[Bioperl-l] bioperl-ext make problems

[Patrice Seyed]

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