[Bioperl-l] bioperl on Mac OSX
Adam Witney
awitney at sghms.ac.uk
Mon Feb 7 13:13:27 EST 2005
Hmm, I am no expert but you may have a problem with your perl installation,
I just downloaded and built HTML::Parser with no problems
How did you install Perl? Or are you using the default?
> I have also tried using fink ... but I run into the same problem:
> won't make, because it can't find -lbundle.o. I imagine I'll have the
> same problem if I install directly from source.
>
>
>
> :~$ fink install html-parser-pm581
> /usr/bin/sudo /sw/bin/fink install html-parser-pm581
> Password:
> Information about 1740 packages read in 0 seconds.
> The following package will be installed or updated:
> html-parser-pm581
> gzip -dc /sw/src/HTML-Parser-3.35.tar.gz | /sw/bin/tar -xf -
> --no-same-owner --no-same-permissions
> perl -pi -e 's,my \$ans = prompt,my \$ans = "y"; #prompt,g' Makefile.PL
> /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
>
> Perl-5.8 provide core support for Unicode strings. You can compile
> HTML::Entities so that Unicode entities like € and € are
> decoded into a string containing "\x{20AC}". If you select no to
> the question below such entities will be left alone and only entities
> in the Latin-1 range is decoded.
>
> Checking if your kit is complete...
> Looks good
> Writing Makefile for HTML::Parser
> make
> cp lib/HTML/Entities.pm blib/lib/HTML/Entities.pm
> cp lib/HTML/Filter.pm blib/lib/HTML/Filter.pm
> cp Parser.pm blib/lib/HTML/Parser.pm
> cp lib/HTML/HeadParser.pm blib/lib/HTML/HeadParser.pm
> cp lib/HTML/LinkExtor.pm blib/lib/HTML/LinkExtor.pm
> cp lib/HTML/PullParser.pm blib/lib/HTML/PullParser.pm
> cp lib/HTML/TokeParser.pm blib/lib/HTML/TokeParser.pm
> /usr/bin/perl5.8.1 /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/perl5.8.1 mkhctype >hctype.h
> /usr/bin/perl5.8.1 mkpfunc >pfunc.h
> cc -c -g -pipe -pipe -fno-common -DPERL_DARWIN -no-cpp-precomp
> -fno-strict-aliasing -I/usr/local/include -Os -DVERSION=\"3.35\"
> -DXS_VERSION=\"3.35\"
> "-I/System/Library/Perl/5.8.1/darwin-thread-multi-2level/CORE"
> -DMARKED_SECTION -DUNICODE_ENTITIES 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: warning -prebind has no effect with -bundle
> ld: can't locate file for: -lbundle1.o
> make: *** [blib/arch/auto/HTML/Parser/Parser.bundle] Error 1
> ### execution of make failed, exit code 2
> Failed: compiling html-parser-pm581-3.35-10 failed
> :~$
>
> On Feb 7, 2005, at 12:57 PM, Adam Witney wrote:
>
>>
>> Well, I often have trouble installing from CPAN on OSX, hence always
>> compiling from source...
>>
>>> 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:
>>
>> Yes I have that HTML directory, but that is fro a different module and
>> not
>> below darwin-2level directory:
>>
>> $site_perl/HTML/Form.pm
>> $site_perl/HTML/Tagset.pm
>> $site_perl/darwin-2level/HTML/HeadParser.pm
>>
>> I can't really help with the problems below as I don't use CPAN much,
>> you
>> might want to try compiling from source, or do what another poster
>> suggested
>> and try fink
>>
>> http://fink.sourceforge.net
>>
>> Which in general is quite good for osx software
>>
>> Cheers
>>
>> Adam
>>
>>
>>> 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+ribonucleop
>>>>>> ro
>>>>>> te
>>>>>> in+A1+(Helix-destabilizing+protein)+(Single-
>>>>>> strand+binding+protein)+(hnRNP+core+protein+A1).%0ASKSESPKEPEQLRKLF
>>>>>> IG
>>>>>> GL
>>>>>> SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR
>>>>>> AV
>>>>>> SR
>>>>>> EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV
>>>>>> DK
>>>>>> IV
>>>>>> IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGG
>>>>>> SR
>>>>>> GG
>>>>>> GGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGG
>>>>>> SG
>>>>>> 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=%3Eg
>>>>>> i%
>>>>>> 7C
>>>>>> 1786183%7Cgb%7CAAC73113.1%7C+(AE000111)+aspartokinase+I%2C+homoseri
>>>>>> ne
>>>>>> +d
>>>>>> ehydrogenase+I+%5BEscherichia+coli%5D%0AMRVLKFGGTSVANAERFLRVADILESN
>>>>>> AR
>>>>>> QG
>>>>>> QVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEF
>>>>>> AQ
>>>>>> IK
>>>>>> HVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAE
>>>>>> ST
>>>>>> RR
>>>>>> IAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
>>>>>> PD
>>>>>> AR
>>>>>> LLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISN
>>>>>> LN
>>>>>> NM
>>>>>> AMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLEL
>>>>>> KE
>>>>>> GL
>>>>>> LEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVR
>>>>>> VT
>>>>>> HQ
>>>>>> MLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEE
>>>>>> LA
>>>>>> QA
>>>>>> KEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYA
>>>>>> AE
>>>>>> KS
>>>>>> RRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYT
>>>>>> EP
>>>>>> DP
>>>>>> RDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKAR
>>>>>> DE
>>>>>> GK
>>>>>> VLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFA
>>>>>> DL
>>>>>> 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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>>>> believed to be clean.
>>>>
>>>
>>
>>
>> --
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>
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