7-mt -lutil -ldl /usr/bin/sqlite3 && : FAILED: hoomd/test/test_vec3 : && /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-stack-protector -std=c++11 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu hoomd/test/CMakeFiles/test_vec3.dir/test_vec3.cc.o -o hoomd/test/test_vec3 -Wl,-rpath,/var/tmp/portage/sci-physics/hoomd-blue-2.0.2/work/hoomd-blue-2.0.2-python2_7/hoomd -rdynamic hoomd/_hoomd.so -lboost_unit_test_framework-mt -lboost_timer-mt -lboost_chrono-mt -lboost_system-mt -lpython2.7 -lboost_signals-mt -lboost_python-2.7-mt -lutil -ldl /usr/bin/sqlite3 && : /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: hoomd/_hoomd.so: etail14iterators_implILb0EE5applyISt6vectorIjSaIjEEE3endERS7_: invalid version 2 (max 0) hoomd/_hoomd.so: error adding symbols: Bad value collect2: error: ld returned 1 exit status ninja: build stopped: subcommand failed.
Portage 2.3.6 (python 3.6.1-final-0, default/linux/amd64/13.0/desktop/gnome/systemd, gcc-5.4.0, glibc-2.23-r4, 4.12.0-gentoo x86_64) ================================================================= System uname: Linux-4.12.0-gentoo-x86_64-Intel-R-_Core-TM-_i7-7700HQ_CPU_@_2.80GHz-with-gentoo-2.3 KiB Mem: 16073288 total, 4304324 free KiB Swap: 5240828 total, 5133308 free Timestamp of repository gentoo: Wed, 12 Jul 2017 18:30:01 +0000 sh bash 4.3_p48-r1 ld GNU ld (Gentoo 2.28 p1.2) 2.28 ccache version 3.2.4 [enabled] app-shells/bash: 4.3_p48-r1::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.1-r2::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo, 3.5.3::gentoo, 3.6.1-r1::gentoo dev-util/ccache: 3.2.4::gentoo dev-util/cmake: 3.7.2::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/openrc: 0.26.3::gentoo sys-apps/sandbox: 2.10-r3::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.28-r2::gentoo sys-devel/gcc: 4.9.4::gentoo, 5.4.0-r3::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6-r3::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.4::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-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 ago location: /hdd/portage/local/layman/ago masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -fno-stack-protector" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/chromium/policies/managed/chrome-gnome-shell.json /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/opt/chrome/policies/managed/chrome-gnome-shell.json /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="-O2 -pipe -march=native -fno-stack-protector" DISTDIR="/hdd/distfiles" EMERGE_DEFAULT_OPTS="--quiet-build=n --autounmask-write --keep-going" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs ccache cgroup compress-build-logs compressdebug config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.heanet.ie/pub/gentoo/" LANG="es_ES.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu" MAKEOPTS="-j9" PKGDIR="/hdd/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 applet avahi avx avx256 bash-completion berkdb bluetooth branding bzip2 cairo ccache cdda cddb cdr chm cli colord cracklib crypt cups cvs cxx dbus djvu dri dts dvd dvdr dvi ebook eds emboss enchant encode evo exif fam fat ffmpeg firefox flac fortran fuse gdbm gif git glamor gnome gnome-keyring gnome-online-accounts google googledrive gphoto2 gpm gromacs gstreamer gtk gtk3 gtkstyle http iconv infinality introspection irc jabber jpeg kpathsea latex lcms ldap libass libnotify libsecret libvisual lyx mad mms mmx mmxext mng mobi modules monolithic-build mp3 mp4 mpeg mtp multilib musicbrainz nautilus ncurses network-cron networkmanager nls nptl ntfs ntp numa nvidia offensive ogg opengl openmp optimized-qmake pam pango pch pdf pdfimport png policykit ppds pulseaudio qt3support qt4 readline reiserfs scanner sdl seccomp sendto session smp sna spell sse sse2 sse3 sse4 sse4_1 ssl ssse3 startup-notification svg systemd t1lib tcpd test theora threads tiff tracker truetype udev udisks unicode upnp upnp-av upower usb v4l vaapi vala vcd vdpau vlc vorbis wifi wxwidgets x264 x265 xattr xcb xfs xml xmpp xv xvid youtube zeroconf 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" 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 isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="es es-ES en en-US fr fr_FR" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="es es_ES en en_US fr fr_FR" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4 python3_5 python3_6" RUBY_TARGETS="ruby21 ruby22" USERLAND="GNU" VIDEO_CARDS="fbdev vesa intel i965 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Live version (9999) work fine. Probably also a newer version of hoomd-blue.
(In reply to Marco Genasci from comment #2) > Live version (9999) work fine. Probably also a newer version of hoomd-blue. I was looking into doing a version bump, but the newer tarballs don't include the mandatory code from the git submodules and hence don't work correctly. The 9999 version works as it comes from git.
Why don't take a snapshot from latest git then? :/
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=87a357c987080a67443e567140482094dd11fef3 commit 87a357c987080a67443e567140482094dd11fef3 Author: Michał Górny <mgorny@gentoo.org> AuthorDate: 2018-07-28 12:03:55 +0000 Commit: Michał Górny <mgorny@gentoo.org> CommitDate: 2018-07-28 12:03:55 +0000 sci-physics/hoomd-blue: Remove last-rited pkg Closes: https://bugs.gentoo.org/624688 profiles/package.mask | 4 -- sci-physics/hoomd-blue/Manifest | 2 - sci-physics/hoomd-blue/hoomd-blue-2.0.2.ebuild | 69 -------------------------- sci-physics/hoomd-blue/hoomd-blue-9999.ebuild | 69 -------------------------- sci-physics/hoomd-blue/metadata.xml | 18 ------- 5 files changed, 162 deletions(-)
