[Bioperl-l] bioperl on Mac OSX

Arya Akmal akmala at nmrc.navy.mil
Mon Feb 7 12:47:04 EST 2005 

Right ... that's what I figured. I have an HTML directory that only  
contains 2 modules: Form.pm and Tagset.pm.  But I'm wondering:

1) Why this module wasn't installed along with everything else in my  
bioperl installation. Did I do something wrong?

2) How I know if there are any other modules that normally would have  
been part of the distribution, but for some reason didn't get  
installed.

3)How do I fix this problem?  I don't seem to be able to make  
HTML::HeadParser

cpan> make HTML::HeadParser
Running make for module HTML::HeadParser
Running make for G/GA/GAAS/HTML-Parser-3.45.tar.gz
   Is already unwrapped into directory  
/Users/aryaakmal/.cpan/build/HTML-Parser-3.45

   CPAN.pm: Going to build G/GA/GAAS/HTML-Parser-3.45.tar.gz

Checking if your kit is complete...
Looks good
Writing Makefile for HTML::Parser
cp lib/HTML/Entities.pm blib/lib/HTML/Entities.pm
cp lib/HTML/LinkExtor.pm blib/lib/HTML/LinkExtor.pm
cp Parser.pm blib/lib/HTML/Parser.pm
cp lib/HTML/Filter.pm blib/lib/HTML/Filter.pm
cp lib/HTML/HeadParser.pm blib/lib/HTML/HeadParser.pm
cp lib/HTML/TokeParser.pm blib/lib/HTML/TokeParser.pm
cp lib/HTML/PullParser.pm blib/lib/HTML/PullParser.pm
/usr/bin/perl /System/Library/Perl/5.8.1/ExtUtils/xsubpp  -typemap  
/System/Library/Perl/5.8.1/ExtUtils/typemap -typemap typemap  Parser.xs  
 > Parser.xsc && mv Parser.xsc Parser.c
/usr/bin/perl mkhctype >hctype.h
/usr/bin/perl mkpfunc >pfunc.h
cc -c   -g -pipe -pipe -fno-common -DPERL_DARWIN -no-cpp-precomp  
-fno-strict-aliasing -I/usr/local/include -Os   -DVERSION=\"3.45\"  
-DXS_VERSION=\"3.45\"   
"-I/System/Library/Perl/5.8.1/darwin-thread-multi-2level/CORE"   
-DMARKED_SECTION Parser.c
Running Mkbootstrap for HTML::Parser ()
chmod 644 Parser.bs
rm -f blib/arch/auto/HTML/Parser/Parser.bundle
LD_RUN_PATH="" MACOSX_DEPLOYMENT_TARGET=10.3 cc  -bundle -undefined  
dynamic_lookup -L/usr/local/lib Parser.o  -o  
blib/arch/auto/HTML/Parser/Parser.bundle
ld: can't locate file for: -lbundle1.o
make: *** [blib/arch/auto/HTML/Parser/Parser.bundle] Error 1
   /usr/bin/make  -- NOT OK

cpan>

On Feb 7, 2005, at 11:40 AM, Adam Witney wrote:

>
> 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+ribonucleopro 
>>> te
>>> in+A1+(Helix-destabilizing+protein)+(Single-
>>> strand+binding+protein)+(hnRNP+core+protein+A1).%0ASKSESPKEPEQLRKLFIG 
>>> GL
>>> SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV 
>>> SR
>>> EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 
>>> IV
>>> IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSR 
>>> GG
>>> GGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGGSG 
>>> SN
>>> FGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF&F 
>>> OR
>>> MAT_OBJECT=Alignment&COMPOSITION_BASED_STATISTICS=off&FILTER=L&CDD_SE 
>>> AR
>>> 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%0AMRVLKFGGTSVANAERFLRVADILESNAR 
>>> QG
>>> QVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQ 
>>> IK
>>> HVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAEST 
>>> RR
>>> IAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPD 
>>> AR
>>> LLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLN 
>>> NM
>>> AMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKE 
>>> GL
>>> LEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVT 
>>> HQ
>>> MLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELA 
>>> QA
>>> KEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAE 
>>> KS
>>> RRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEP 
>>> DP
>>> RDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDE 
>>> GK
>>> VLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADL 
>>> LR
>>> 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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