[Bioperl-l] bioperl on Mac OSX

Mon Feb 7 11:40:26 EST 2005

Have you installed HTML::Parser?

I have BioPerl running on OSX nicely. I always compile from source and
haven't had any problems for several versions of BioPerl now.

If installed correctly HeadParser.pm will appear here

$site_perl/darwin-2level/HTML/HeadParser.pm

Where $site_perl is probably for you

/Library/Perl/5.8.1

Cheers

Adam

>> The modules you mentions can be loaded:
>> 
>>> :~$ perl /Library/Perl/5.8.1/IO/String.pm
>>> :~$ perl /Library/Perl/5.8.1/LWP
>>> :~$ perl /Library/Perl/5.8.1/LWP.pm
>>> :~$ perl /Library/Perl/5.8.1/LWP/UserAgent.pm
>>> :~$
>> 
>> The problem seems to be with HTML::Parser:
>> 
>>> :~$ perldoc HTML::Parser
>>> No documentation found for "HTML::Parser".
>>> :~$
>> 
>> The only modules I have under HTML are Form.pm and Tagset.pm.
>> Apparently, I am missing a module called HeadParser.pm:
>> 
>>  DB<4> use Bio::Perl;
>> 
>>  DB<5> $seq_object = get_sequence('swissprot',"ROA1_HUMAN");
>> 
>>  DB<6> $blast_result = blast_sequence($seq_object)
>> 
>>  -------------------- WARNING ---------------------
>>  MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
>>  User-Agent: libwww-perl/5.803
>>  Content-Length: 666
>>  Content-Type: application/x-www-form-urlencoded
>> 
>> SERVICE=plain&QUERY=%3EROA1_HUMAN+Heterogeneous+nuclear+ribonucleoprote
>> in+A1+(Helix-destabilizing+protein)+(Single-
>> strand+binding+protein)+(hnRNP+core+protein+A1).%0ASKSESPKEPEQLRKLFIGGL
>> SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR
>> EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV
>> IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGG
>> GGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGGSGSN
>> FGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF&FOR
>> MAT_OBJECT=Alignment&COMPOSITION_BASED_STATISTICS=off&FILTER=L&CDD_SEAR
>> CH=off&PROGRAM=blastp&CMD=Put&DATABASE=nr&EXPECT=1e-10
>> 
>> <HTML>
>> <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
>> <BODY>
>> <H1>An Error Occurred</H1>
>> 500 Can't locate HTML/HeadParser.pm in @INC (@INC contains:
>> /sw/lib/perl5 /sw/lib/perl5/darwin
>> /System/Library/Perl/5.8.1/darwin-thread-multi-2level
>> /System/Library/Perl/5.8.1
>> /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1
>> /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level
>> /Network/Library/Perl/5.8.1 /Network/Library/Perl .)
>> </BODY>
>> </HTML>
>> 
>> ---------------------------------------------------
>> Submitted Blast for [ROA1_HUMAN]
>> 
>> Finally, here are the results of running the Remote Blast tests:
>> 
>> :~/Desktop$ perl -I. -Ilib t/RemoteBlast.t
>> 1..6
>> ok 1
>> ok 2
>> 
>> -------------------- WARNING ---------------------
>> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
>> User-Agent: libwww-perl/5.803
>> Content-Length: 1091
>> Content-Type: application/x-www-form-urlencoded
>> 
>> COMPOSITION_BASED_STATISTICS=off&CDD_SEARCH=off&FILTER=L&QUERY=%3Egi%7C
>> 1786183%7Cgb%7CAAC73113.1%7C+(AE000111)+aspartokinase+I%2C+homoserine+d
>> ehydrogenase+I+%5BEscherichia+coli%5D%0AMRVLKFGGTSVANAERFLRVADILESNARQG
>> QVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIK
>> HVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRR
>> IAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDAR
>> LLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNM
>> AMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGL
>> LEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQ
>> MLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQA
>> KEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKS
>> RRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDP
>> RDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGK
>> VLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLR
>> TLSWKLGV&FORMAT_OBJECT=Alignment&EXPECT=1e
>> -10&DATABASE=ecoli&SERVICE=plain&CMD=Put&PROGRAM=blastp
>> 
>> <HTML>
>> <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
>> <BODY>
>> <H1>An Error Occurred</H1>
>> 500 Can't locate HTML/HeadParser.pm in @INC (@INC contains: t . lib
>> /sw/lib/perl5 /sw/lib/perl5/darwin
>> /System/Library/Perl/5.8.1/darwin-thread-multi-2level
>> /System/Library/Perl/5.8.1
>> /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1
>> /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level
>> /Network/Library/Perl/5.8.1 /Network/Library/Perl)
>> </BODY>
>> </HTML>
>> 
>> ---------------------------------------------------
>> ok 3
>> ok 4 # Unable to run RemoteBlast tests - probably no network
>> connection.
>> ok 5 # Unable to run RemoteBlast tests - probably no network
>> connection.
>> ok 6 # Unable to run RemoteBlast tests - probably no network
>> connection.
>> :~/Desktop$
>> 

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