[Bioperl-l] bioperl-ext make problems

[Aaron J. Mackey]

So do you actually have the Staden io-lib "Read" library installed?  If 
not, this isn't going to work.

-Aaron

Patrice Seyed wrote:

> Here goes:
> 
> ~] sudo perl -MCPAN -eshell
> Undefined value assigned to typeglob at (eval 16) line 15, <RC> line 11.
> Warning [/etc/inputrc line 11]:
>   Invalid variable `mark-symlinked-directories'
> 
> cpan shell -- CPAN exploration and modules installation (v1.7601)
> ReadLine support enabled
> 
> cpan>
> 
> after typing "look Bio::Ext::Align" it scanned cache and then dumped into:
> Removing previously used /root/.cpan/build/bioperl-ext-1.4
> Working directory is /root/.cpan/build/bioperl-ext-1.4
> <prompt>
> 
> # perl Makefile.PL
> Checking if your kit is complete...
> Looks good
> Writing Makefile for Bio::Ext::Align
> Please tell us where your Staden io_lib "read" library is installed:
> [/usr/local/lib]
> Please tell us where your Staden io_lib "Read.h" header is installed:
> [/usr/local/include/io_lib]
> Writing Makefile for Bio::SeqIO::staden::read
> Writing Makefile for Bio
> One or more DATA sections were not processed by Inline.
> 
> "make" ended like this:
> 
> read.xs:91: request for member `NBases' in something not a structure or
> union
> read.xs:91: request for member `NBases' in something not a structure or
> union
> read.xs:93: request for member `base' in something not a structure or union
> read.xs:94: request for member `prob_A' in something not a structure or
> union
> read.xs:94: request for member `prob_C' in something not a structure or
> union
> read.xs:95: request for member `prob_G' in something not a structure or
> union
> read.xs:95: request for member `prob_T' in something not a structure or
> union
> read.xs:144: request for member `ident' in something not a structure or
> union
> read.xs:145: request for member `info' in something not a structure or union
> make[2]: *** [read.o] Error 1
> make[2]: Leaving directory
> `/root/.cpan/build/bioperl-ext-1.4/Bio/SeqIO/staden/_
> Inline/build/Bio/SeqIO/staden/read'
> 
> A problem was encountered while attempting to compile and install your
> Inline
> C code. The command that failed was:
>   make
> 
> The build directory was:
> /root/.cpan/build/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/s
> tade
> n/read
> 
> To debug the problem, cd to the build directory, and inspect the output
> files.
> 
>  at -e line 0
> INIT failed--call queue aborted.
> make[1]: *** [read.inl] Error 2
> make[1]: Leaving directory
> `/root/.cpan/build/bioperl-ext-1.4/Bio/SeqIO/staden'
> make: *** [subdirs] Error 2
> 
> 
> 
> -Patrice
> 
> -----Original Message-----
> From: Aaron J. Mackey [mailto:amackey at pcbi.upenn.edu] 
> Sent: Monday, February 07, 2005 11:22 AM
> To: Patrice Seyed
> Cc: bioperl-l
> Subject: Re: [Bioperl-l] bioperl-ext make problems
> 
>  From the CPAN prompt, type "look Bio::Ext::Align".  Then: "perl 
> Makefile.PL; make; make test" and see if you get more descriptive error 
> messages.  From your report we can't really figure out what's going on.
> 
> -Aaron
> 
> On Feb 7, 2005, at 10:01 AM, Patrice Seyed wrote:
> 
> 
>>Hello,
>>
>>I'm getting error when trying to install bioperl-ext, wondering if you 
>>could
>>point me in the right direction. I run -eshell and -MCPAN, and then 
>>try to
>>install the module:
>>
>>CPAN.pm: Going to build B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
>>
>>Checking if your kit is complete...
>>Looks good
>>Writing Makefile for Bio::Ext::Align
>>ERROR from evaluation of
>>/root/.cpan/build/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't 
>>locate
>>Inline/MakeMaker.pm in @INC (@INC contains:
>>/usr/local/IT/perl-5.8.6/lib/5.8.6/i686-linux
>>/usr/local/IT/perl-5.8.6/lib/5.8.6
>>/usr/local/IT/perl-5.8.6/lib/site_perl/5.8.6/i686-linux
>>/usr/local/IT/perl-5.8.6/lib/site_perl/5.8.6
>>/usr/local/IT/perl-5.8.6/lib/site_perl 
>>/root/.cpan/build/bioperl-ext-1.4 .)
>>at ./Makefile.PL line 1.
>>BEGIN failed--compilation aborted at ./Makefile.PL line 1.
>>Running make test
>>  Make had some problems, maybe interrupted? Won't test
>>Running make install
>>  Make had some problems, maybe interrupted? Won't install
>>
>>
>>I then installed I/IN/INGY/Inline-0.44.tar.gz without complaint, and 
>>tried
>>again:
>>
>>cpan> install B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
>>Running make for B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
>>  Is already unwrapped into directory /root/.cpan/build/bioperl-ext-1.4
>>  Makefile.PL returned status 512
>>Running make test
>>  Make had some problems, maybe interrupted? Won't test
>>Running make install
>>  Make had some problems, maybe interrupted? Won't install
>>
>>
>>Another thing worth noting is that I had to do a force install for 
>>bioperl,
>>bioperl-run, bioperl-db, bioperl-microarray, and bioperl-gui, because 
>>of
>>make test errors for each one. I am running perl v5.8.6 and RHEL 3 
>>variant
>>with the 2.4.21-4.0.1.ELsmp kernel. Thanks in advance for any tips of 
>>this
>>problem or getting around this type of problem.
>>
>>Patrice
>>
>>Patrice Seyed
>>Linux System Administrator - LinGA
>>RHCE, SCSA
>>Boston University Medical Campus
>>
>>
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> 
> --
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  amackey at pcbi.upenn.edu
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
> 
> 
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