[Bioperl-l] bioperl-live install issue on unix

Sean O'Keeffe limericksean at gmail.com
Wed Dec 10 07:56:57 EST 2008

Ok I tried setting the cpan make and build directives as follows:

> perl -e shell -MCPAN
CPAN: File::HomeDir loaded ok (v0.66)

cpan shell -- CPAN exploration and modules installation (v1.9205)
ReadLine support enabled

cpan[1]> o conf makepl_arg PREFIX=/home/okeeffe/perllib
    makepl_arg         [PREFIX=/home/okeeffe/perllib]
Please use 'o conf commit' to make the config permanent!

cpan[2]> o conf mbuildpl_arg "--prefix /home/okeeffe/perllib"
    mbuildpl_arg       [--prefix /home/okeeffe/perllib]
Please use 'o conf commit' to make the config permanent!

However, commit failed:

cpan[3]> o conf commit
Catching error: "/usr/local/lib/perl5/5.8.7/CPAN/Config.pm is not
writable at /usr/local/lib/perl5/5.8.7/CPAN/HandleConfig.pm line
286\cJ\cICPAN::HandleConfig::commit('CPAN::HandleConfig', 'args',
'ARRAY(0x667060)') called at
/usr/local/lib/perl5/5.8.7/CPAN/HandleConfig.pm line
128\cJ\cICPAN::HandleConfig::edit('CPAN::HandleConfig', 'commit')
called at /usr/local/lib/perl5/5.8.7/CPAN.pm line
2029\cJ\cICPAN::Shell::o('CPAN::Shell', 'conf', 'commit') called at
/usr/local/lib/perl5/5.8.7/CPAN.pm line 274\cJ\cIeval {...} called at
/usr/local/lib/perl5/5.8.7/CPAN.pm line 274\cJ\cICPAN::shell() called
at -e line 1\cJ" at /usr/local/lib/perl5/5.8.7/CPAN.pm line 281
        CPAN::shell() called at -e line 1

2008/12/10 Dave Messina <David.Messina at sbc.su.se>:
> Following on to what Dave H. said, cpan itself needs to know that you want
> to install in a personal module area; it, too, defaults to the system
> location.
> From the CPAN man page:
>  5)  I am not root, how can I install a module in a personal directory?
>            You will most probably like something like this:
>              o conf makepl_arg "LIB=~/myperl/lib \
>                                INSTALLMAN1DIR=~/myperl/man/man1 \
>                                INSTALLMAN3DIR=~/myperl/man/man3"
>              install Sybase::Sybperl
>            You can make this setting permanent like all "o conf" settings
> with "o conf commit".
>            You will have to add ~/myperl/man to the MANPATH environment
> variable and also tell your perl programs to look into
>            ~/myperl/lib, e.g. by including
>              use lib "$ENV{HOME}/myperl/lib";
>            or setting the PERL5LIB environment variable.
>            Another thing you should bear in mind is that the UNINST
> parameter should never be set if you are not root.
> So, now that you've wiped your cpan configuration parameters, you need to
> set some new ones, even before you update CPAN.
> Actually, the advice on the BioPerl Installation page is better than the
> above. Do the following:
> % cpan
> cpan>o conf makepl_arg PREFIX=/home/users/dag/My_Local_Perl_Modules
> cpan>o conf mbuildpl_arg "--prefix /home/users/dag/My_Local_Perl_Modules"
> cpan>o conf commit
> Here's the whole section of the installation instructions that deal with
> personal installations:
> http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA
> By the way, just a bit below that section are the instructions on how to set
> your PERL5LIB environmental variable.
> Dave

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