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

alison waller alison.waller at utoronto.ca
Thu Nov 29 11:20:59 EST 2007


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

  

 



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