[Bioperl-l] bioperl on Mac OSX

Mon Feb 7 14:54:29 EST 2005

Appears you need to install Xcode.
http://www.talkaboutmac.com/group/perl.macosx/messages/4773.html

-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

On Feb 7, 2005, at 12:47 PM, Arya Akmal wrote:

> 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+ribonucleopr 
>>>> ote
>>>> in+A1+(Helix-destabilizing+protein)+(Single-
>>>> strand+binding+protein)+(hnRNP+core+protein+A1).%0ASKSESPKEPEQLRKLFI 
>>>> GGL
>>>> SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA 
>>>> VSR
>>>> EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 
>>>> KIV
>>>> IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGS 
>>>> RGG
>>>> GGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGGS 
>>>> GSN
>>>> FGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF& 
>>>> FOR
>>>> MAT_OBJECT=Alignment&COMPOSITION_BASED_STATISTICS=off&FILTER=L&CDD_S 
>>>> EAR
>>>> 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+homoserin 
>>>> e+d
>>>> ehydrogenase+I+%5BEscherichia+coli%5D%0AMRVLKFGGTSVANAERFLRVADILESNA 
>>>> RQG
>>>> QVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFA 
>>>> QIK
>>>> HVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAES 
>>>> TRR
>>>> IAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVP 
>>>> DAR
>>>> LLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNL 
>>>> NNM
>>>> AMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELK 
>>>> EGL
>>>> LEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRV 
>>>> THQ
>>>> MLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEEL 
>>>> AQA
>>>> KEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAA 
>>>> EKS
>>>> RRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTE 
>>>> PDP
>>>> RDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARD 
>>>> EGK
>>>> VLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFAD 
>>>> LLR
>>>> 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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>>
>
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