Guilherme Amadio | 20 Feb 16:43 2015
Picon

Formal request to join the team

Hello everyone,

I think my announcement is still a bit fresh, so you probably know that
I recently became a Gentoo dev.

One of the areas of interest for me is gentoo-science, more
specifically, sci-physics packages, as I actually work on development of
a geant sucessor, called geantv. So I would like to formally request to
join the science team and possibly I would like to maintain geant and
related packages on Gentoo if there isn't already someone maintaining
these packages. Here are some packages I am interested in maintaining:

sci-phyiscs/geant and related geant-docs, geant-data, etc.
sci-physics/root and related packages
dev-libs/vc (currently maintained by kde herd for some reason, used in geantv)
sci-physics/clhep, dependency of geant

If there is any of you around, I'm currently working at Fermilab (as a
visitor, as I'm a postdoc at a Brazilian university).

Well, nice to "meet" you all!

Best regards,
—Guilherme

christoph irrenfried | 5 Feb 16:03 2015
Picon
Picon

Re: Mathematica issue

On 02/05/2015 03:52 PM, Markus Oehme wrote:
> (a) Does the license server still operate (maybe your university changed the
>     setup)?
All the others on in my department have no problem with the connection
to the server. The only difference is that they are using Debian.
>
> (b) Are you able to reach the license server on the network (issue a ping or
>     similar)?
yes if i ping the server i get a positive response!
>
> (c) If both have positive answers I would contact the operator of the
>     license server for further trouble shooting.
I contacted than with the answer: That you get from using gentoo (not
the same words but it was what they meant ;( ).

The wired thing is that when I installed it after I had a fresh
installation of gentoo it worked but than I installed other stuff and it
stopped working. I installed gentoo a couple of times but it looks like
it always stops after different installations. It definitely is caused
by gentoo.

Therefore I wanted to know if someone else works with mathematica on
gentoo and if that person can give me his configuration to check it
against mine.

Thanks!

christoph irrenfried | 5 Feb 14:40 2015
Picon
Picon

Mathematica issue

Hello,
my name is Chris and I have a huge Mathemaica problem. I need it for
work on a daily bases but after I did my regular update a couple mounths
ago it just wont start again. I filed this issue on the gentoo forum but
I cant find a way to get rid of this problem. The error message is as a
pic included.
Than a couple weeks ago I bought a laptop and installed gentoo with
gnome on it but there aswell and I got the same error. I have
no idea what's the problem. I wanted to ask you if someone has a
gentoo/gnome system with mathematica running and if so if it is possible
to get the USE flags from your make.conf or I don't know if there is a
way to compare my settings with your system and see if maybe (or
definitely) I messed something up e.g. fonts or something ....

Thanks in advance,
chi

Justin Bronder | 4 Feb 07:05 2015
Picon

sys-cluster/torque needs a new {proxy,}maintainer

I haven't seriously run torque since 2007 and I'm already not so great
with keeping up with the packages I maintain.  I'd really love to see
the package handed off to someone who is running it day to day.  I do
have contacts upstream that are very responsive and would be happy to
continue to help as much as my free time allows.

--

-- 
Justin Bronder
JC D | 26 Jan 14:42 2015
Picon

Question before setting up sage-on-gentoo

Hi!
I want to install sage-on-gentoo using gentoo_prefix on a Mac OS 10.10.
My first try was not successful and it seems it was related to the "kind of outdated" gcc-apple compiler that is originally used in gentoo_prefix on Mac.
I have a question: Would it be possible to install a more recent gcc such as gcc-4.8 (as soon as it is unmasked) and then build the whole sage-on-gentoo with this compiler, but keeping the rest untouched?
And how could I do this? Would it be possible to set up layman using the gcc-4.8 for everything in the overlay or could I use /etc/portage/env for that?
Best regards from a newbie

Jan Marten Simons | 22 Dec 11:49 2014
Picon
Picon

Sci-Overlay down?

Hi,

I'm experiencing prblems with the Sci-Overlay:

http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git

seems to be down. Also Layman cannot check out the git repo due to a timeout.

Is anybody else here having those problems as well?

Cheers,
Jan

François Bissey | 7 Dec 10:14 2014
Picon

fplll sources

Hi all,

I have been in contact over the last few days with a sage-on-gentoo
user who is in deep trouble trying to use flto.
But in the last emails we exchanged came this:
My only other thought was, since the lattice tests are failing, maybe it was related to fplll.  The ebuid for
that tried to download source from a page that no longer existed so I converted an src.rpm to tar.gz for
that.  It seems that fplll was moved to github (https://github.com/dstehle/fplll) and I couldn't figure
out how to make that work in an ebuild.

So he couldn’t fetch the sources for fplll which is in the main tree.
Can anyone check if the sources are properly mirrored. If not
I can provide the appropriate tarball.

François

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

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Jeramia Poland | 18 Nov 14:54 2014
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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
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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" 

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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()
  


Gmane