[Bioperl-l] bioperl installation

[Xiang Deng]

Jason,

Thanks for trying that for me.

I already downloaded and installed Inline-0.44 under directory 
"my_bioperl/bioperl-ext-1.4" and staden library io_lib-1.8.12 under 
directory "my_bioperl/".
but I still have following errors when installing bioperl-ext-1.4


mendel 297% perl Makefile.PL 
LIB=/v0/users/deng0007/my_bioperl/bioperl-ext-1.4
Writing Makefile for Bio::Ext::Align
Warning: prerequisite Bio::SeqIO::abi 0 not found.
Please tell us where your Staden io_lib "read" library is installed: 
[/usr/local/lib] [/v0/users/deng0007/my_bioperl]
Please tell us where your Staden io_lib "Read.h" header is installed: 
[[/v0/users/deng0007/my_bioperl]/io_lib] [/v0/users/deng0007/my_bioperl]
Writing Makefile for Bio::SeqIO::staden::read
Writing Makefile for Bio
mendel 298% make 


        DEFINE='-DPOSIX -DNOERROR'; CC='cc -n32'; export DEFINE INC CC; \
        cd libs && make CC=cc -n32 libsw.a -e
Usage: make [-f makefile] [-p] [-i] [-k] [-s] [-r] [-n] [-u]
        [-d] [-D] [-S] [-g] [-w] [-P] [-B] [-b] [-O] [-e] [-t] [-q] [-M] 
[-N] [names]
*** Error code 1 (bu21)
*** Error code 1 (bu21)

Do you know what is the problem here? I just followed the install 
instruction, do I miss any parameters there?

thanks,

Xiang

Department of Pharmacology and Cancer Biology
Duke University Medical Center
Durham, NC 27710
Phone: 919-4792339




Jason Stajich <jason at cgt.duhs.duke.edu> 
07/22/2004 02:38 PM

To
Xiang Deng <xiang.deng at duke.edu>
cc
Bioperl <bioperl-l at bioperl.org>
Subject
RE: [Bioperl-l] bioperl installation






Someone has already setup CPAN on the machine - you need to coordinate
with the sysadmin or else download the modules by hand and do the install
manualy.

for each module (Inline::C, et)
% perl Makefile.PL LIB=~/lib/perl
% make
% make install

I have logged into mendel and had the same problems, but I don't have time
to figure out the best workaround for you other than downloading the
modules by hand for now or else getting the admin to install these for
you.

 -jason

 On Thu, 22 Jul 2004, Xiang Deng wrote:

> Brian,
>
> I tried that, but I could not enter CPAN shell,
>
> mendel 215% perl -e shell -MCPAN
>
>
> Your configuration suggests that CPAN.pm should use a working
> directory of
>     /.cpan
> Unfortunately we could not create the lock file
>     /.cpan/.lock
> due to permission problems.
>
> Please make sure that the configuration variable
>     $CPAN::Config->{cpan_home}
> points to a directory where you can write a .lock file. You can set
> this variable in either
>     /usr/local/lib/perl5/5.6.1/CPAN/Config.pm
> or
>     /v0/users/deng0007/.cpan/CPAN/MyConfig.pm
>
> Could not open >/.cpan/.lock: Permission denied
>
> Do I need to create all of those ".cpan/CPAN/MyConfig.pm"? I do not even
> have the .cpan directory.
>
> thanks
>
> Xiang
>
> Department of Pharmacology and Cancer Biology
> Duke University Medical Center
> Durham, NC 27710
> Phone: 919-4792339
>
>
>
>
> "Brian Osborne" <brian_osborne at cognia.com>
> Sent by: bioperl-l-bounces at portal.open-bio.org
> 07/22/2004 12:01 PM
>
> To
> "Xiang Deng" <xiang.deng at duke.edu>, "Jason Stajich"
> <jason at cgt.duhs.duke.edu>
> cc
> bioperl-l-bounces at portal.open-bio.org, bioperl-l at bioperl.org
> Subject
> RE: [Bioperl-l] bioperl installation
>
>
>
>
>
>
> Xiang,
>
> The section in the on-line instruction, the INSTALL page, talking about
> installing in a personal area using CPAN is called "INSTALLING BIOPERL 
IN
> A
> PERSONAL MODULE AREA":
>
> You can also use CPAN to install accessory modules in your
> local directory. First enter the CPAN shell, then set the
> arguments for the command "perl Makefile.PL", like this:
>
> >perl -e shell -MCPAN
> cpan>o conf makepl_arg LIB=/home/users/dag/My_Local_Perl_Modules
>
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Xiang Deng
> Sent: Thursday, July 22, 2004 11:42 AM
> To: Jason Stajich
> Cc: bioperl-l-bounces at portal.open-bio.org; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] bioperl installation
>
> Thanks for your message, Jason.
>
> The problem is I don't have permission to install bioperl into the
> standard site_perl/system area. From the on-line instruction at
> bioperl.org the only way I can get it installed is to use "make", not
> CPAN.
>
> So could you please let me know where I can download Inline::MakeMaker 
and
> Inline::C module. Everything I downloaded is from bioperl.org. I did not
> see where I can get these two. And if I get it which directory I should
> put them in.
>
> thanks,
>
> Xiang
>
> Department of Pharmacology and Cancer Biology
> Duke University Medical Center
> Durham, NC 27710
> Phone: 919-4792339
>
>
>
>
> Jason Stajich <jason at cgt.duhs.duke.edu>
> Sent by: bioperl-l-bounces at portal.open-bio.org
> 07/22/2004 11:25 AM
>
> To
> Xiang Deng <xiang.deng at duke.edu>
> cc
> bioperl-l at bioperl.org
> Subject
> Re: [Bioperl-l] bioperl installation
>
>
>
>
>
>
>
> Did you install Inline::C?
> >From the README in bioperl-ext directory
>   o Installing
>
>  Depending on your choise of extensions, you might need
>  Inline::MakeMaker and Inline::C to create the makefile. Use for
>  example the cpan program to install Inline::MakeMaker and answer yes
>  when prompted to install Inline::C.
>
> This line gives you a hint:
> > Can't locate Inline/MakeMaker.pm in @INC (@INC contains:
>
> Did you also install the staden library?
> -jason
> On Thu, 22 Jul 2004, Xiang Deng wrote:
>
> > To whom it may concern,
> >
> > I am trying to install bioperl locally under my peronal folder. The 
core
> > modules were successfully installed. I ran through a simple perl 
script
> to
> > use bio::perl or bio::seq without complain. but I got problem with
> > installing bioperl-ext-1.4.
> >
> > When I installed core modules I used this
> > >perl Makefile.PL LIB=/my_local_directory/
> >
> > My first question is whether or not I have to use the same way to deal
> > with ext modules too and I can use the same directory or a separate 
one.
> >
> > Actually I tried both and both failed with error message as follows:
> >
> > mendel 207% perl Makefile.PL
> > Checking if your kit is complete...
> > Looks good
> > Writing Makefile for Bio::Ext::Align
> > ERROR from evaluation of
> >
> 
/v0/users/deng0007/my_bioperl/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL:
> > Can't locate Inline/MakeMaker.pm in @INC (@INC contains:
> > /usr/local/lib/perl5/5.6.1/IP27-irix /usr/local/lib/perl5/5.6.1
> > /usr/local/lib/perl5/site_perl/5.6.1/IP27-irix
> > /usr/local/lib/perl5/site_perl/5.6.1 /usr/local/lib/perl5/site_perl
> > /v0/users/deng0007/my_bioperl/bioperl-ext-1.4 .) at ./Makefile.PL line
> 1.
> > BEGIN failed--compilation aborted at ./Makefile.PL line 1.
> >
> > could you please let me know what I did wrong or miss in there? thanks 
a
> > lot,
> >
> > Xiang
> >
> > Department of Pharmacology and Cancer Biology
> > Duke University Medical Center
> > Durham, NC 27710
> > Phone: 919-4792339
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu