[Bioperl-l] Re: [Bug 1837] Bio::Ext::Align

Brian Osborne osborne1 at optonline.net
Fri Dec 16 10:08:22 EST 2005


Jouni,

What happens when you change "1.5.1" to "1.51" in Bio/SeqIO/staden/read.pm?
Does "perl Makefile.PL" work?

Brian O


On 12/16/05 3:04 AM, "Jouni Valiaho" <Jouni.Valiaho at uta.fi> wrote:

> Hi Brian,
> 
> Thank you for your answer.
> I tried again to install the latest bioperl-ext package. The procedure
> is shown below.
> 
> $ wget http://bioperl.org/DIST/current_ext_unstable.tar.gz
> --08:57:25--  http://bioperl.org/DIST/current_ext_unstable.tar.gz
>           => `current_ext_unstable.tar.gz'
> Resolving bioperl.org... 65.246.187.176
> Connecting to bioperl.org|65.246.187.176|:80... connected.
> HTTP request sent, awaiting response... 200 OK
> Length: 398,120 (389K) [application/x-gzip]
> 
> 100%[====================================>] 398,120       98.74K/s
> ETA 00:00
> 
> 08:57:29 (98.51 KB/s) - `current_ext_unstable.tar.gz' saved [398120/398120]
> 
> $  tar -zxvf current_ext_unstable.tar.gz
> bioperl-ext-1.5.1/
> bioperl-ext-1.5.1/CVS/
> bioperl-ext-1.5.1/CVS/Root
> bioperl-ext-1.5.1/CVS/Repository
> bioperl-ext-1.5.1/CVS/Entries
> bioperl-ext-1.5.1/CVS/Tag
> bioperl-ext-1.5.1/Makefile.PL
> bioperl-ext-1.5.1/README
> bioperl-ext-1.5.1/Bio/
> bioperl-ext-1.5.1/Bio/CVS/
> bioperl-ext-1.5.1/Bio/CVS/Root
> bioperl-ext-1.5.1/Bio/CVS/Repository
> bioperl-ext-1.5.1/Bio/CVS/Entries
> bioperl-ext-1.5.1/Bio/CVS/Tag
> bioperl-ext-1.5.1/Bio/Ext/
> bioperl-ext-1.5.1/Bio/Ext/CVS/
> bioperl-ext-1.5.1/Bio/Ext/CVS/Root
> bioperl-ext-1.5.1/Bio/Ext/CVS/Repository
> bioperl-ext-1.5.1/Bio/Ext/CVS/Entries
> bioperl-ext-1.5.1/Bio/Ext/CVS/Tag
> bioperl-ext-1.5.1/Bio/Ext/Align/
> bioperl-ext-1.5.1/Bio/Ext/Align/CVS/
> bioperl-ext-1.5.1/Bio/Ext/Align/CVS/Root
> bioperl-ext-1.5.1/Bio/Ext/Align/CVS/Repository
> bioperl-ext-1.5.1/Bio/Ext/Align/CVS/Entries
> bioperl-ext-1.5.1/Bio/Ext/Align/CVS/Tag
> bioperl-ext-1.5.1/Bio/Ext/Align/Align.pm
> bioperl-ext-1.5.1/Bio/Ext/Align/Align.xs
> bioperl-ext-1.5.1/Bio/Ext/Align/Makefile.PL
> bioperl-ext-1.5.1/Bio/Ext/Align/blosum45.mat
> bioperl-ext-1.5.1/Bio/Ext/Align/blosum50.mat
> bioperl-ext-1.5.1/Bio/Ext/Align/blosum62.bla
> bioperl-ext-1.5.1/Bio/Ext/Align/blosum62.mat
> bioperl-ext-1.5.1/Bio/Ext/Align/md_20.mat
> bioperl-ext-1.5.1/Bio/Ext/Align/test.pl
> bioperl-ext-1.5.1/Bio/Ext/Align/typemap
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/CVS/
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/CVS/Root
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/CVS/Repository
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/CVS/Entries
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/CVS/Tag
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/aln.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/aln.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/alnconvert.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/alnconvert.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/alnrange.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/alnrange.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/asciibtcanvas.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/asciibtcanvas.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/basematrix.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/basematrix.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/btcanvas.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/btcanvas.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/codon.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/codon.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/commandline.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/commandline.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/complexconsensi.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/complexconsensi.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/complexevalset.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/complexevalset.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/complexsequence.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/complexsequence.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/compmat.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/compmat.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/database.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dna.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dna.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dnamatrix.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dnamatrix.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dpalign.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dpalign.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dpenvelope.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dpenvelope.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dyna.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dynlibcross.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/dynlibcross.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/histogram.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/histogram.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/hscore.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/hscore.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/linesubs.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/linesubs.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/linspc.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/makefile
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/packaln.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/packaln.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/probability.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/probability.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/protein.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/protein.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/proteindb.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/proteindb.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/proteinsw.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/proteinsw.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/seqaligndisplay.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/seqaligndisplay.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/sequence.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/sequence.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/sequencedb.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/sequencedb.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/sw.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/sw_wrap.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/sw_wrap.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wisebase.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wiseconfig.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wiseconfig.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wiseerror.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wiseerror.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wisefile.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wisefile.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wisememman.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wisememman.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wiseoverlay.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wiseoverlay.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wiserandom.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wiserandom.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wisestring.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wisestring.h
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wisetime.c
> bioperl-ext-1.5.1/Bio/Ext/Align/libs/wisetime.h
> bioperl-ext-1.5.1/Bio/Ext/HMM/
> bioperl-ext-1.5.1/Bio/Ext/HMM/CVS/
> bioperl-ext-1.5.1/Bio/Ext/HMM/CVS/Root
> bioperl-ext-1.5.1/Bio/Ext/HMM/CVS/Repository
> bioperl-ext-1.5.1/Bio/Ext/HMM/CVS/Entries
> bioperl-ext-1.5.1/Bio/Ext/HMM/CVS/Tag
> bioperl-ext-1.5.1/Bio/Ext/HMM/HMM.pm
> bioperl-ext-1.5.1/Bio/Ext/HMM/HMM.xs
> bioperl-ext-1.5.1/Bio/Ext/HMM/Makefile.PL
> bioperl-ext-1.5.1/Bio/Ext/HMM/hmm.h
> bioperl-ext-1.5.1/Bio/Ext/HMM/hmmlib.c
> bioperl-ext-1.5.1/Bio/Ext/HMM/test.pl
> bioperl-ext-1.5.1/Bio/Ext/HMM/typemap
> bioperl-ext-1.5.1/Bio/SeqIO/
> bioperl-ext-1.5.1/Bio/SeqIO/CVS/
> bioperl-ext-1.5.1/Bio/SeqIO/CVS/Root
> bioperl-ext-1.5.1/Bio/SeqIO/CVS/Repository
> bioperl-ext-1.5.1/Bio/SeqIO/CVS/Entries
> bioperl-ext-1.5.1/Bio/SeqIO/CVS/Tag
> bioperl-ext-1.5.1/Bio/SeqIO/staden/
> bioperl-ext-1.5.1/Bio/SeqIO/staden/CVS/
> bioperl-ext-1.5.1/Bio/SeqIO/staden/CVS/Root
> bioperl-ext-1.5.1/Bio/SeqIO/staden/CVS/Repository
> bioperl-ext-1.5.1/Bio/SeqIO/staden/CVS/Entries
> bioperl-ext-1.5.1/Bio/SeqIO/staden/CVS/Tag
> bioperl-ext-1.5.1/Bio/SeqIO/staden/Makefile.PL
> bioperl-ext-1.5.1/Bio/SeqIO/staden/read.pm
> bioperl-ext-1.5.1/Bio/SeqIO/staden/test.pl
> bioperl-ext-1.5.1/t/
> bioperl-ext-1.5.1/t/CVS/
> bioperl-ext-1.5.1/t/CVS/Root
> bioperl-ext-1.5.1/t/CVS/Repository
> bioperl-ext-1.5.1/t/CVS/Entries
> bioperl-ext-1.5.1/t/CVS/Tag
> bioperl-ext-1.5.1/t/Test.pm
> bioperl-ext-1.5.1/t/basic.t
> bioperl-ext-1.5.1/t/data/
> bioperl-ext-1.5.1/t/data/CVS/
> bioperl-ext-1.5.1/t/data/CVS/Root
> bioperl-ext-1.5.1/t/data/CVS/Repository
> bioperl-ext-1.5.1/t/data/CVS/Entries
> bioperl-ext-1.5.1/t/data/CVS/Tag
> bioperl-ext-1.5.1/t/data/readtest.abi
> bioperl-ext-1.5.1/t/data/readtest.ctf
> bioperl-ext-1.5.1/t/data/readtest.exp
> bioperl-ext-1.5.1/t/data/readtest.pln
> bioperl-ext-1.5.1/t/data/readtest.ztr
> bioperl-ext-1.5.1/t/data/readtestabi.fa
> bioperl-ext-1.5.1/t/data/readtestref.scf
> 
> $ cd bioperl-ext-1.5.1/
> 
> $ perl Makefile.PL
> Writing Makefile for Bio::Ext::Align
> ERROR from evaluation of
> /home/java/perl/bioperl-ext-1.5.1/Bio/SeqIO/staden/Makefile.PL:
> Invalid version '' for Bio::SeqIO::staden::read.
> Must be of the form '#.##'. (For instance '1.23')
> at ./Makefile.PL line 4
> 
> It didn't make makefile
> 
> $ ls -a
> .  ..  Bio  CVS  Makefile.PL  README  t
> 
> 
> I guess that the problem above may not related to the bug I previously
> reported.
> I am sorry about minor information that I provided for bug report.
> I have only limited experiences about using perl and I have no
> experience about Perl
> Inline. I had no idea what kind information could be useful related to bug.
> 
> Regards,
> Jouni Väliaho
> 
> 
> Quoting bugzilla-daemon at portal.open-bio.org:
> 
>> http://bugzilla.open-bio.org/show_bug.cgi?id=1837
>> 
>> 
>> osborne1 at optonline.net changed:
>> 
>>           What    |Removed                     |Added
>> ----------------------------------------------------------------------------
>>             Status|NEW                         |RESOLVED
>>         Resolution|                            |WORKSFORME
>> 
>> 
>> 
>> 
>> ------- Comment #1 from osborne1 at optonline.net  2005-12-15 09:38 -------
>> Jouni, thank you for the submission. I think that I'll close this bug as I've
>> been able to install bioperl-ext without the manual copy you used. Without a
>> bit more information it's difficult to determine what went wrong with your
>> install and since everything works for you now...
>> 
>> 
>> 
>> 
>> ------- You are receiving this mail because: -------
>> You reported the bug, or are watching the reporter.
>> 
> 
> 
> 
> --------------------------------------------------------------------
> Jouni Väliaho, Research scientist       Phone: +358-3-215 8916
> Institute of Medical Technology         Fax: +358-3-215 7710
> FI-33014 University of Tampere          E-mail: jouni.valiaho at uta.fi
> Finland                                 http://bioinf.uta.fi/
> --------------------------------------------------------------------





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