https://tinderboxlogs.s3.amazonaws.com/tbamd64.excelsior.flameeyes.eu/sci-chemistry%3Afreeon-1.0.8-r1%3A20141025-074634.html Portage 2.2.14_rc1 (python 2.7.8-final-0, default/linux/amd64/13.0, gcc-4.9.1-asneeded, glibc-2.20, 3.15.5-hardened-r2 x86_64) ================================================================= System uname: Linux-3.15.5-hardened-r2-x86_64-AMD_Opteron-TM-_Processor_6272-with-gentoo-2.2 KiB Mem: 65962672 total, 16391156 free KiB Swap: 0 total, 0 free Timestamp of tree: Unknown ld ld di GNU (Gentoo 2.24 p1.4) 2.24 distcc 3.1 x86_64-pc-linux-gnu [disabled] ccache version 3.1.9 [disabled] app-shells/bash: 4.2_p53 dev-java/java-config: 2.2.0 dev-lang/perl: 5.18.2-r2 dev-lang/python: 2.7.8, 3.2.5-r6, 3.3.5-r1, 3.4.1 dev-util/ccache: 3.1.9 dev-util/cmake: 2.8.12.2-r2 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.13.1 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.4_p6-r1, 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.13.2, 1.14.1 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.6.4, 4.7.4, 4.8.3, 4.9.1 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2-r1 sys-devel/make: 4.1 sys-kernel/linux-headers: 3.17 (virtual/os-headers) sys-libs/glibc: 2.20 Repositories: gentoo ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/entropy /opt/openjms/config /usr/share/bufrtables /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/themes/oxygen-gtk/gtk-2.0 /var/bind /var/lib/hsqldb /var/lib/neatx/home /var/spool/torque /var/yp/Makefile" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/games/angband/edit/ /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="-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches" DISTDIR="/var/cache/portage/distfiles" FCFLAGS="-O2 -pipe -ggdb -march=native -frecord-gcc-switches" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fail-clean fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict test test-fail-continue unknown-features-warn unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe -ggdb -march=native -frecord-gcc-switches" GENTOO_MIRRORS="http://ftp.ucsb.edu/pub/mirrors/linux/gentoo/ http://gentoo.mirrors.hoobly.com/ http://gentoo.llarian.net/" LANG="en_US.utf8" LC_ALL="C" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j24" 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" PORTAGE_TMPDIR="/tmp" PORTDIR="/var/cache/tinderbox/tree" PORTDIR_OVERLAY="" SYNC="rsync://excelsior.flameeyes.eu/gentoo-portage" USE="3dnow 3dnowex acl amd64 berkdb blas bzip2 cli cracklib crypt cxx doc dri emacs ffmpeg fortran freetype iconv icu intl introspection ipv6 lapack mmx modules multilib ncurses nls nptl openmp pam pax_kernel pcre pdf plasma qt3support readline semantic-desktop session snmp sse sse2 sse3 sse4 ssl ssse3 tcmalloc tcpd truetype udev unicode vhosts xft zlib" 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" 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" 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_3" RUBY_TARGETS="ruby19" USERLAND="GNU" 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Please attach the config.log. Which USE and version are you using for hdf5?
Created attachment 388052 [details] build.log Autoattach of build.log -- if there are any issues with this file please add bug to tracker bug 527870
Comment on attachment 388052 [details] build.log Hi Ian, I can't reproduce this problem here. However, there are a few things in the build.log that seem strange: /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: 40: /usr/share/config.site: [[: Permission denied and /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: 25266: /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: declare: Permission denied What kind of build environment is your tinderbox using? Is it using bash as sh? Or some other shell? Did it install sci-libs/hdf5? Which version? Is there a /usr/bin/h5cc? Thanks, nick
This is with dash as sh.
@Justin How is this typically fixed? If I run autoreconf would that pick up dash?
(In reply to Nicolas Bock from comment #5) > @Justin How is this typically fixed? If I run autoreconf would that pick up > dash? Use app-eselect/eselect-sh and dash to temporarily set /bin/sh to dash and test the build. You need to fix configure.ac to be posix compliant.
Thanks for the advice. I will do that.
I switched to sh -> dash and sci-chemistry/freeon-1.0.8-r1 builds now. I didn't change anything in the ebuild. Maybe something else changed?
@Justin, thanks for the blas/lapack patch! It's in the master branch now :) https://github.com/FreeON/freeon/commit/424fe7418c8e91c89e55947c8e5fcaf31739e11e
Closing.
