[Bioperl-l] bioperl installation problems with CPAN

Sheila Zuñiga Trejos sheila.zuniga at sistemasgenomicos.com
Tue Feb 26 06:11:09 EST 2008


Hi Dave,
Thanks for your quick reply.

Here is the output:
cpan> o conf
CPAN::Config options from /etc/perl/CPAN/Config.pm:
commit Commit changes to disk
defaults Reload defaults from disk
init Interactive setting of all options
build_cache 10
build_dir /root/.cpan/build
cache_metadata 1
cpan_home /root/.cpan
cpan_version_check 1
dontload_hash
ftp /usr/bin/ftp
ftp_proxy
getcwd cwd
gpg /usr/bin/gpg
gzip /bin/gzip
histfile /root/.cpan/histfile
histsize 100
http_proxy
inactivity_timeout 0
index_expire 1
inhibit_startup_message 0
keep_source_where /root/.cpan/sources
lynx
make /usr/bin/make
make_arg dual processor system
make_install_arg to always uninstall potentially conflicting files
makepl_arg
ncftpget /usr/bin/ncftpget
no_proxy
pager /usr/bin/less
prefer_installer MB
prerequisites_policy ask
scan_cache atstart
shell /bin/bash
tar /bin/tar
term_is_latin 1
unzip /usr/bin/unzip
urllist
 <ftp://ftp.rediris.es/mirror/CPAN/> ftp://ftp.rediris.es/mirror/CPAN/
wget /usr/bin/wget

 
Sheila

  _____  

De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave
Messina
Enviado el: martes, 26 de febrero de 2008 11:48
Para: Sheila Zuñiga Trejos
CC: bioperl-l at bioperl.org
Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN


Hi Sheila,

Please be sure to keep bioperl-l on the Cc so that everyone can follow along
the discussion.

I don't think this is a BioPerl-specific problem. Can you successfully
install other modules from CPAN?

Could you type "o conf" in cpan and paste the results into your reply to
this message?


Dave




On 2/26/08, Sheila Zuñiga Trejos <sheila.zuniga at sistemasgenomicos.com>
wrote: 

Hi Dave,
I've tried the two options and in both cases I got the same error message. I
even restart the server both times in case it could make any difference but
nothing changed.
First attempt:

Type: cpan> o conf makepl_arg ""
Return: makepl_arg
Type: cpan> o conf commit
Return: commit: wrote /etc/perl/CPAN/Config.pm
Type: cpan> install Bundle::CPAN
Return: error message attached (same as before)

Second attempt:

Type: cpan> o conf defaults
(did not return anything)
Type: cpan> o conf commit
Return: commit: wrote /etc/perl/CPAN/Config.pm
Type: cpan> install Bundle::CPAN
Return: error message attached (same as before)

I installed Bioperl in Debian Sarge before and I never had any problem with
CPAN but with Debian Etch... Well, I hope you have other ideas.

 
Thanks very much for your help.
 
Sheila

  _____  

De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave
Messina
Enviado el: martes, 26 de febrero de 2008 0:47
Para: Sheila Zuñiga Trejos
CC: bioperl-l at bioperl.org
Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN



Hi Sheila,

It looks like your cpan configuration has gotten messed up. It's giving
invalid parameters to the make command:


make: *** No hay ninguna regla para construir el objetivo `dual'.  Alto.

  /usr/bin/make dual processor system -- NOT OK


Go to the command line on your system. Enter the cpan shell:

% cpan

Type the following:

cpan> o conf makepl_arg ""
cpan> o conf commit


That should reset the arguments that cpan adds to the make command. If that
doesn't fix your problem, reset everything by typing

cpan> o conf defaults
cpan> o conf commit

and see if that does it.


Dave








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