[Bioperl-l] Problems installing bioperl (bioperl-live tarball from CVS)

Chris Fields cjfields at uiuc.edu
Thu Nov 29 23:53:09 EST 2007


Alison,

There are directions on how to do this here:

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA

(TinyURL link)
http://tinyurl.com/3263dd

Note the additional configuration for CPAN in that section; you'll  
need to set up CPAN so it installs everything locally.

chris

On Nov 29, 2007, at 10:20 AM, alison waller wrote:

> Hi all,
>
>
>
> I would like to install the CVS version of bioperl  as I know of  
> some code
> changes that will be useful to me.  However, I am having problems  
> installing
> it.
>
> I am trying to install bioperl in my home directly on a linux cluster.
>
>
>
> I used
>
>
>
>> cd bioperl-live
>
> *       perl Build.PL -install /home/awaller
>
>
>
> However after the build command I got a lot of errors.  Do I have to  
> also
> have perl installed in my home directory??  There is perl installed  
> on the
> cluster in /usr/bin.  Do I need to point to this or does Build.PL
> automatically look there?  I noticed a few errors about not having
> permission and a few about not being able to connect. I've copied a  
> portion
> of the messages after my Build.pl command.
>
>
>
> Any help would be appreciated,
>
>
>
> alison
>
>
>
>
>
> Issuing "/usr/bin/ftp -n"
>
> ftp: mirror.isurf.ca: Unknown host
>
> Not connected.
>
> Local directory now /root/.cpan/sources/modules
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Bad luck... Still failed!
>
> Can't access URL
> ftp://mirror.isurf.ca/pub/CPAN/modules/02packages.details.txt.gz.
>
>
>
> Please check, if the URLs I found in your configuration file
>
> (ftp://ftp.nrc.ca/pub/CPAN/, ftp://cpan.sunsite.ualberta.ca/pub/CPAN/,
>
> ftp://cpan.mirror.cygnal.ca/pub/CPAN/, ftp://mirror.isurf.ca/pub/ 
> CPAN) are
>
> valid. The urllist can be edited. E.g. with 'o conf urllist push
>
> ftp://myurl/'
>
>
>
> Could not fetch modules/02packages.details.txt.gz
>
> Trying to get away with old file:
>
> 3604718  584 -rw-r--r--  1 0        0          592967 Nov 12 22:53
> /root/.cpan/sources/modules/02packages.details.txt.gz
>
> Going to read /root/.cpan/sources/modules/02packages.details.txt.gz
>
>  Database was generated on Sat, 10 Nov 2007 22:36:34 GMT
>
>
>
>  There's a new CPAN.pm version (v1.9204) available!
>
>  [Current version is v1.7601]
>
>  You might want to try
>
>    install Bundle::CPAN
>
>    reload cpan
>
>  without quitting the current session. It should be a seamless upgrade
>
>  while we are running...
>
>
>
> Warning: You are not allowed to write into directory
> "/root/.cpan/sources/modules".
>
>    I'll continue, but if you encounter problems, they may be due
>
>    to insufficient permissions.
>
> Fetching with LWP:
>
>  ftp://ftp.nrc.ca/pub/CPAN/modules/03modlist.data.gz
>
> LWP failed with code[500] message[Cannot write to
> '/root/.cpan/sources/modules/03modlist.data.gz-25787': Permission  
> denied]
>
> Fetching with Net::FTP:
>
>  ftp://ftp.nrc.ca/pub/CPAN/modules/03modlist.data.gz
>
> Cannot open Local file /root/.cpan/sources/modules/03modlist.data.gz:
> Permission denied
>
> at /usr/share/perl/5.8/CPAN.pm line 2265
>
> Couldn't fetch 03modlist.data.gz from ftp.nrc.ca
>
> Fetching with LWP:
>
>  ftp://cpan.sunsite.ualberta.ca/pub/CPAN/modules/03modlist.data.gz
>
> LWP failed with code[500] message[FTP close response: 500 Network  
> seems to
> have barfed - Let's all phone our ISP and go postal!
>
> Unknown command.
>
> ]
>
> Fetching with Net::FTP:
>
>  ftp://cpan.sunsite.ualberta.ca/pub/CPAN/modules/03modlist.data.gz
>
> Cannot open Local file /root/.cpan/sources/modules/03modlist.data.gz:
> Permission denied
>
> at /usr/share/perl/5.8/CPAN.pm line 2265
>
> Couldn't fetch 03modlist.data.gz from cpan.sunsite.ualberta.ca
>
> Fetching with LWP:
>
>  ftp://cpan.mirror.cygnal.ca/pub/CPAN/modules/03modlist.data.gz
>
> LWP failed with code[500] message[LWP::Protocol::MyFTP: Bad hostname
> 'cpan.mirror.cygnal.ca']
>
> Fetching with Net::FTP:
>
>  ftp://cpan.mirror.cygnal.ca/pub/CPAN/modules/03modlist.data.gz
>
> Fetching with LWP:
>
>  ftp://mirror.isurf.ca/pub/CPAN/modules/03modlist.data.gz
>
> LWP failed with code[500] message[LWP::Protocol::MyFTP: Bad hostname
> 'mirror.isurf.ca']
>
> Fetching with Net::FTP:
>
>  ftp://mirror.isurf.ca/pub/CPAN/modules/03modlist.data.gz
>
>
>
> Trying with "/usr/bin/lynx -source" to get
>
>    ftp://ftp.nrc.ca/pub/CPAN/modules/03modlist.data.gz
>
> sh: line 1: /root/.cpan/sources/modules/03modlist.data: Permission  
> denied
>
>
>
> System call "/usr/bin/lynx -source
> "ftp://ftp.nrc.ca/pub/CPAN/modules/03modlist.data.gz"  >
> /root/.cpan/sources/modules/03modlist.data"
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/ncftp" to get
>
>    ftp://ftp.nrc.ca/pub/CPAN/modules/03modlist.data.gz
>
> Use ncftpget or ncftpput to handle file URLs.
>
>
>
> System call "cd /root/.cpan/sources/modules && /usr/bin/ncftp
> "ftp://ftp.nrc.ca/pub/CPAN/modules/03modlist.data.gz" "
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/wget -O -" to get
>
>    ftp://ftp.nrc.ca/pub/CPAN/modules/03modlist.data.gz
>
> sh: line 1: /root/.cpan/sources/modules/03modlist.data: Permission  
> denied
>
>
>
> System call "/usr/bin/wget -O -
> "ftp://ftp.nrc.ca/pub/CPAN/modules/03modlist.data.gz"  >
> /root/.cpan/sources/modules/03modlist.data"
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/lynx -source" to get
>
>    ftp://cpan.sunsite.ualberta.ca/pub/CPAN/modules/03modlist.data.gz
>
> sh: line 1: /root/.cpan/sources/modules/03modlist.data: Permission  
> denied
>
>
>
> System call "/usr/bin/lynx -source
> "ftp://cpan.sunsite.ualberta.ca/pub/CPAN/modules/03modlist.data.gz"  >
> /root/.cpan/sources/modules/03modlist.data"
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/ncftp" to get
>
>    ftp://cpan.sunsite.ualberta.ca/pub/CPAN/modules/03modlist.data.gz
>
> Use ncftpget or ncftpput to handle file URLs.
>
>
>
> System call "cd /root/.cpan/sources/modules && /usr/bin/ncftp
> "ftp://cpan.sunsite.ualberta.ca/pub/CPAN/modules/03modlist.data.gz" "
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/wget -O -" to get
>
>    ftp://cpan.sunsite.ualberta.ca/pub/CPAN/modules/03modlist.data.gz
>
> sh: line 1: /root/.cpan/sources/modules/03modlist.data: Permission  
> denied
>
>
>
> System call "/usr/bin/wget -O -
> "ftp://cpan.sunsite.ualberta.ca/pub/CPAN/modules/03modlist.data.gz"  >
> /root/.cpan/sources/modules/03modlist.data"
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/lynx -source" to get
>
>    ftp://cpan.mirror.cygnal.ca/pub/CPAN/modules/03modlist.data.gz
>
> sh: line 1: /root/.cpan/sources/modules/03modlist.data: Permission  
> denied
>
>
>
> System call "/usr/bin/lynx -source
> "ftp://cpan.mirror.cygnal.ca/pub/CPAN/modules/03modlist.data.gz"  >
> /root/.cpan/sources/modules/03modlist.data"
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/ncftp" to get
>
>    ftp://cpan.mirror.cygnal.ca/pub/CPAN/modules/03modlist.data.gz
>
> Use ncftpget or ncftpput to handle file URLs.
>
>
>
> System call "cd /root/.cpan/sources/modules && /usr/bin/ncftp
> "ftp://cpan.mirror.cygnal.ca/pub/CPAN/modules/03modlist.data.gz" "
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/wget -O -" to get
>
>    ftp://cpan.mirror.cygnal.ca/pub/CPAN/modules/03modlist.data.gz
>
> sh: line 1: /root/.cpan/sources/modules/03modlist.data: Permission  
> denied
>
>
>
> System call "/usr/bin/wget -O -
> "ftp://cpan.mirror.cygnal.ca/pub/CPAN/modules/03modlist.data.gz"  >
> /root/.cpan/sources/modules/03modlist.data"
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/lynx -source" to get
>
>    ftp://mirror.isurf.ca/pub/CPAN/modules/03modlist.data.gz
>
> sh: line 1: /root/.cpan/sources/modules/03modlist.data: Permission  
> denied
>
>
>
> System call "/usr/bin/lynx -source
> "ftp://mirror.isurf.ca/pub/CPAN/modules/03modlist.data.gz"  >
> /root/.cpan/sources/modules/03modlist.data"
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/ncftp" to get
>
>    ftp://mirror.isurf.ca/pub/CPAN/modules/03modlist.data.gz
>
> Use ncftpget or ncftpput to handle file URLs.
>
>
>
> System call "cd /root/.cpan/sources/modules && /usr/bin/ncftp
> "ftp://mirror.isurf.ca/pub/CPAN/modules/03modlist.data.gz" "
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
>
>
> Trying with "/usr/bin/wget -O -" to get
>
>    ftp://mirror.isurf.ca/pub/CPAN/modules/03modlist.data.gz
>
> sh: line 1: /root/.cpan/sources/modules/03modlist.data: Permission  
> denied
>
>
>
> System call "/usr/bin/wget -O -
> "ftp://mirror.isurf.ca/pub/CPAN/modules/03modlist.data.gz"  >
> /root/.cpan/sources/modules/03modlist.data"
>
> returned status 1 (wstat 256), left
>
> /root/.cpan/sources/modules/03modlist.data.gz with size 141973
>
> Issuing "/usr/bin/ftp -n"
>
> Local directory now /root/.cpan/sources/modules
>
> local: 03modlist.data.gz: Permission denied
>
> Bad luck... Still failed!
>
> Can't access URL ftp://ftp.nrc.ca/pub/CPAN/modules/03modlist.data.gz.
>
>
>
> Issuing "/usr/bin/ftp -n"
>
> Local directory now /root/.cpan/sources/modules
>
> local: 03modlist.data.gz: Permission denied
>
> Bad luck... Still failed!
>
> Can't access URL
> ftp://cpan.sunsite.ualberta.ca/pub/CPAN/modules/03modlist.data.gz.
>
>
>
> Issuing "/usr/bin/ftp -n"
>
> ftp: cpan.mirror.cygnal.ca: Unknown host
>
> Not connected.
>
> Local directory now /root/.cpan/sources/modules
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Bad luck... Still failed!
>
> Can't access URL
> ftp://cpan.mirror.cygnal.ca/pub/CPAN/modules/03modlist.data.gz.
>
>
>
> Issuing "/usr/bin/ftp -n"
>
> ftp: mirror.isurf.ca: Unknown host
>
> Not connected.
>
> Local directory now /root/.cpan/sources/modules
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Not connected.
>
> Bad luck... Still failed!
>
> Can't access URL ftp://mirror.isurf.ca/pub/CPAN/modules/03modlist.data.gz 
> .
>
>
>
> Please check, if the URLs I found in your configuration file
>
> (ftp://ftp.nrc.ca/pub/CPAN/, ftp://cpan.sunsite.ualberta.ca/pub/CPAN/,
>
> ftp://cpan.mirror.cygnal.ca/pub/CPAN/, ftp://mirror.isurf.ca/pub/ 
> CPAN) are
>
> valid. The urllist can be edited. E.g. with 'o conf urllist push
>
> ftp://myurl/'
>
>
>
> Could not fetch modules/03modlist.data.gz
>
> Trying to get away with old file:
>
> 3604719  144 -rw-r--r--  1 0        0          141973 Nov 12 22:53
> /root/.cpan/sources/modules/03modlist.data.gz
>
> Going to read /root/.cpan/sources/modules/03modlist.data.gz
>
> Going to write /root/.cpan/Metadata
>
> can't create /root/.cpan/Metadata: Permission denied at
> /usr/share/perl/5.8/CPAN.pm line 3432
>
> Running install for module Test::Harness
>
> Running make for A/AN/ANDYA/Test-Harness-3.00.tar.gz
>
> mkdir /root/.cpan/sources/authors/id/A/AN: Permission denied at
> /usr/share/perl/5.8/CPAN.pm line 2342
>
> ******************************************
> Alison S. Waller  M.A.Sc.
> Doctoral Candidate
> awaller at chem-eng.utoronto.ca
> 416-978-4222 (lab)
> Department of Chemical Engineering
> Wallberg Building
> 200 College st.
> Toronto, ON
> M5S 3E5
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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