Bug 394961 – sci-biology/mrbayes-3.1.2-r1: fails to compile

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Agostino Sarubbo 2011-12-16 18:03:11 UTC]

Created attachment 296061 [details]
build.log

Portage 2.1.10.11 (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.13-r4, 3.0.6-gentoo x86_64)
=================================================================
System uname: Linux-3.0.6-gentoo-x86_64-Intel-R-_Core-TM-_i3_CPU_540_@_3.07GHz-with-gentoo-2.0.3
Timestamp of tree: Fri, 16 Dec 2011 17:00:01 +0000
app-shells/bash:          4.1_p9
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r3, 3.1.4-r3
dev-util/cmake:           2.8.4-r1
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.9.4
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.68
sys-devel/automake:       1.10.3, 1.11.1
sys-devel/binutils:       2.21.1-r1
sys-devel/gcc:            4.5.3-r1
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.39 (virtual/os-headers)
sys-libs/glibc:           2.13-r4
Repositories: gentoo x-portage
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -g0"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/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="-march=native -O2"
DISTDIR="/media/sources"
EMERGE_DEFAULT_OPTS="--with-bdeps y --quiet-build n"
FEATURES="assume-digests binpkg-logs collision-protect distlocks ebuild-locks fixlafiles fixpackages multilib-strict news parallel-fetch protect-owned sandbox sfperms split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O1"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="it_IT.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
LINGUAS="am fil zh af ca cs da de el es et gl hu nb nl pl pt ro ru sk sl sv uk bg cy en eo fo ga he id ku lt lv mk ms nn sw tn zu ja zh_TW en_GB pt_BR ko zh_CN ar en_CA fi kk oc sr tr fa wa nds as be bn bn_BD bn_IN en_US es_AR es_CL es_ES es_MX eu fy fy_NL ga_IE gu gu_IN hi hi_IN is ka kn ml mr nn_NO or pa pa_IN pt_PT rm si sq sv_SE ta ta_LK te th vi ast dz km my om sh ug uz ca@valencia sr@ijekavian sr@ijekavianlatin sr@latin csb hne mai se es_LA fr_CA zh_HK br la no es_CR et_EE sr_CS bo hsb hy mn sr@Latn lb ne bs tg uz@cyrillic xh be_BY brx ca_XV dgo en_ZA gd kok ks ky lo mni nr ns pap ps rw sa_IN sat sd ss st sw_TZ ti ts ve mt ia az me tl ak hy_AM lg nso son ur_PK it fr nb nb_NO hr nan ur"
MAKEOPTS="-j4"
PKGDIR="/media/sources/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X aac acl acpi alsa amd64 apng bash-completion berkdb bzip2 cairo cli cracklib crypt cups cxx dbus device-mapper dri extras ffmpeg fortran gdbm gpm gtk iconv ipv6 jpeg jpeg2k kde lame mmx modules mp3 mudflap multilib ncurses nls nptl nptlonly nsplugin ogg opengl openmp pam pcre png policykit pppd qt3support qt4 readline sdl semantic-desktop session sse sse2 ssl svg sysfs tcpd tiff unicode vorbis xorg zlib" ALSA_CARDS="hda-intel" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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 stage tables krita karbon braindump" 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 ubx" INPUT_DEVICES="mouse evdev keyboard" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="am fil zh af ca cs da de el es et gl hu nb nl pl pt ro ru sk sl sv uk bg cy en eo fo ga he id ku lt lv mk ms nn sw tn zu ja zh_TW en_GB pt_BR ko zh_CN ar en_CA fi kk oc sr tr fa wa nds as be bn bn_BD bn_IN en_US es_AR es_CL es_ES es_MX eu fy fy_NL ga_IE gu gu_IN hi hi_IN is ka kn ml mr nn_NO or pa pa_IN pt_PT rm si sq sv_SE ta ta_LK te th vi ast dz km my om sh ug uz ca@valencia sr@ijekavian sr@ijekavianlatin sr@latin csb hne mai se es_LA fr_CA zh_HK br la no es_CR et_EE sr_CS bo hsb hy mn sr@Latn lb ne bs tg uz@cyrillic xh be_BY brx ca_XV dgo en_ZA gd kok ks ky lo mni nr ns pap ps rw sa_IN sat sd ss st sw_TZ ti ts ve mt ia az me tl ak hy_AM lg nso son ur_PK it fr nb nb_NO hr nan ur" NGINX_MODULES_HTTP="access auth_basic autoindex browser charset empty_gif fastcgi geo gzip limit_req limit_zone map memcached proxy referer rewrite scgi split_clients ssi upstream_ip_hash userid uwsgi addition cache_purge dav degradation flv geoip gzip_static headers_more image_filter perl push random_index realip secure_link stub_status sub xslt ey_balancer slowfs_cache upload" NGINX_MODULES_MAIL="imap pop3 smtp" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ree18 ruby18" USERLAND="GNU" VIDEO_CARDS="nouveau"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Justin Lecher (RETIRED) 2011-12-17 13:45:22 UTC]

+  17 Dec 2011; Justin Lecher <[e-mail]> mrbayes-3.1.2-r1.ebuild:
+  Use mpicc with USE=mpi, #394961
+