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hgecol
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Joined: 31 Jul 2011
Posts: 16

PostPosted: Tue Sep 20, 2011 3:30 am    Post subject: [sovled] Failed to emerge R and Grass Reply with quote

R
Code:

make[3]: Leaving directory `/var/tmp/portage/dev-lang/R-2.10.1/work/R-2.10.1/src/modules/lapack'
make[2]: Leaving directory `/var/tmp/portage/dev-lang/R-2.10.1/work/R-2.10.1/src/modules'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/var/tmp/portage/dev-lang/R-2.10.1/work/R-2.10.1/src'
make: *** [R] Error 1
emake failed
 * ERROR: dev-lang/R-2.10.1 failed (compile phase):
 *   emake failed
 *
 * Call stack:
 *     ebuild.sh, line  56:  Called src_compile
 *   environment, line 3045:  Called die
 * The specific snippet of code:
 *       emake || die "emake failed";
 *
 * If you need support, post the output of 'emerge --info =dev-lang/R-2.10.1',
 * the complete build log and the output of 'emerge -pqv =dev-lang/R-2.10.1'.
 * The complete build log is located at '/var/tmp/portage/dev-lang/R-2.10.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-lang/R-2.10.1/temp/environment'.
 * S: '/var/tmp/portage/dev-lang/R-2.10.1/work/R-2.10.1'

>>> Failed to emerge dev-lang/R-2.10.1, Log file:

>>>  '/var/tmp/portage/dev-lang/R-2.10.1/temp/build.log'

 * Messages for package sci-libs/blas-reference-20070226:

 * blas has been eselected to reference

 * Messages for package dev-lang/R-2.10.1:

 * ERROR: dev-lang/R-2.10.1 failed (compile phase):
 *   emake failed
 *
 * Call stack:
 *     ebuild.sh, line  56:  Called src_compile
 *   environment, line 3045:  Called die
 * The specific snippet of code:
 *       emake || die "emake failed";
 *
 * If you need support, post the output of 'emerge --info =dev-lang/R-2.10.1',
 * the complete build log and the output of 'emerge -pqv =dev-lang/R-2.10.1'.
 * The complete build log is located at '/var/tmp/portage/dev-lang/R-2.10.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-lang/R-2.10.1/temp/environment'.
 * S: '/var/tmp/portage/dev-lang/R-2.10.1/work/R-2.10.1'

 * GNU info directory index is up-to-date.


GRASS: Failed to emerge gdal-1.6.3
Code:

make: *** [frmts-target] Error 2
emake failed
 * ERROR: sci-libs/gdal-1.6.3-r1 failed (compile phase):
 *   emake failed
 *
 * Call stack:
 *     ebuild.sh, line  56:  Called src_compile
 *   environment, line 5961:  Called die
 * The specific snippet of code:
 *       emake -j1 || die "emake failed";
 *
 * If you need support, post the output of 'emerge --info =sci-libs/gdal-1.6.3-r1',
 * the complete build log and the output of 'emerge -pqv =sci-libs/gdal-1.6.3-r1'.
 * The complete build log is located at '/var/tmp/portage/sci-libs/gdal-1.6.3-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/gdal-1.6.3-r1/temp/environment'.
 * S: '/var/tmp/portage/sci-libs/gdal-1.6.3-r1/work/gdal-1.6.3'

>>> Failed to emerge sci-libs/gdal-1.6.3-r1, Log file:

>>>  '/var/tmp/portage/sci-libs/gdal-1.6.3-r1/temp/build.log'

 * Messages for package sci-libs/gdal-1.6.3-r1:

 * User-specified configure options are not set.
 * If needed, set GDAL_CONFIGURE_OPTS to enable grass support.
 * ERROR: sci-libs/gdal-1.6.3-r1 failed (compile phase):
 *   emake failed
 *
 * Call stack:
 *     ebuild.sh, line  56:  Called src_compile
 *   environment, line 5961:  Called die
 * The specific snippet of code:
 *       emake -j1 || die "emake failed";
 *
 * If you need support, post the output of 'emerge --info =sci-libs/gdal-1.6.3-r1',
 * the complete build log and the output of 'emerge -pqv =sci-libs/gdal-1.6.3-r1'.
 * The complete build log is located at '/var/tmp/portage/sci-libs/gdal-1.6.3-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/gdal-1.6.3-r1/temp/environment'.
 * S: '/var/tmp/portage/sci-libs/gdal-1.6.3-r1/work/gdal-1.6.3'

 * GNU info directory index is up-to-date.



emerge --info =dev-lang/R-2.10.1
Code:

Portage 2.1.10.11 (default/linux/amd64/10.0/desktop, gcc-4.4.5, glibc-2.12.2-r0, 2.6.39-gentoo-r3 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-2.6.39-gentoo-r3-x86_64-Intel-R-_Core-TM-_i5_CPU_M_520_@_2.40GHz-with-gentoo-2.0.3
Timestamp of tree: Mon, 19 Sep 2011 23:30:01 +0000
app-shells/bash:          4.1_p9
dev-lang/python:          2.6.6-r2, 2.7.1-r1, 3.1.3-r1
dev-util/cmake:           2.8.4-r1
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.8.3-r1
sys-apps/sandbox:         2.4
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.11.1
sys-devel/binutils:       2.21.1-r1
sys-devel/gcc:            4.4.5
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.36.1 (virtual/os-headers)
sys-libs/glibc:           2.12.2
Repositories: gentoo gentoo-zh science
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA PUEL"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -mtune=core2 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /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="-march=core2 -mtune=core2 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://mirrors.163.com/gentoo/ ftp://mirrors.sohu.com/gentoo/ http://mirrors.sohu.com/gentoo/ "
LC_ALL=""
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/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="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/gentoo-zh /var/lib/layman/science"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus device-mapper dri dts dvd dvdr encode exif fam firefox flac fortran gdbm gdu gif iconv ipv6 jpeg lcms ldap libnotify lock mad minimal mmx mng modules mp3 mp4 mpeg mplayer mudflap multilib ncurses nls nptl nptlonly ogg opengl openmp pam pango pcre pdf perl png policykit ppds pppd python readline sdl session spell sse sse2 ssl startup-notification svg sysfs tcpd thunar tiff truetype udev unicode usb vorbis x264 xcb xml xorg xulrunner xv xvid zlib" ALSA_CARDS="hda-intel usb-audio" 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="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia nouveau intel" 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, LANG, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS


Last edited by hgecol on Tue Sep 27, 2011 6:02 am; edited 1 time in total
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Bones McCracker
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PostPosted: Tue Sep 20, 2011 7:58 pm    Post subject: Reply with quote

Did you recently emerge sys-libs/zlib-1.2.5.1-r1 ? It included a change that broke a number of packages. Check out Bug 383179.

Specific to R and gdal, see Bug 383431 and Bug 383569.

Temporary work-around:
Code:
CPPFLAGS='-DOF=_Z_OF' emerge -1a <package>

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hgecol
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Joined: 31 Jul 2011
Posts: 16

PostPosted: Wed Sep 21, 2011 12:14 am    Post subject: Reply with quote

Thanks a lot.

But I did not emerged zlib-1.2.5.1.
'gdal-1.8.1 (~amd64)' and 'R-2.13.1(~amd64)' could be emerged, however, grass-6.4.1 can not emerged.
The problem of grass-6.4.1 just seems similar.
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hgecol
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Joined: 31 Jul 2011
Posts: 16

PostPosted: Tue Sep 27, 2011 6:01 am    Post subject: Reply with quote

I found out the problem today.
'R' & 'GRASS' were conflicted with ' media-libs/libpng-1.5.5'
I has emerged an unstable version of libpng for some reason.
I changed 'package.keywords' and installed the stable version, then 'R' & 'Grass' can be installed now.
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Bones McCracker
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PostPosted: Tue Sep 27, 2011 7:36 am    Post subject: Reply with quote

Ah, yes. Best to keep the system as much as you can one way or the other.
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