[Bioperl-l] Re: Installing BioPerl under Mac OS X

[Madeleine Lemieux]

Koen,

>> I have also installed (following each package's installation  
>> instructions) wwwBlast (latest OS X version from NCBI), t-coffee (the  
>> Unix version, not the Mac one), clustalw (the OS X version) and  
>> EMBOSS.
>
> Just as a note, all three, as well as pTk (804.026) are also availble  
> through fink.
My fink (0.7.1) does not list clustalw, pTk, t-coffee or wwwBlast among  
its packages so I just downloaded the source or executables that were  
available. I've used fink several times but don't know much about it.  
Is there some way other than using the list option to find out what  
packages are available?

> Madeleine, I am curious why didn't use fink to install bioperl.  
> Version 1.4 has been available for a few months, and is actually part  
> of the most recent binary release (Fink 0.7.1). Did you get any  
> particular errors when you tried to install it? I am the  
> fink-maintainer of bioperl, so if there are any problems please let me  
> know, so I can try to fix the package.
I was quite pleased to see bioperl as one of the fink packages but see  
below for what happens when I try use fink to install bioperl-pm581. Is  
there a log file somewhere that might contain more useful information?

Madeleine

-----------
LeMeiLin:~ $ fink install bioperl-pm581
/usr/bin/sudo /sw/bin/fink  install bioperl-pm581
Password:
Information about 1853 packages read in 1 seconds.
The following package will be installed or updated:
  bioperl-pm581
The following 10 additional packages will be installed:
  libwww-pm581 libxml-pm581 soap-lite-pm581 uri-pm581 xml-dom-pm581
  xml-node-pm581 xml-parser-pm581 xml-regexp-pm xml-twig-pm581  
xml-writer-pm
Do you want to continue? [Y/n] Y
gzip -dc /sw/src/URI-1.30.tar.gz | /sw/bin/tar -xf -  --no-same-owner  
--no-same-permissions
/usr/bin/perl5.8.1 Makefile.PL PERL=/usr/bin/perl5.8.1 PREFIX=/sw  
INSTALLPRIVLIB=/sw/lib/perl5/5.8.1  
INSTALLARCHLIB=/sw/lib/perl5/5.8.1/darwin-thread-multi-2level  
INSTALLSITELIB=/sw/lib/perl5/5.8.1  
INSTALLSITEARCH=/sw/lib/perl5/5.8.1/darwin-thread-multi-2level  
INSTALLMAN1DIR=/sw/share/man/man1 INSTALLMAN3DIR=/sw/share/man/man3  
INSTALLSITEMAN1DIR=/sw/share/man/man1  
INSTALLSITEMAN3DIR=/sw/share/man/man3 INSTALLBIN=/sw/bin  
INSTALLSITEBIN=/sw/bin INSTALLSCRIPT=/sw/bin
Checking if your kit is complete...
Looks good
Writing Makefile for URI
make
cp URI/nntp.pm blib/lib/URI/nntp.pm
cp URI/gopher.pm blib/lib/URI/gopher.pm
cp URI/rlogin.pm blib/lib/URI/rlogin.pm
cp URI/https.pm blib/lib/URI/https.pm
cp URI/snews.pm blib/lib/URI/snews.pm
cp URI/URL.pm blib/lib/URI/URL.pm
cp URI/Split.pm blib/lib/URI/Split.pm
cp URI/_userpass.pm blib/lib/URI/_userpass.pm
cp URI/urn/isbn.pm blib/lib/URI/urn/isbn.pm
cp URI/mailto.pm blib/lib/URI/mailto.pm
cp URI/file/QNX.pm blib/lib/URI/file/QNX.pm
cp URI/_login.pm blib/lib/URI/_login.pm
cp URI/ldapi.pm blib/lib/URI/ldapi.pm
cp URI/file/Unix.pm blib/lib/URI/file/Unix.pm
cp URI/_segment.pm blib/lib/URI/_segment.pm
cp URI/_query.pm blib/lib/URI/_query.pm
cp URI/mms.pm blib/lib/URI/mms.pm
cp URI/file/Mac.pm blib/lib/URI/file/Mac.pm
cp URI/urn.pm blib/lib/URI/urn.pm
cp URI/_ldap.pm blib/lib/URI/_ldap.pm
cp URI/Heuristic.pm blib/lib/URI/Heuristic.pm
cp URI/rsync.pm blib/lib/URI/rsync.pm
cp URI/ssh.pm blib/lib/URI/ssh.pm
cp URI/WithBase.pm blib/lib/URI/WithBase.pm
cp URI/pop.pm blib/lib/URI/pop.pm
cp URI/file/Base.pm blib/lib/URI/file/Base.pm
cp URI/file/Win32.pm blib/lib/URI/file/Win32.pm
cp URI/_foreign.pm blib/lib/URI/_foreign.pm
cp URI.pm blib/lib/URI.pm
cp URI/file/FAT.pm blib/lib/URI/file/FAT.pm
cp URI/news.pm blib/lib/URI/news.pm
cp URI/ldap.pm blib/lib/URI/ldap.pm
cp URI/_generic.pm blib/lib/URI/_generic.pm
cp URI/rtsp.pm blib/lib/URI/rtsp.pm
cp URI/ftp.pm blib/lib/URI/ftp.pm
cp URI/Escape.pm blib/lib/URI/Escape.pm
cp URI/_server.pm blib/lib/URI/_server.pm
cp URI/http.pm blib/lib/URI/http.pm
cp URI/ldaps.pm blib/lib/URI/ldaps.pm
cp URI/file.pm blib/lib/URI/file.pm
cp URI/QueryParam.pm blib/lib/URI/QueryParam.pm
cp URI/file/OS2.pm blib/lib/URI/file/OS2.pm
cp URI/sip.pm blib/lib/URI/sip.pm
cp URI/urn/oid.pm blib/lib/URI/urn/oid.pm
cp URI/telnet.pm blib/lib/URI/telnet.pm
cp URI/tn3270.pm blib/lib/URI/tn3270.pm
cp URI/rtspu.pm blib/lib/URI/rtspu.pm
cp URI/sips.pm blib/lib/URI/sips.pm
cp URI/data.pm blib/lib/URI/data.pm
Manifying blib/man3/URI::Escape.3pm
Manifying blib/man3/URI.3pm
Manifying blib/man3/URI::URL.3pm
Manifying blib/man3/URI::ldap.3pm
Manifying blib/man3/URI::file.3pm
Manifying blib/man3/URI::data.3pm
Manifying blib/man3/URI::WithBase.3pm
Manifying blib/man3/URI::QueryParam.3pm
Manifying blib/man3/URI::Heuristic.3pm
Manifying blib/man3/URI::Split.3pm
make test
PERL_DL_NONLAZY=1 /usr/bin/perl5.8.1 "-MExtUtils::Command::MM" "-e"  
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/abs............ok
t/clone..........ok
t/data...........ok
t/escape.........ok
t/file...........ok
t/ftp............ok
t/generic........ok
t/heuristic......FAILED test 7
         Failed 1/15 tests, 93.33% okay
t/http...........ok
t/ldap...........ok
t/mailto.........ok
t/mix............ok
t/mms............ok
t/news...........ok
t/old-absconf....ok
t/old-base.......ok
t/old-relbase....ok
t/pop............ok
t/query-param....ok
t/query..........ok
t/rel............ok
t/rfc2732........ok
t/roy-test.......ok
t/rsync..........ok
t/rtsp...........ok
t/sip............ok
t/split..........ok
t/storable.......ok
t/urn-isbn.......skipped
         all skipped: Needs the Business::ISBN module installed
t/urn-oid........ok
Failed Test   Stat Wstat Total Fail  Failed  List of Failed
------------------------------------------------------------------------ 
-------
t/heuristic.t               15    1   6.67%  7
1 test skipped.
Failed 1/30 test scripts, 96.67% okay. 1/447 subtests failed, 99.78%  
okay.
make: *** [test_dynamic] Error 2
### execution of make failed, exit code 2
Failed: compiling uri-pm581-1.30-11 failed
LeMeiLin:~ $