Bug 547816 – sci-chemistry/apbs-1.4.1-r2 fails to build on ppc

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Pacho Ramos 2015-04-26 14:02:12 UTC]

Created attachment 402048 [details]
build.log

Linking C shared library /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_routines.so
cd /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1
/usr/lib/ccache/bin/powerpc-unknown-linux-gnu-gcc  -fPIC -std=c99  -Wl,-O1 -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so -o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_routines.so CMakeFiles/apbs_routines.dir/routines.c.o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_mg.so -lapbs_fem /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_generic.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_pmgc.so /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_geoflow.so -lmaloc -lm -fopenmp 
/usr/lib/gcc/powerpc-unknown-linux-gnu/4.8.4/../../../../powerpc-unknown-linux-gnu/bin/ld: cannot find -lapbs_fem
make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build'
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build/CMakeFiles  1 2
collect2: error: ld returned 1 exit status
src/CMakeFiles/apbs_routines.dir/build.make:92: recipe for target '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_routines.so' failed
make[2]: *** [/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-pdb2pqr-74fcb8676de69ed04ddab8976a8b05a6caaf4d65/apbs/lib/libapbs_routines.so] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build'
CMakeFiles/Makefile2:132: recipe for target 'src/CMakeFiles/apbs_routines.dir/all' failed
make[1]: *** [src/CMakeFiles/apbs_routines.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[100%] Built target apbs
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/apbs-1.4.1-r2/work/apbs-1.4.1_build'
Makefile:116: recipe for target 'all' failed
make: *** [all] Error 2

Portage 2.2.18 (python 2.7.9-final-0, default/linux/powerpc/ppc32/13.0/desktop/gnome/systemd, gcc-4.8.4, glibc-2.20-r2, 3.12.20-gentoo ppc64)
=================================================================
System uname: Linux-3.12.20-gentoo-ppc64-POWER7_-architected-with-gentoo-2.2
KiB Mem:    16514732 total,   3620732 free
KiB Swap:    7814548 total,   7791568 free
Timestamp of repository gentoo: Sun, 26 Apr 2015 10:00:01 +0000
sh bash 4.2_p53
ld GNU ld (Gentoo 2.24 p1.4) 2.24
ccache version 3.1.9 [enabled]
app-shells/bash:          4.2_p53::gentoo
dev-java/java-config:     2.2.0::gentoo
dev-lang/perl:            5.20.2::gentoo
dev-lang/python:          2.7.9-r1::gentoo, 3.4.1::gentoo
dev-util/ccache:          3.1.9-r4::gentoo
dev-util/cmake:           2.8.12.2-r1::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.13.11::gentoo
sys-apps/sandbox:         2.6-r1::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.11.6-r1::gentoo, 1.12.6::gentoo, 1.13.4::gentoo
sys-devel/binutils:       2.24-r3::gentoo
sys-devel/gcc:            4.8.4::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: 3.18::gentoo (virtual/os-headers)
sys-libs/glibc:           2.20-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

ACCEPT_KEYWORDS="ppc"
ACCEPT_LICENSE="*"
CBUILD="powerpc-unknown-linux-gnu"
CFLAGS="-O2 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector"
CHOST="powerpc-unknown-linux-gnu"
CONFIG_PROTECT="/etc /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/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 -mcpu=powerpc -mtune=powerpc -pipe -fno-stack-protector"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--quiet-build=n --autounmask-write --keep-going"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs ccache config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms split-log strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j33"
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="/var/tmp"
USE="X a52 aac acl alsa berkdb bluetooth branding bzip2 cairo cdda cdr cli colord cracklib crypt cups cxx dbus dri dts dvd dvdr eds 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 mng modules mp3 mp4 mpeg nautilus ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppc ppds pulseaudio qt3support qt4 readline sdl session socialweb spell ssl startup-notification svg systemd tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xml xv xvid zlib" ABI_PPC="32" ALSA_CARDS="aoa aoa-fabric-layout aoa-onyx aoa-soundbus aoa-soundbus-i2s aoa-tas aoa-toonie powermac usb-audio via82xx" 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" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_US" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="fbdev glint mach64 mga nv r128 radeon savage tdfx trident 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:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Justin Lecher (RETIRED) 2015-05-05 08:53:20 UTC]

Could you please check whether this is a parallel make issue?

[Comment 2 Pacho Ramos 2015-05-07 18:11:38 UTC]

Created attachment 402840 [details]
build.log

Yes, it still fails :(

[Comment 3 Justin Lecher (RETIRED) 2015-05-08 10:01:41 UTC]

+  08 May 2015; Justin Lecher <[e-mail]> apbs-1.4.1-r2.ebuild:
+  Disable iAPBS to fix compilation problems, bug #547816
+

[Comment 4 Pacho Ramos 2015-05-08 17:21:35 UTC]

It works! :)