Jeramia Poland | 21 Nov 19:09 2014
Picon

Emerge Sage-doc-6.3 fails 3.16.5-sources gcc-4.8.3 with lto and graphite

I've emerge sage-6.3 but the last package sage-doc is failing.  I though sage might work without it but it crashes when I attempt to run it saying that pynac.so is an undefined symbol.

It seems like sage-doc is complaining of a symbol issue which I assume is related to my "bizarre" gcc flag configuration.  I've attempted to emerge with no graphite and no lto flags but it still is not working. I attempted changing to the 'vanilla' profile through gcc-config but that did not work either.

What should I try next?

Attached are:

info output
build log
whatever -pqv outputs 
environment

Thanks,
Jeramia
Portage 2.2.8-r2 (hardened/linux/amd64, gcc-4.8.3, glibc-2.19-r1, 3.16.5-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.16.5-gentoo-x86_64-AMD_A10-5700_APU_with_Radeon-tm-_HD_Graphics-with-gentoo-2.2
KiB Mem:    15873608 total,   9231428 free
KiB Swap:          0 total,         0 free
Timestamp of tree: Sun, 09 Nov 2014 08:00:01 +0000
ld GNU gold (Gentoo 2.24 p1.4 2.24) 1.11
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:          2.7.7, 3.3.5-r1, 3.4.1
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.13.4
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.13 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo CloogPatch science sage-on-gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* - <at> EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release
/etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks
fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict
unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.aditsu.net:8000/ http://gentoo.modulix.net/gentoo/ http://gentoo.gg3.net/"
LANG="en_US.utf8"
LDFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize -fuse-linker-plugin"
MAKEOPTS="-j5"
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"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage /var/lib/layman/science /var/lib/layman/sage-on-gentoo"
USE="acl amd64 bash-completion bcmath berkdb bindist blas bzip2 cli cracklib crypt cxx dri emacs fftw
gdbm graphite hardened iconv ipv6 justify lapack lm_sensors lto lzma lzo mmx modules multilib ncurses
nls nptl openmp pam pax_kernel pcre python readline session smp sse sse2 sse3 sse4_1 ssl symlink syslog
tcpd threads truetype udev unicode urandom usb xattr xtpax 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" INPUT_DEVICES="evdev" 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
ruby20" USERLAND="GNU" VIDEO_CARDS="fglrx" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

Portage 2.2.8-r2 (hardened/linux/amd64, gcc-4.8.3, glibc-2.19-r1, 3.16.5-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.16.5-gentoo-x86_64-AMD_A10-5700_APU_with_Radeon-tm-_HD_Graphics-with-gentoo-2.2
KiB Mem:    15873608 total,   5727044 free
KiB Swap:          0 total,         0 free
Timestamp of tree: Mon, 17 Nov 2014 11:00:01 +0000
ld GNU gold (Gentoo 2.24 p1.4 2.24) 1.11
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:          2.7.7, 3.3.5-r1, 3.4.1
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.13.4
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.13 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo CloogPatch science sage-on-gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* - <at> EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
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=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks
fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict
unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.aditsu.net:8000/ http://gentoo.modulix.net/gentoo/ http://gentoo.gg3.net/"
LANG="en_US.utf8"
LDFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize -fuse-linker-plugin"
MAKEOPTS="-j5"
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"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage /var/lib/layman/science /var/lib/layman/sage-on-gentoo"
USE="acl amd64 bash-completion bcmath berkdb bindist blas bzip2 cli cracklib crypt cxx dri emacs fftw
gdbm graphite hardened iconv ipv6 justify lapack lm_sensors lto lzma lzo mmx modules multilib ncurses
nls nptl openmp pam pax_kernel pcre python readline session smp sse sse2 sse3 sse4_1 ssl symlink syslog
tcpd threads truetype udev unicode urandom usb xattr xtpax 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" INPUT_DEVICES="evdev" 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
ruby20" USERLAND="GNU" VIDEO_CARDS="fglrx" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

Portage 2.2.8-r2 (hardened/linux/amd64, gcc-4.8.3, glibc-2.19-r1, 3.16.5-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.16.5-gentoo-x86_64-AMD_A10-5700_APU_with_Radeon-tm-_HD_Graphics-with-gentoo-2.2
KiB Mem:    15870928 total,  13074708 free
KiB Swap:          0 total,         0 free
Timestamp of tree: Fri, 21 Nov 2014 11:30:01 +0000
ld GNU gold (Gentoo 2.24 p1.4 2.24) 1.11
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:          2.7.7, 3.3.5-r1, 3.4.1
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.13.4
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.16 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo CloogPatch science sage-on-gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* - <at> EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
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=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks
fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict
unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.aditsu.net:8000/ http://gentoo.modulix.net/gentoo/ http://gentoo.gg3.net/"
LANG="en_US.utf8"
LDFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize -fuse-linker-plugin"
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"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage /var/lib/layman/science /var/lib/layman/sage-on-gentoo"
USE="acl amd64 bash-completion bcmath berkdb bindist blas bzip2 cli cracklib crypt cxx dri emacs fftw
gdbm graphite hardened iconv ipv6 justify lapack lm_sensors lto lzma lzo mmx modules multilib ncurses
nls nptl openmp pam pax_kernel pcre python readline session smp sse sse2 sse3 sse4_1 ssl symlink syslog
tcpd threads truetype udev unicode urandom usb xattr xtpax 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" INPUT_DEVICES="evdev" 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
ruby20" USERLAND="GNU" VIDEO_CARDS="radeon" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

=================================================================
                        Package Settings
=================================================================

sci-mathematics/sage-doc-6.3 was built with the following:
USE="-html" ABI_X86="64" PYTHON_TARGETS="python2_7"

Attachment (build.log): text/x-log, 6050 bytes
Attachment (environment): application/octet-stream, 184 KiB
[ebuild  N    ] sci-mathematics/singular-3.1.6  USE="boost emacs flint python readline -doc -examples
{-test}" PYTHON_TARGETS="python2_7" 

 * IMPORTANT: 1 news items need reading for repository 'gentoo'.
 * Use eselect news to read news items.

[ebuild  N    ] x11-drivers/ati-drivers-14.4_p1  USE="modules multilib pax_kernel -debug -qt4
-static-libs" 

 * IMPORTANT: 1 news items need reading for repository 'gentoo'.
 * Use eselect news to read news items.

[ebuild   R   ] sci-mathematics/sage-doc-6.3  USE="html*" PYTHON_TARGETS="python2_7" 

 * IMPORTANT: 1 news items need reading for repository 'gentoo'.
 * Use eselect news to read news items.

Jeramia Poland | 18 Nov 14:54 2014
Picon

Atlas not listed under eselect blas with eselect-1.4.3-r100 and atlas-3.10.1-r2

Atlas is not listed in the output for "eselect blas list" now, hence unselectable.  These two, atlas and eselect, updated together and Atlas is still listed in the "eselect cblas list" output.  Perhaps my memory is incorrect but I thought on my last machine that atlas was selectable under blas through eselect.

Jeramia
Jeramia Poland | 14 Nov 16:50 2014
Picon

Emerge singular-3.1.6::sage-on-gentoo fails on gentoo-3.16.5 gcc 4.8.3 with graphite and lto

I have a relatively fresh install of 3.16.5 that I've been trying to get Sage installed on for the past 5 days.

After install I followed these instructions for enabling graphite and lto:


Since then I've been attempting to finish a sage emerge.
Singular is failing and it seems to be an ld exit status 1 type fail so I'm pretty sure its lto.

Thing is I've got singular in package.env with no-lto.conf (as set out by the instructions above).

It seems singular is just ignoring my no-lto flags like in this bug:


I can't really tell from that bug if there was a resolution or workaround, so I don't know where to go from here.

Anybody have any idea how to fix or get around this?

attached are:

info output
build log
whatever -pqv outputs 
environment

Thanks,
Jeramia
Portage 2.2.8-r2 (hardened/linux/amd64, gcc-4.8.3, glibc-2.19-r1, 3.16.5-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.16.5-gentoo-x86_64-AMD_A10-5700_APU_with_Radeon-tm-_HD_Graphics-with-gentoo-2.2
KiB Mem:    15873608 total,   9231428 free
KiB Swap:          0 total,         0 free
Timestamp of tree: Sun, 09 Nov 2014 08:00:01 +0000
ld GNU gold (Gentoo 2.24 p1.4 2.24) 1.11
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:          2.7.7, 3.3.5-r1, 3.4.1
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.13.4
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.13 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo CloogPatch science sage-on-gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* - <at> EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release
/etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks
fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict
unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.aditsu.net:8000/ http://gentoo.modulix.net/gentoo/ http://gentoo.gg3.net/"
LANG="en_US.utf8"
LDFLAGS="-march=native -O2 -pipe -flto=4 -floop-interchange -ftree-loop-distribution
-floop-strip-mine -floop-block -ftree-vectorize -fuse-linker-plugin"
MAKEOPTS="-j5"
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"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage /var/lib/layman/science /var/lib/layman/sage-on-gentoo"
USE="acl amd64 bash-completion bcmath berkdb bindist blas bzip2 cli cracklib crypt cxx dri emacs fftw
gdbm graphite hardened iconv ipv6 justify lapack lm_sensors lto lzma lzo mmx modules multilib ncurses
nls nptl openmp pam pax_kernel pcre python readline session smp sse sse2 sse3 sse4_1 ssl symlink syslog
tcpd threads truetype udev unicode urandom usb xattr xtpax 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" INPUT_DEVICES="evdev" 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
ruby20" USERLAND="GNU" VIDEO_CARDS="fglrx" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

Attachment (build.log): text/x-log, 401 KiB
[ebuild  N    ] sci-mathematics/singular-3.1.6  USE="boost emacs flint python readline -doc -examples
{-test}" PYTHON_TARGETS="python2_7" 

 * IMPORTANT: 1 news items need reading for repository 'gentoo'.
 * Use eselect news to read news items.

Attachment (environment): application/octet-stream, 205 KiB
ferreirafm | 17 Oct 15:52 2014
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science not syncing

Hi Gentoo Scientists,
I'm frequently getting the following error when syncing science overlay.
Is git.overlay.gentoo.org dead?
Best,
Fred



####################### 
receiving file list ... 
 100 files...
... 
...
 62600 files...
 62700 files...
                    
sent 76 bytes  received 1,480,180 bytes  328,945.78 bytes/sec
total size is 40,893,007  speedup is 27.63

 Fetching remote list...
 Fetch Ok

 Syncing selected overlay(s)...
 Running Rsync... # /usr/bin/rsync -rlptDvz --progress --delete --delete-after --timeout=180 --exclude=distfiles/* --exclude=local/* --exclude=packages/* rsync://roverlay.dev.gentoo.org/roverlay/ /var/lib/layman/roverlay
 Running Git... # ( cd /var/lib/layman/science  && /usr/bin/git pull )
 Failure result returned from Git
  
 Succeeded:
 ------
 Successfully synchronized overlay "roverlay".
  
  
 Errors:
 ------
 Failed to sync overlay "science".
 Error was: Syncing overlay "science" returned status 1!
 db.sync()
  

 CLI: Errors occurred processing action sync_all
  
 Errors:
 ------
 Failed to sync overlay "science".
 Syncing overlay "science" returned status 1!
 db.sync()
  

François Bissey | 17 Oct 03:43 2014
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git migration guide

Hi all,

Do we have a migration guide from git-2 to git-r3.
Google was lacking in providing info.

Francois

v_2e | 20 Sep 11:56 2014
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[sage-on-gentoo] Cannot install sage-doc: insufficient memory

  Hello!
  I have been experiencing a problem trying to install sage-doc for
several months. I have 2GB of RAM on my laptop, and it turns out not
sufficient to build Sage documentation. Each time it fails with a
message "Cannot allocate memory". I use Xfce, so the system itself does
not consume too much memory. Therefore I do not understand if this is a
sage-doc problem or not.

  Regards,
    Vladimir

----- 
 <v_2e <at> ukr.net>

ferreirafm | 18 Sep 17:33 2014
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hdf-java

Hi GentooSci, 
Can't emerge hdf-java. The file hdf-java-2.9-src.tar can't be found in the tree.

Build.log is as follows:

>>> Downloading 'ftp://ftp.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar'
pathconf: Permission denied
--2014-09-18 12:25:56--  ftp://ftp.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar
           => ‘/usr/portage/distfiles/hdf-java-2.9-src.tar’
Resolving ftp.las.ic.unicamp.br... 143.106.60.118
Connecting to ftp.las.ic.unicamp.br|143.106.60.118|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/gentoo/distfiles ... done.
==> SIZE hdf-java-2.9-src.tar ... done.
==> PASV ... done.    ==> RETR hdf-java-2.9-src.tar ... 
No such file ‘hdf-java-2.9-src.tar’.

>>> Downloading 'http://www.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar'
--2014-09-18 12:26:04--  http://www.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar
Resolving www.las.ic.unicamp.br... 143.106.60.118
Connecting to www.las.ic.unicamp.br|143.106.60.118|:80... connected.
HTTP request sent, awaiting response... Read error (Connection timed out) in headers.
Retrying.

--2014-09-18 12:27:05--  (try: 2)  http://www.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar
Connecting to www.las.ic.unicamp.br|143.106.60.118|:80... connected.
HTTP request sent, awaiting response... Read error (Connection timed out) in headers.
Retrying.

--2014-09-18 12:28:14--  (try: 3)  http://www.las.ic.unicamp.br/pub/gentoo/distfiles/hdf-java-2.9-src.tar
Connecting to www.las.ic.unicamp.br|143.106.60.118|:80... connected.
HTTP request sent, awaiting response... Read error (Connection timed out) in headers.
Giving up.

>>> Downloading 'ftp://ftp.ussg.iu.edu/pub/linux/gentoo/distfiles/hdf-java-2.9-src.tar'
pathconf: Permission denied
--2014-09-18 12:29:16--  ftp://ftp.ussg.iu.edu/pub/linux/gentoo/distfiles/hdf-java-2.9-src.tar
           => ‘/usr/portage/distfiles/hdf-java-2.9-src.tar’
Resolving ftp.ussg.iu.edu... 156.56.247.193
Connecting to ftp.ussg.iu.edu|156.56.247.193|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/linux/gentoo/distfiles ... done.
==> SIZE hdf-java-2.9-src.tar ... done.
==> PASV ... done.    ==> RETR hdf-java-2.9-src.tar ... 
No such file ‘hdf-java-2.9-src.tar’.

>>> Downloading 'ftp://mirror.iawnet.sandia.gov/pub/gentoo/distfiles/hdf-java-2.9-src.tar'
pathconf: Permission denied
--2014-09-18 12:29:22--  ftp://mirror.iawnet.sandia.gov/pub/gentoo/distfiles/hdf-java-2.9-src.tar
           => ‘/usr/portage/distfiles/hdf-java-2.9-src.tar’
Resolving mirror.iawnet.sandia.gov... 192.160.227.246
Connecting to mirror.iawnet.sandia.gov|192.160.227.246|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/gentoo/distfiles ... done.
==> SIZE hdf-java-2.9-src.tar ... done.
==> PASV ... done.    ==> RETR hdf-java-2.9-src.tar ... 
No such file ‘hdf-java-2.9-src.tar’.

>>> Downloading 'http://www.hdfgroup.org/ftp/HDF5/hdf-java/src/hdf-java-2.9-src.tar'
--2014-09-18 12:29:34--  http://www.hdfgroup.org/ftp/HDF5/hdf-java/src/hdf-java-2.9-src.tar
Resolving www.hdfgroup.org... 50.28.50.143
Connecting to www.hdfgroup.org|50.28.50.143|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2014-09-18 12:29:35 ERROR 404: Not Found.

[31;01m * [39;49;00mFetch failed for 'dev-java/hdf-java-2.9', Log file:
[31;01m * [39;49;00m '/var/tmp/portage/dev-java/hdf-java-2.9/temp/build.log'

Jauhien Piatlicki | 11 Sep 17:57 2014
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science eselect fork

Hi,

I'm just wondering what is the status of our eselect fork and what
blocks adding patches back to the upstream?

--
Jauhien

Jauhien Piatlicki | 2 Sep 18:42 2014
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packages with invalid SRC_URI and compilation failures

Hi,

I would ask an opinion about what to do with packages that have invalid
SRC_URI (pointing to non-existent sources) and severe compilation problems.

I'm trying to fix ebuilds that lead to `repoman full` failures now, so
we will be able to have automatic repoman checks for pull requests. Some
ebuilds are really outdated and quite hard to fix (e.g. I tried to do
version bump for sci-physics/bigdft, but I failed as new version does
not compile and error is in fortran code, that I do not understand).

So what to do with such outdated not working stuff? As nobody makes
issues/bugs about it, I think, we can just remove unmaintained broken
packages from the overlay.

--
Jauhien

Thomas Kahle | 18 Aug 13:43 2014
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Sage keyword files

Hi,

here are two additions to the provided keyword files (one keyword one
USE actually) that seem necessary for sage-6.3 on stable Gentoo:

The following keyword changes are necessary to proceed:
 (see "package.accept_keywords" in the portage(5) man page for more details)
# required by sci-mathematics/sage-6.3::sage-on-gentoo
# required by sci-mathematics/sage-doc-6.3::sage-on-gentoo
=dev-python/numpy-1.8.1 ~amd64

The following USE changes are necessary to proceed:
 (see "package.use" in the portage(5) man page for more details)
# required by sci-mathematics/sage-6.3::sage-on-gentoo
# required by sci-mathematics/sage-doc-6.3::sage-on-gentoo
>=sci-libs/libsingular-3.1.6-r3 flint

Thanks,
Thomas

marco restelli | 29 Jul 15:43 2014
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petsc-3.5.1, missing fortran includes

Hi all,
   I notice that  petsc-3.5.1.ebuild  does not install some include
files which are useful when using the fortran interface of PETSC; for
me the problem is solved adding

191a192,196
> 		doins include/finclude/*.h90
> 		insinto /usr/include/${PN}/finclude/ftn-auto
> 		doins include/finclude/ftn-auto/*
> 		insinto /usr/include/${PN}/finclude/ftn-custom
> 		doins include/finclude/ftn-custom/*

Regards,
   Marco


Gmane