[gentoo-science] Re: AW: sage-on-gentoo

[gentoo-science] Re: AW: sage-on-gentoo

[Christopher Schwan]

Hi Mark,

On Wednesday 03 March 2010 23:45:01 you wrote:
> Hi Chris
> 
> As before I spared some unused cpu cycles to emerge --depclean all sage
> dependences and emerged sage again. Everything went smooth but sage emerge
> still freezes at
> 
> >>> Install sage-4.3.3 into
> >>> /var/tmp/portage/sci-mathematics/sage-4.3.3/image/ category
> 
> sci-mathematics
> make -j3 DESTDIR=/var/tmp/portage/sci-mathematics/sage-4.3.3/image//opt
> install echo "Experimental use only!"
> Experimental use only!
> if [ "/var/tmp/portage/sci-mathematics/sage-4.3.3/image//opt" = "" ]; then
> \ echo "Set DESTDIR"; \
>                 exit 1; \
>         fi
> mkdir -p /var/tmp/portage/sci-mathematics/sage-4.3.3/image//opt
> mkdir -p /var/tmp/portage/sci-mathematics/sage-4.3.3/image//opt/sage
> mkdir -p /var/tmp/portage/sci-mathematics/sage-4.3.3/image//opt/bin/
> cp -r --preserve=mode,links *
> /var/tmp/portage/sci-mathematics/sage-4.3.3/image//opt/sage/ python
> local/bin/sage-hardcode_sage_root /var/tmp/portage/sci-
> mathematics/sage-4.3.3/image//opt/sage/sage "/var/tmp/portage/sci-
> mathematics/sage-4.3.3/image//opt"/sage
> cp /var/tmp/portage/sci-mathematics/sage-4.3.3/image//opt/sage/sage
> /var/tmp/portage/sci- mathematics/sage-4.3.3/image//opt/bin/
> cd /var/tmp/portage/sci-mathematics/sage-4.3.3/image//opt/bin/; ./sage -c
> Setting permissions of DOT_SAGE directory so only you can read and write
> it.
> 
> 
> build log is the same -- no errors, just stop at this point.
> I examined list of processes and found that gap is running at pts/4
> [although emerge sage is on pts/0?]
> 
> Name, Username, PID, TTY, Niceness, Virtual Size, Memory, Shared Mem,
> Command, gap,  root,     3139,pts/4,19,      53564,        38376,  1472,  
>     /usr/libexec/gap/gap -m 32m -l /usr/share/gap -r -b -p -T -o 9999G
> /var/tmp/portage/sci-
> mathematics/sage-4.3.3/image/opt/sage/data//extcode/gap/sage.g
> 
> here is the list of all processes running on pts/0:
> 
> Name, Username, PID, TTY, Niceness, CPU %, IO Read, IO Write, Virtual Size,
> Memory, Shared Mem, Command, Window Title
> sandbox, root, 1826, pts/0, 19, 0, 0, 0, 3840, 140, 456,
> [sci-mathematics/sage-4.3.3] sandbox "/usr/lib64/portage/bin/ebuild.sh"
> install ,
> ebuild.sh, root, 1827, pts/0, 19, 0, 0, 0, 25540, 2572, 1432, /bin/bash
> /usr/lib64/portage/bin/ebuild.sh install ,
> ebuild.sh, root, 1860, pts/0, 19, 0, 0, 0, 25720, 2704, 880, /bin/bash
> /usr/lib64/portage/bin/ebuild.sh install ,
> make, root, 2084, pts/0, 19, 0, 0, 0, 14272, 572, 864, make -j3
> DESTDIR=/var/tmp/portage/sci-mathematics/sage-4.3.3/image//opt install ,
> sh, root, 2472, pts/0, 19, 0, 0, 0, 23452, 552, 1320, /bin/sh -c cd
> /var/tmp/portage/sci- mathematics/sage-4.3.3/image//opt/bin/; ./sage -c ,
> bash, root, 2473, pts/0, 19, 0, 0, 0, 23584, 564, 1364, bash ./sage -c ,
> bash, root, 2476, pts/0, 19, 0, 0, 0, 23584, 656, 1400, bash
> /var/tmp/portage/sci-
> mathematics/sage-4.3.3/image/opt/sage/local/bin/sage-sage -c ,
> python2.6, root, 2491, pts/0, 19, 0, 0, 0, 38900, 3000, 2600,
> /usr/bin/python2.6
> /var/tmp/portage/sci-mathematics/sage-4.3.3/image/opt/sage/local/bin/sage-
> cleaner , python2.6, root, 2492, pts/0, 19, 0, 0, 0, 276496, 19720, 8684,
> /usr/bin/python2.6
> /var/tmp/portage/sci-mathematics/sage-4.3.3/image/opt/sage/local/bin/sage-
> eval , bash, marek, 3482, pts/0, 0, 0, 0, 0, 20948, 4, 548, /bin/bash ,
> su, root, 4257, pts/0, 0, 0, 0, 0, 44820, 4, 560, su ,
> bash, root, 4263, pts/0, 0, 0, 0, 0, 20948, 4, 548, bash ,
> python2.6, root, 4270, pts/0, 19, 0, 0, 0, 175648, 84740, 1776,
> /usr/bin/python2.6 /usr/bin/emerge sage
> 
> best regards
> 
> m

thank you for investigating yourself on this problem - so we should check if 
gap is running correctly on your pc. I dont know much about gap, but you could 
try to start gap manually and then to exit the program (type gap and inside 
gap "quit;" ).

I will forward this mail to the science mailing list which will be the place 
to discuss problems regarding Sage-on-Gentoo (at least for a while).

Cheers,

Christopher

[gentoo-science] AW: AW: sage-on-gentoo

[Schwan, Christopher]

Hi Marek,

thank you for your mail - I currently do not have an idea how to fix this, but I will forward this mail to the science mailing list and have a closer look at the problem later. The gentoo-science list is the list where you should send your questions in future, so that Francois can read them, too. You can find info on the list here: http://www.gentoo.org/main/en/lists.xml

Also please send us a list of versions of the following programs you have installed:

- dev-lang/python (also its USE-flags)
- dev-python/cython
- dev-python/mpmath

Cheers,

Christopher

________________________________________
Von: Marek Kaluba [mk224@st.amu.edu.pl]
Gesendet: Dienstag, 23. März 2010 00:00
An: Schwan, Christopher
Betreff: Re: AW: sage-on-gentoo

Hi Chris

This time after version bump to 4.3.4 i got following error:
(attachment contains build log)


python `which cython` --embed-positions --directive cdivision=True -I/var/tmp/portage/sci-
mathematics/sage-4.3.4/work/sage-4.3.4/devel/sage-main -o
sage/libs/symmetrica/symmetrica.c sage/libs/symmetrica/symmetrica.pyx
sage/libs/symmetrica/symmetrica.pyx --> /var/tmp/portage/sci-
mathematics/sage-4.3.4/work/sage-4.3.4/local//lib64/python/site-
packages//sage/libs/symmetrica/symmetrica.pyx
python `which cython` --embed-positions --directive cdivision=True -I/var/tmp/portage/sci-
mathematics/sage-4.3.4/work/sage-4.3.4/devel/sage-main -o sage/libs/mpmath/utils.c
sage/libs/mpmath/utils.pyx
sage/libs/mpmath/utils.pyx --> /var/tmp/portage/sci-
mathematics/sage-4.3.4/work/sage-4.3.4/local//lib64/python/site-
packages//sage/libs/mpmath/utils.pyx
python `which cython` --embed-positions --directive cdivision=True -I/var/tmp/portage/sci-
mathematics/sage-4.3.4/work/sage-4.3.4/devel/sage-main -o sage/libs/mpmath/ext_impl.c
sage/libs/mpmath/ext_impl.pyx

Error converting Pyrex file to C:
------------------------------------------------------------
...
from sage.libs.gmp.all cimport mpz_t
                                   ^
------------------------------------------------------------

/var/tmp/portage/sci-mathematics/sage-4.3.4/work/sage-4.3.4/devel/sage-
main/sage/libs/mpmath/ext_impl.pxd:1:36: Unrecognized character

Error converting Pyrex file to C:


Error running command, failed with status 256.
sage: There was an error installing modified sage library code.

ERROR installing SAGE

real    5m6.568s
user    4m32.119s
sys     0m16.169s
sage: An error occurred while installing sage-4.3.4
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /var/tmp/portage/sci-mathematics/sage-4.3.4/work/sage-4.3.4/install.log.  Describe your
computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/var/tmp/portage/sci-mathematics/sage-4.3.4/work/sage-4.3.4/spkg/build/sage-4.3.4 and type
'make check' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/var/tmp/portage/sci-mathematics/sage-4.3.4/work/sage-4.3.4/spkg/build/sage-4.3.4' &&
'/var/tmp/portage/sci-mathematics/sage-4.3.4/work/sage-4.3.4/sage' -sh)
When you are done debugging, you can type "exit" to leave the
subshell.
make: *** [installed/sage-4.3.4] Error 1

real    27m11.521s
user    21m43.418s
sys     1m59.049s
Error building Sage.
 * ERROR: sci-mathematics/sage-4.3.4 failed:
 *   install failed
 *
 * Call stack:
 *     ebuild.sh, line  54:  Called src_compile
 *   environment, line 4726:  Called die
 * The specific snippet of code:
 *       ./install || die "install failed";
 *
 * If you need support, post the output of 'emerge --info =sci-mathematics/sage-4.3.4',
 * the complete build log and the output of 'emerge -pqv =sci-mathematics/sage-4.3.4'.
 * This ebuild used the following eclasses from overlays:
 *   /var/lib/layman/sage-on-gentoo/eclass/sage.eclass
 * This ebuild is from an overlay named 'sage-on-gentoo': '/var/lib/layman/sage-on-
gentoo/'
 * The complete build log is located at '/var/tmp/portage/sci-
mathematics/sage-4.3.4/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-
mathematics/sage-4.3.4/temp/environment'.
 * S: '/var/tmp/portage/sci-mathematics/sage-4.3.4/work/sage-4.3.4'

best regards

mark