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Ubuntu 12.04: Sage fails to install from PPA - Error installing package gap_packages-4.4.12.p
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Johannes  
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 More options Nov 18 2012, 2:04 pm
From: Johannes <dajo.m...@web.de>
Date: Sun, 18 Nov 2012 20:04:20 +0100
Local: Sun, Nov 18 2012 2:04 pm
Subject: Ubuntu 12.04: Sage fails to install from PPA - Error installing package gap_packages-4.4.12.p
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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 ďż˝../../Makefileďż˝ 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 ďż˝../../bin/leonďż˝ 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

  gap_packages-4.4.12.p0.log
79K Download

 
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Jan Groenewald  
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 More options Nov 18 2012, 2:23 pm
From: Jan Groenewald <j...@aims.ac.za>
Date: Sun, 18 Nov 2012 21:23:20 +0200
Local: Sun, Nov 18 2012 2:23 pm
Subject: Re: [sage-devel] Ubuntu 12.04: Sage fails to install from PPA - Error installing package gap_packages-4.4.12.p
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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

On 18 November 2012 21:04, Johannes <dajo.m...@web.de> wrote:

--
  .~.
  /V\     Jan Groenewald
 /( )\    www.aims.ac.za
 ^^-^^

 
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Johannes  
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 More options Nov 18 2012, 2:42 pm
From: Johannes <dajo.m...@web.de>
Date: Sun, 18 Nov 2012 20:42:11 +0100
Local: Sun, Nov 18 2012 2:42 pm
Subject: Re: [sage-devel] Ubuntu 12.04: Sage fails to install from PPA - Error installing package gap_packages-4.4.12.p
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Hey,
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
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


 
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Jan Groenewald  
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 More options Nov 18 2012, 10:47 pm
From: Jan Groenewald <j...@aims.ac.za>
Date: Mon, 19 Nov 2012 05:47:19 +0200
Local: Sun, Nov 18 2012 10:47 pm
Subject: Re: [sage-devel] Ubuntu 12.04: Sage fails to install from PPA - Error installing package gap_packages-4.4.12.p
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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

On 18 November 2012 21:42, Johannes <dajo.m...@web.de> wrote:

--
  .~.
  /V\     Jan Groenewald
 /( )\    www.aims.ac.za
 ^^-^^

 
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Johannes  
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 More options Nov 21 2012, 11:32 am
From: Johannes <dajo.m...@web.de>
Date: Wed, 21 Nov 2012 17:32:05 +0100
Local: Wed, Nov 21 2012 11:32 am
Subject: Re: [sage-devel] Ubuntu 12.04: Sage fails to install from PPA - Error installing package gap_packages-4.4.12.p
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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


 
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Jan Groenewald  
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 More options Nov 21 2012, 11:28 pm
From: Jan Groenewald <j...@aims.ac.za>
Date: Thu, 22 Nov 2012 06:28:29 +0200
Local: Wed, Nov 21 2012 11:28 pm
Subject: Re: [sage-devel] Ubuntu 12.04: Sage fails to install from PPA - Error installing package gap_packages-4.4.12.p
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Hi Johannes,

I suggest removing sagemath-optional, with this command
sudo apt-get purge sagemath-optional

Regards,
Jan

On 21 November 2012 18:32, Johannes <dajo.m...@web.de> wrote:

--
  .~.
  /V\     Jan Groenewald
 /( )\    www.aims.ac.za
 ^^-^^

 
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