[Bioperl-l] bioperl on Mac OSX
Arya Akmal
akmala at nmrc.navy.mil
Mon Feb 7 13:04:22 EST 2005
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$
>>>>>
>>>
>>>
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>>>
>>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
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