Ubuntu 12.04: Sage fails to install from PPA - Error installing package gap_packages-4.4.12.p
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Johannes
Nov 18, 2012, 2:04:20 PM11/18/12
to sage-...@googlegroups.com
Hi list,
I tried to upgrade my sage installation, but it fails to build:
make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/grape/nauty22'
gcc -c -O4 -march=i686 -DBIGNAUTY -o naututilB.o naututil.c
gcc -c -O4 -march=i686 -DBIGNAUTY -o nautyB.o nauty.c
gcc -c -O4 -march=i686 -DBIGNAUTY -o nautilB.o nautil.c
gcc -c -O4 -march=i686 -DBIGNAUTY -o nautinvB.o nautinv.c
gcc -c -O4 -march=i686 -DBIGNAUTY -o naugraphB.o naugraph.c
gcc -c -O4 -march=i686 rng.c
gcc -o dreadnautB -O4 -march=i686 -DBIGNAUTY dreadnaut.c naututilB.o \
nautyB.o nautilB.o nautinvB.o naugraphB.o rng.o
make[1]: Verlasse Verzeichnis
'/usr/lib/sagemath/local/lib/pkg/grape/nauty22'
( cd src; make BINDIR="" )
make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/grape/src'
gcc -O -o ../bin//drcanon4 drcanon4.c
gcc -O -o ../bin//drtogap4 drtogap4.c
gcc -O -o ../bin//gap4todr gap4todr.c
make[1]: Verlasse Verzeichnis '/usr/lib/sagemath/local/lib/pkg/grape/src'
cat: ../..//sysinfo.gap: Datei oder Verzeichnis nicht gefunden
( test -d bin || mkdir bin; \
test -d bin/ || mkdir bin/; cd bin/; \
make -f ../../Makefile all2 CC="gcc" CFLAGS="-O2"; \
cd ../../src/leon/src/../; ./configure; make; mkdir
../../bin/leon; \
cp cent ../../bin/leon; cp cjrndper ../../bin/leon; \
cp commut ../../bin/leon; cp compgrp ../../bin/leon; \
cp desauto ../../bin/leon; cp fndelt ../../bin/leon; \
cp generate ../../bin/leon; cp inter ../../bin/leon; \
cp orbdes ../../bin/leon; cp orblist ../../bin/leon; \
cp randobj ../../bin/leon; cp setstab ../../bin/leon; \
cp wtdist ../../bin/leon; cp src/*.sh ../../bin/leon; \
cp wtdist ../../bin; cp desauto ../../bin; \
cp wtdist ../../bin/; cp desauto ../../bin/ \
)
make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
make[1]: ../../Makefile: Datei oder Verzeichnis nicht gefunden
make[1]: *** Keine Regel, um �../../Makefile� zu erstellen. Schluss.
make[1]: Verlasse Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
/bin/sh: 4: cd: can't cd to ../../src/leon/src/../
/bin/sh: 4: ./configure: not found
make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
make[1]: *** Keine Targets angegeben und keine �make�-Steuerdatei
gefunden. Schluss.
make[1]: Verlasse Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
mkdir: kann Verzeichnis �../../bin/leon� nicht anlegen: Datei oder
Verzeichnis nicht gefunden
my setup:
Ubuntu 12.04
Linux neo 3.2.0-31-generic #50-Ubuntu SMP Fri Sep 7 16:17:36 UTC 2012
i686 i686 i386 GNU/Linux
if you need any more information, just ask, and I'll tell you.
greatz and thnx,
Johannes
I tried to upgrade my sage installation, but it fails to build:
make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/grape/nauty22'
gcc -c -O4 -march=i686 -DBIGNAUTY -o naututilB.o naututil.c
gcc -c -O4 -march=i686 -DBIGNAUTY -o nautyB.o nauty.c
gcc -c -O4 -march=i686 -DBIGNAUTY -o nautilB.o nautil.c
gcc -c -O4 -march=i686 -DBIGNAUTY -o nautinvB.o nautinv.c
gcc -c -O4 -march=i686 -DBIGNAUTY -o naugraphB.o naugraph.c
gcc -c -O4 -march=i686 rng.c
gcc -o dreadnautB -O4 -march=i686 -DBIGNAUTY dreadnaut.c naututilB.o \
nautyB.o nautilB.o nautinvB.o naugraphB.o rng.o
make[1]: Verlasse Verzeichnis
'/usr/lib/sagemath/local/lib/pkg/grape/nauty22'
( cd src; make BINDIR="" )
make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/grape/src'
gcc -O -o ../bin//drcanon4 drcanon4.c
gcc -O -o ../bin//drtogap4 drtogap4.c
gcc -O -o ../bin//gap4todr gap4todr.c
make[1]: Verlasse Verzeichnis '/usr/lib/sagemath/local/lib/pkg/grape/src'
cat: ../..//sysinfo.gap: Datei oder Verzeichnis nicht gefunden
( test -d bin || mkdir bin; \
test -d bin/ || mkdir bin/; cd bin/; \
make -f ../../Makefile all2 CC="gcc" CFLAGS="-O2"; \
cd ../../src/leon/src/../; ./configure; make; mkdir
../../bin/leon; \
cp cent ../../bin/leon; cp cjrndper ../../bin/leon; \
cp commut ../../bin/leon; cp compgrp ../../bin/leon; \
cp desauto ../../bin/leon; cp fndelt ../../bin/leon; \
cp generate ../../bin/leon; cp inter ../../bin/leon; \
cp orbdes ../../bin/leon; cp orblist ../../bin/leon; \
cp randobj ../../bin/leon; cp setstab ../../bin/leon; \
cp wtdist ../../bin/leon; cp src/*.sh ../../bin/leon; \
cp wtdist ../../bin; cp desauto ../../bin; \
cp wtdist ../../bin/; cp desauto ../../bin/ \
)
make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
make[1]: ../../Makefile: Datei oder Verzeichnis nicht gefunden
make[1]: *** Keine Regel, um �../../Makefile� zu erstellen. Schluss.
make[1]: Verlasse Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
/bin/sh: 4: cd: can't cd to ../../src/leon/src/../
/bin/sh: 4: ./configure: not found
make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
make[1]: *** Keine Targets angegeben und keine �make�-Steuerdatei
gefunden. Schluss.
make[1]: Verlasse Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
mkdir: kann Verzeichnis �../../bin/leon� nicht anlegen: Datei oder
Verzeichnis nicht gefunden
my setup:
Ubuntu 12.04
Linux neo 3.2.0-31-generic #50-Ubuntu SMP Fri Sep 7 16:17:36 UTC 2012
i686 i686 i386 GNU/Linux
if you need any more information, just ask, and I'll tell you.
greatz and thnx,
Johannes
Jan Groenewald
Nov 18, 2012, 2:23:20 PM11/18/12
to sage-...@googlegroups.com
Dear Johannes,
How did you install? From the PPA? Is this the sagemath-optional trying to build?
Note that this package might be discontinued in future as I see this message:
"Installing optional GAP packages, which may not be open source."
and free PPAs are only for open source. It's also not well designed, it currently
builds packages as root, which is bad practice and dangerous to your system;
but that can be fixed.
For others: sagemath-optional currently installs these:
0 jan@osprey:~$ls /usr/lib/sagemath/spkg/optional/
biopython-1.60.spkg database_odlyzko_zeta.spkg
database_cremona_ellcurve-20120827.spkg database_sloane_oeis-2005-12.spkg
database_gap-4.4.12.p1.spkg database_symbolic_data-20070206.spkg
database_jones_numfield-v4.spkg dot2tex-2.8.7-2.spkg
database_kohel-20060803.spkg gap_packages-4.4.12.p1.spkg
Johannes, please list the installed PPA packages:
dpkg -l |grep sagemath
This package compiled for me on an up-to-date 64bit system. Your sage can work
perfectly without sagemath-optional, which is not yet a reliable package. You can remove
it with
sudo apt-get purge sagemath-optional
But if you want to help test, and understand the risks, can you do this
sudo apt-get update
sudo apt-get dist-upgrade
sudo sage -f /usr/lib/sagemath/spkg/optional/gap_packages-4.4.12.p1.spkg
Regards,
Jan
--
.~.
/V\ Jan Groenewald
/( )\ www.aims.ac.za
^^-^^
How did you install? From the PPA? Is this the sagemath-optional trying to build?
Note that this package might be discontinued in future as I see this message:
"Installing optional GAP packages, which may not be open source."
and free PPAs are only for open source. It's also not well designed, it currently
builds packages as root, which is bad practice and dangerous to your system;
but that can be fixed.
For others: sagemath-optional currently installs these:
0 jan@osprey:~$ls /usr/lib/sagemath/spkg/optional/
biopython-1.60.spkg database_odlyzko_zeta.spkg
database_cremona_ellcurve-20120827.spkg database_sloane_oeis-2005-12.spkg
database_gap-4.4.12.p1.spkg database_symbolic_data-20070206.spkg
database_jones_numfield-v4.spkg dot2tex-2.8.7-2.spkg
database_kohel-20060803.spkg gap_packages-4.4.12.p1.spkg
Johannes, please list the installed PPA packages:
dpkg -l |grep sagemath
This package compiled for me on an up-to-date 64bit system. Your sage can work
perfectly without sagemath-optional, which is not yet a reliable package. You can remove
it with
sudo apt-get purge sagemath-optional
But if you want to help test, and understand the risks, can you do this
sudo apt-get update
sudo apt-get dist-upgrade
sudo sage -f /usr/lib/sagemath/spkg/optional/gap_packages-4.4.12.p1.spkg
Regards,
Jan
make[1]: *** Keine Regel, um »../../Makefile« zu erstellen. Schluss.
make[1]: Verlasse Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
/bin/sh: 4: cd: can't cd to ../../src/leon/src/../
/bin/sh: 4: ./configure: not found
make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
make[1]: *** Keine Targets angegeben und keine »make«-Steuerdatei
gefunden. Schluss.
make[1]: Verlasse Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
mkdir: kann Verzeichnis »../../bin/leon“ nicht anlegen: Datei oder
Verzeichnis nicht gefunden
my setup:
Ubuntu 12.04
Linux neo 3.2.0-31-generic #50-Ubuntu SMP Fri Sep 7 16:17:36 UTC 2012
i686 i686 i386 GNU/Linux
if you need any more information, just ask, and I'll tell you.
greatz and thnx,
Johannes
--
You received this message because you are subscribed to the Google Groups "sage-devel" group.
To post to this group, send email to sage-...@googlegroups.com.
To unsubscribe from this group, send email to sage-devel+...@googlegroups.com.
Visit this group at http://groups.google.com/group/sage-devel?hl=en.
--
.~.
/V\ Jan Groenewald
/( )\ www.aims.ac.za
^^-^^
Johannes
Nov 18, 2012, 2:42:11 PM11/18/12
to sage-...@googlegroups.com
Hey,
sagemath-upstream-binary`
>
> Johannes, please list the installed PPA packages:
> dpkg -l |grep sagemath
dpkg -l |grep sagemath
iF sagemath-optional 5.4
ii sagemath-upstream-binary 5.4ubuntu1
> sudo apt-get update
> sudo apt-get dist-upgrade
> sudo sage -f /usr/lib/sagemath/spkg/optional/gap_packages-4.4.12.p1.spkg
Installing the package by `sage -f ..` as above seems to work fine.
greatz
Johannes
> make[1]: *** Keine Regel, um �../../Makefile� zu erstellen. Schluss.
> <mailto:sage-devel%2Bunsu...@googlegroups.com>.
> ^^-^^
On 18.11.2012 20:23, Jan Groenewald wrote:
> Dear Johannes,
>
> How did you install? From the PPA? Is this the sagemath-optional trying
> to build?
I once installed Sage by `apt-get install sagemath-optional
> Dear Johannes,
>
> How did you install? From the PPA? Is this the sagemath-optional trying
> to build?
sagemath-upstream-binary`
>
> Johannes, please list the installed PPA packages:
> dpkg -l |grep sagemath
iF sagemath-optional 5.4
ii sagemath-upstream-binary 5.4ubuntu1
> sudo apt-get update
> sudo apt-get dist-upgrade
> sudo sage -f /usr/lib/sagemath/spkg/optional/gap_packages-4.4.12.p1.spkg
greatz
Johannes
> make[1]: Verlasse Verzeichnis
> '/usr/lib/sagemath/local/lib/pkg/guava/bin'
> /bin/sh: 4: cd: can't cd to ../../src/leon/src/../
> /bin/sh: 4: ./configure: not found
> make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
> make[1]: *** Keine Targets angegeben und keine �make�-Steuerdatei
> '/usr/lib/sagemath/local/lib/pkg/guava/bin'
> /bin/sh: 4: cd: can't cd to ../../src/leon/src/../
> /bin/sh: 4: ./configure: not found
> make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
> gefunden. Schluss.
> make[1]: Verlasse Verzeichnis
> '/usr/lib/sagemath/local/lib/pkg/guava/bin'
> mkdir: kann Verzeichnis �../../bin/leon� nicht anlegen: Datei oder
> make[1]: Verlasse Verzeichnis
> '/usr/lib/sagemath/local/lib/pkg/guava/bin'
> Verzeichnis nicht gefunden
>
> my setup:
> Ubuntu 12.04
> Linux neo 3.2.0-31-generic #50-Ubuntu SMP Fri Sep 7 16:17:36 UTC 2012
> i686 i686 i386 GNU/Linux
>
> if you need any more information, just ask, and I'll tell you.
>
> greatz and thnx,
> Johannes
>
> --
> You received this message because you are subscribed to the Google
> Groups "sage-devel" group.
> To post to this group, send email to sage-...@googlegroups.com
> <mailto:sage-...@googlegroups.com>.
>
> my setup:
> Ubuntu 12.04
> Linux neo 3.2.0-31-generic #50-Ubuntu SMP Fri Sep 7 16:17:36 UTC 2012
> i686 i686 i386 GNU/Linux
>
> if you need any more information, just ask, and I'll tell you.
>
> greatz and thnx,
> Johannes
>
> --
> You received this message because you are subscribed to the Google
> Groups "sage-devel" group.
> To post to this group, send email to sage-...@googlegroups.com
> <mailto:sage-devel%2Bunsu...@googlegroups.com>.
> Visit this group at http://groups.google.com/group/sage-devel?hl=en.
>
>
>
>
>
> --
> .~.
> /V\ Jan Groenewald
> /( )\ www.aims.ac.za <http://www.aims.ac.za>
>
>
>
>
>
> --
> .~.
> /V\ Jan Groenewald
> ^^-^^
Jan Groenewald
Nov 18, 2012, 10:47:19 PM11/18/12
to sage-...@googlegroups.com
Hi Johannes,
If gap_packages managed to install with sage -f, then you can complete the sagemath-optional installation with
dpkg-reconfigure sagemath-optional
Until you do this your package manager will stay in a broken state.
When you run dpkg -l sagemath-optional, it should also say "ii"
next to it, once you are finished.
Regards,
Jan
--
If gap_packages managed to install with sage -f, then you can complete the sagemath-optional installation with
dpkg-reconfigure sagemath-optional
Until you do this your package manager will stay in a broken state.
When you run dpkg -l sagemath-optional, it should also say "ii"
next to it, once you are finished.
Regards,
Jan
> make[1]: *** Keine Regel, um »../../Makefile« zu erstellen. Schluss.
> make[1]: Verlasse Verzeichnis
> '/usr/lib/sagemath/local/lib/pkg/guava/bin'
> /bin/sh: 4: cd: can't cd to ../../src/leon/src/../
> /bin/sh: 4: ./configure: not found
> make[1]: Betrete Verzeichnis '/usr/lib/sagemath/local/lib/pkg/guava/bin'
> make[1]: *** Keine Targets angegeben und keine »make«-Steuerdatei
> gefunden. Schluss.
> make[1]: Verlasse Verzeichnis
> '/usr/lib/sagemath/local/lib/pkg/guava/bin'
> mkdir: kann Verzeichnis »../../bin/leon“ nicht anlegen: Datei oder
--
^^-^^
Johannes
Nov 21, 2012, 11:32:05 AM11/21/12
to sage-...@googlegroups.com
Hi
Am Mo 19 Nov 2012 04:47:19 CET schrieb Jan Groenewald:
> dpkg-reconfigure sagemath-optional
that does not work:
/usr/sbin/dpkg-reconfigure: sagemath-optional ist kaputt oder nicht
komplett installiert
(package is defect or not completely installed)
if I try
dpkg-reconfigure --force sagemath-optional
I get get exactly the same error as before.
greatz Johannes
> Until you do this your package manager will stay in a broken state.
> When you run dpkg -l sagemath-optional, it should also say "ii"
> next to it, once you are finished.
>
> Regards,
> Jan
>
>
>
> On 18 November 2012 21:42, Johannes <dajo...@web.de
> > <mailto:sage-...@googlegroups.com
> <mailto:sage-devel%252Buns...@googlegroups.com>>.
Am Mo 19 Nov 2012 04:47:19 CET schrieb Jan Groenewald:
> dpkg-reconfigure sagemath-optional
that does not work:
/usr/sbin/dpkg-reconfigure: sagemath-optional ist kaputt oder nicht
komplett installiert
(package is defect or not completely installed)
if I try
dpkg-reconfigure --force sagemath-optional
I get get exactly the same error as before.
greatz Johannes
> Until you do this your package manager will stay in a broken state.
> When you run dpkg -l sagemath-optional, it should also say "ii"
> next to it, once you are finished.
>
> Regards,
> Jan
>
>
>
> On 18 November 2012 21:42, Johannes <dajo...@web.de
> <mailto:sage-...@googlegroups.com>>.
> > To unsubscribe from this group, send email to
> > sage-devel+...@googlegroups.com
> <mailto:sage-devel%2Bunsu...@googlegroups.com>
> > <mailto:sage-devel%2Bunsu...@googlegroups.com
> > To unsubscribe from this group, send email to
> > sage-devel+...@googlegroups.com
> <mailto:sage-devel%2Bunsu...@googlegroups.com>
> <mailto:sage-devel%252Buns...@googlegroups.com>>.
Jan Groenewald
Nov 21, 2012, 11:28:29 PM11/21/12
to sage-...@googlegroups.com
Hi Johannes,
I suggest removing sagemath-optional, with this command
sudo apt-get purge sagemath-optional
Regards,
Jan
I suggest removing sagemath-optional, with this command
sudo apt-get purge sagemath-optional
Regards,
Jan
^^-^^
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