f951: Fatal Error: Reading module ‘h5global’ at line 1959 column 58: Unexpected EOF compilation terminated. make[3]: *** [Makefile:1007: H5_ff.lo] Error 1 make[3]: Leaving directory '/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18_build/fortran/src' ----------------------------------------------------------------- This is an unstable amd64 chroot image (named desktop-unstable_20161231-204545) at a hardened host acting as a tinderbox. ----------------------------------------------------------------- from make.conf: USE=" pax_kernel xtpax -cdinstall -oci8 -bindist ssp cgroups -clang -compat consolekit declarative dnssec fax ffmpeg freetds -gnuplot gtk2 -gui -gzip havege help -ibus icu isag libinput mikmod minimal -ncurses -ois openssl plasma -plotutils postproc source spice system-cairo -system-libs -uxa xinerama xslt xvmc -xz zip" gcc-config -l: [1] x86_64-pc-linux-gnu-5.4.0 * llvm-config --version: 3.9.1 Available Java Virtual Machines: [1] icedtea-bin-8 system-vm Available Python interpreters, in order of preference: [1] python3.4 [2] python2.7 (fallback) Available Ruby profiles: [1] ruby21 (with Rubygems) * java-config: The following VMs are available for generation-2: *) IcedTea JDK 3.2.0 [icedtea-bin-8] ----------------------------------------------------------------- $ cat emerge-info.txt Portage 2.3.3 (python 3.4.5-final-0, default/linux/amd64/13.0/desktop, gcc-5.4.0, glibc-2.24, 4.8.15-hardened x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.8.15-hardened-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.3 KiB Mem: 65285560 total, 1866096 free KiB Swap: 67108860 total, 67091632 free Timestamp of repository gentoo: Mon, 02 Jan 2017 11:22:44 +0000 sh bash 4.4_p5-r1 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 app-shells/bash: 4.4_p5-r1::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.1_rc4::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo dev-util/cmake: 3.7.1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/openrc: 0.23::gentoo sys-apps/sandbox: 2.10-r3::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.25.1-r1::gentoo, 2.27::gentoo sys-devel/gcc: 5.4.0-r2::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: 4.9::gentoo (virtual/os-headers) sys-libs/glibc: 2.24::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: 1 tinderbox location: /tmp/tb/data/portage masters: gentoo priority: 2 local location: /usr/local/portage masters: gentoo priority: 99 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -Wall" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /opt/openfire/resources/security/ /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/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="-O2 -pipe -march=native" 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 cdda cdr cgroups cli consolekit convert cracklib crypt cups cxx dbus declarative dnssec dri dts dvd dvdr emboss encode exif fam fax ffmpeg firefox flac fortran freetds gd gdbm gif glamor gpm gtk gtk2 havege help iconv icu ipv6 isag jpeg lcms ldap libinput libnotify mad messages mikmod minimal mmx mmxext mng mod modules mp3 mp4 mpeg multilib nls nptl ogg opengl openmp openssl pam pango pax_kernel pcre pdf plasma png policykit postproc ppds python qml qt3support qt4 readline sdl seccomp session source spell spice sse sse2 ssl ssp startup-notification svc svg system-cairo system-ffmpeg tcpd tiff truetype udev udisks unicode upower usb video vorbis wxwidgets x264 xattr xcb xinerama xml 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" L10N="ca kk" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" 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 458340 [details] config.log.bz2
Created attachment 458342 [details] emerge-history.txt
Created attachment 458344 [details] environment
Created attachment 458346 [details] etc.portage.tbz2
Created attachment 458348 [details] sci-libs:hdf5-1.8.18:20170102-113724.log.bz2
This is not a GCC-6 issue. From the build log: > compiler 'x86_64-pc-linux-gnu-gcc' is GNU gcc-5.4.0 > checking for Fortran libraries of x86_64-pc-linux-gnu-gfortran... -L/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/ It wasn't using gcc-6. I'm not able to reproduce the issue with gcc-6.3.0 or gcc-5.4.0.
and b/c it builds fine recently I'll close this as invalid as long as the root cause can't be proven being a different one ?
