Created attachment 524392 [details] build.log /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -march=native -pipe -fomit-frame-pointer -flto -fuse-linker-plugin -pthread -Wl,-O1 -Wl,--as-needed -flto -o exrheader main.o -lImath -lHalf -lIex -lIexMath -lIlmThread -pthread ../IlmImf/libIlmImf.la -lz -pthread libtool: link: x86_64-pc-linux-gnu-g++ -O2 -march=native -pipe -fomit-frame-pointer -flto -fuse-linker-plugin -pthread -Wl,-O1 -flto -o .libs/exrheader main.o -pthread -pthread -Wl,--as-needed -L/usr/lib64 ../IlmImf/.libs/libIlmImf.so /usr/lib64/libImath.so /usr/lib64/libHalf.so /usr/lib64/libIexMath.so /usr/lib64/libIlmThread.so /usr/lib64/libIex.so -lz -pthread /usr/lib64/libIlmThread.so: undefined reference to `pthread_create' /usr/lib64/libIlmThread.so: undefined reference to `sem_wait' /usr/lib64/libIlmThread.so: undefined reference to `sem_init' /usr/lib64/libIlmThread.so: undefined reference to `sem_destroy' /usr/lib64/libIlmThread.so: undefined reference to `sem_getvalue' /usr/lib64/libIlmThread.so: undefined reference to `sem_post' /usr/lib64/libIlmThread.so: undefined reference to `sem_trywait' /usr/lib64/libIlmThread.so: undefined reference to `pthread_join' collect2: error: ld returned 1 exit status make[1]: *** [Makefile:414: exrheader] Error 1 make[1]: Leaving directory '/var/tmp/portage/media-libs/openexr-2.2.0-r2/work/openexr-2.2.0-abi_x86_64.amd64/exrheader' # emerge --info Portage 2.3.24 (python 3.5.4-final-0, default/linux/amd64/17.1/systemd, gcc-7.3.0, glibc-2.26-r6, 4.16.0-rc5 x86_64) ================================================================= System uname: Linux-4.16.0-rc5-x86_64-Intel-R-_Core-TM-_i5-6500_CPU_@_3.20GHz-with-gentoo-2.4.1 KiB Mem: 16021848 total, 1530636 free KiB Swap: 12337144 total, 11967992 free Timestamp of repository gentoo: Mon, 19 Mar 2018 13:00:02 +0000 Head commit of repository gentoo: 1170a57f0a741ea9a0ccefc4e6ff1a83997a2763 sh bash 4.4_p19 ld GNU ld (Gentoo 2.30 p1) 2.30.0 ccache version 3.3.4 [disabled] app-shells/bash: 4.4_p19::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.26.1-r2::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.4.6-r1::gentoo, 3.5.4-r1::gentoo dev-util/ccache: 3.3.4-r1::gentoo dev-util/cmake: 3.10.3::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.4.1-r2::gentoo sys-apps/sandbox: 2.13::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.11.6-r3::gentoo, 1.16.1-r1::gentoo sys-devel/binutils: 2.30::gentoo sys-devel/gcc: 7.3.0-r1::gentoo sys-devel/gcc-config: 1.9.1::gentoo sys-devel/libtool: 2.4.6-r4::gentoo sys-devel/make: 4.2.1-r3::gentoo sys-kernel/linux-headers: 4.15::gentoo (virtual/os-headers) sys-libs/glibc: 2.26-r6::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-extra-opts: sync-rsync-verify-metamanifest: no x-portage location: /usr/local/portage masters: gentoo priority: 0 mv location: /var/lib/layman/mv sync-type: laymansync sync-uri: git://anongit.gentoo.org/user/mv.git masters: gentoo priority: 50 rust location: /var/lib/layman/rust sync-type: laymansync sync-uri: git://github.com/gentoo/gentoo-rust.git masters: gentoo priority: 50 steam-overlay location: /var/lib/layman/steam-overlay sync-type: laymansync sync-uri: git://github.com/anyc/steam-overlay.git masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA Intel-SDP Oracle-BCLA-JavaSE Oracle-EADLA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=native -pipe -fomit-frame-pointer -flto -fuse-linker-plugin" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/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-php7.2/ext-active/ /etc/php/cgi-php7.2/ext-active/ /etc/php/cli-php7.2/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -march=native -pipe -fomit-frame-pointer -flto -fuse-linker-plugin" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--jobs=4 --load-average=4.5" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs candy cgroup clean-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms splitdebug strict strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync webrsync-gpg xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -flto" LINGUAS="en" MAKEOPTS="-j5" 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 aacs acl acpi aiglx alac alsa amd64 amr amrnb amrwb animation apache2 apng argon2 artworkextra asf aspnet2 asyncns authdaemond avahi avi bash-completion bcmath berkdb bitmap-fonts bluetooth bluray bmp bonjour brotli btrfs bzip2 cairo caps cdda cddb cdparanoia cdr celt chm clang cli crypt cryptsetup css cups curl cxx daap dbus device-mapper dga dhclient dirac divx4linux dlloader dns dnssec dovecot-sasl dpms dri dri3 dts dv dvb dvd dvdr dvdread egl enca encode exif ext4 faac fam fame fat fbcondecor fbsplash ffmpeg fftw firefox flac fontconfig foomaticdb fortran freetype ftp fuse gaim gd gdbm geoip gif gimpprint glamor gles gles1 gles2 glib glibc-omitfp glitz glut gost gphoto2 gsm gstreamer gstreamer10 gtk gtk2 gudev hardenedphp hbci howl howl-compat http2 https hwdb iconv icu idn imagemagick imap imlib innodb ipv6 java java5 javafx jbig jce joystick jpeg jpeg2k junit kdbus kdehiddenvisibility kvm lapack lcms libfame libkms libnotify librtmp libusb lirc live llvm lm_sensors lvm lz4 lzma lzo mad maildir mdadm mdnsresponder-compat metalink mjpeg mmap mms mng modules motif mozilla mozsvg mp3 mpeg mpeg2 mplayer mpx multilib musepack mysql mythtv natspec ncurses nemesi network networkmanager nls nptl nptlonly ntfs ocl-icd offensive ofx ogg oggvorbis openal opencl openexr opengl openmp openvg opus pam pango pcre pcre16 pcre32 pdf pdflib perl pgo phonon pic pie png pnp policykit ppd ppds pulseaudio python qt qt3 qt3support qt4 quicktime quvi rar readline resolvconf rtc rtmp schroedinger screensaver sctp sdl seccomp session sftp sharedmem shout smp sna sni sox speex spell sqlite ssh ssl steamruntime suspend2 svg systemd theora threads tiff tls transcode truetype truetype-fonts type-fonts udev udisks unicode unzip upnp ups usb user-session uxa v4l2 vaapi vcd vdpau videos virgl vorbis vpx vulkan wayland webdav webp webservices wifi win32codecs wmf wv x264 x265 xanim xattr xcb xcomposite xdg xinerama xml xml2 xpm xprint xrandr xv xvfb xvid xvmc zeroconf zip zlib" ABI_X86="64" ALSA_CARDS="hda-intel" APACHE2_MODULES="actions alias auth_basic authn_core authz_core cache_disk authn_alias authn_anon authn_dbm authn_file authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex brotli cache dav dav_fs dav_lock dconf deflate dir env expires ext_filter file_cache filter headers include info log_config logio mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias auth_digest proxy proxy_ajp proxy_connect proxy_http proxy_fcgi reqtimeout cgi cgid unixd socache_shmcb proxy_html xml2enc" 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" CURL_SSL="openssl" 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" GRUB_PLATFORMS="efi-64 pc" INPUT_DEVICES="evdev joystick keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LIRC_DEVICES="userspace" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-1" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7 python3_5" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby25" USERLAND="GNU" VIDEO_CARDS="intel i965 amdgpu radeon radeonsi" 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
This is another failure due to -flto being enabled.
> /usr/lib64/libIlmThread.so: undefined reference to `pthread_create' I think this but is really underlinking against pthread in media-libs/ilmbase (/usr/lib64/libIlmThread.so) and should be worked around there. Note there is no libpthread in NEEDED depends: $ lddtree /usr/lib64/libIlmThread.so libIlmThread.so => /usr/lib64/libIlmThread.so (interpreter => none) libIex-2_2.so.12 => /usr/lib64/libIex-2_2.so.12 libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/libstdc++.so.6 ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2 libm.so.6 => /lib64/libm.so.6 libc.so.6 => /lib64/libc.so.6 libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/libgcc_s.so.1 Slightly simpler reproducer on ilmbase: $ LDFLAGS="$(portageq envvar LDFLAGS) -Wl,--no-undefined" emerge -v1 media-libs/ilmbase /bin/sh ../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -pipe -O2 -pipe -flto -pthread -version-info 12:0:0 -no-undefined -release 2_2 -Wl,-O1 -Wl,--as-needed -O2 -pipe -flto -Wl,--hash-style=gnu -Wl,--no-undefined -o libIlmThread.la -rpath /usr/lib64 IlmThreadPool.lo IlmThread.lo IlmThreadSemaphore.lo IlmThreadMutex.lo IlmThreadPosix.lo IlmThreadSemaphorePosix.lo IlmThreadSemaphorePosixCompat.lo IlmThreadMutexPosix.lo ../Iex/libIex.la -pthread ... /dev/shm/portage/media-libs/ilmbase-2.2.0-r1/temp/ccHtIfsh.ltrans0.ltrans.o: In function `IlmThread_2_2::Thread::start()': <artificial>:(.text+0x747): undefined reference to `pthread_create'
> Slightly simpler reproducer on ilmbase: > > $ LDFLAGS="$(portageq envvar LDFLAGS) -Wl,--no-undefined" emerge -v1 > media-libs/ilmbase This fails for me even on non-lto systems.
Vague consensus it's a libtool bug of mis-handling -pthread (-lpthread would work) for c++ libraries: https://bugzilla.redhat.com/show_bug.cgi?id=661333
Upstream bug report: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=15646 Gentoo might want to apply the patch: http://permalink.gmane.org/gmane.comp.gnu.libtool.patches/11704 It's a hack but non-invasive one.
Created attachment 525216 [details, diff] libtool-2.4.6-pthread.patch Used this to apply/test the patch: --- a/sys-devel/libtool/libtool-2.4.6-r4.ebuild +++ b/sys-devel/libtool/libtool-2.4.6-r4.ebuild @@ -60,2 +60,3 @@ src_prepare() { epatch "${FILESDIR}"/${PN}-2.4.6-darwin-use-linux-version.patch + epatch "${FILESDIR}"/${PN}-2.4.6-pthread.patch if use prefix ; then @@ -81,3 +82,3 @@ src_prepare() { touch doc/*.1 - export HELP2MAN=false + export HELP2MAN=true fi I guess it will need to be applied to as well https://gitweb.gentoo.org/proj/elt-patches.git/
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5690e822e589b92b4225c8c8b671ff8db5faf605 commit 5690e822e589b92b4225c8c8b671ff8db5faf605 Author: Lars Wendler <polynomial-c@gentoo.org> AuthorDate: 2018-03-26 08:37:26 +0000 Commit: Lars Wendler <polynomial-c@gentoo.org> CommitDate: 2018-03-26 08:38:31 +0000 sys-devel/libtool: Revbump to add pthread patch. Bug: https://bugs.gentoo.org/650876 Package-Manager: Portage-2.3.24, Repoman-2.3.6 .../files/libtool-2.4.6-libtoolize-slow.patch | 6 +- .../libtool/files/libtool-2.4.6-pthread.patch | 43 +++++++ .../files/libtool-2.4.6-pthread_bootstrapped.patch | 21 ++++ sys-devel/libtool/libtool-2.4.6-r5.ebuild | 124 +++++++++++++++++++++ sys-devel/libtool/libtool-9999.ebuild | 5 + 5 files changed, 196 insertions(+), 3 deletions(-)}
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61fedd15b0dbf3df6a37eae73cd1e931b17b9220 commit 61fedd15b0dbf3df6a37eae73cd1e931b17b9220 Author: Craig Andrews <candrews@gentoo.org> AuthorDate: 2018-03-24 01:23:08 +0000 Commit: Craig Andrews <candrews@gentoo.org> CommitDate: 2018-03-26 13:51:17 +0000 media-libs/openexr: Strip lto flag Closes: https://bugs.gentoo.org/650876 Package-Manager: Portage-2.3.24, Repoman-2.3.6 media-libs/openexr/openexr-2.2.0-r2.ebuild | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-)
*** Bug 651630 has been marked as a duplicate of this bug. ***
