[Bioperl-l] bioperl-ext installation

[Renxue Wang]

Hi, There,

 

I am trying to install bioperl-ext package, but the hit a lot of
problems. We follow the instructions of README and some points in some
web postings, but it did not go through properly. I thought someone
might have some better ideas on what is going on there and what to do
next. Would you let me know if you do? I attach the error messages
below. 

 

Thanks a lot, 

 

Renxue

 

_______________________________________________________________

Here is what I got,

 

> perl Makefile.PL

Writing Makefile for Bio::Ext::Align

Found Staden io_lib "libread" in /usr/local/lib ...

Automatically using the Read.h found in /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.

 

[root at VLING010 bioperl-ext]#

 

also, in "make", I got this in the end,

 

read.xs:145: request for member `info' in something not a structure or
union

make[2]: *** [read.o] Error 1

make[2]: Leaving directory
`/home/hok/bioperl-ext/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/r
ead'

 

A problem was encountered while attempting to compile and install your
Inline

C code. The command that failed was:

  make

 

The build directory was:

/home/hok/bioperl-ext/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/re
ad

 

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 `/home/hok/bioperl-ext/Bio/SeqIO/staden'

make: *** [subdirs] Error 2

 

in "make test", this came up,

 

[root at VLING010 Align]# make test

PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl

1..9

# Running under perl version 5.008 for linux

# Current time local: Thu Nov 17 13:21:45 2005

# Current time GMT:   Thu Nov 17 21:21:45 2005

# Using Test.pm version 1.23

Can't locate Bio/Ext/Align.pm in @INC (@INC contains: blib/lib blib/arch
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at
test.pl line 14.

BEGIN failed--compilation aborted at test.pl line 14.

make: *** [test_dynamic] Error 2

[root at VLING010 Align]#

 

I ignored these and went ahead with make install. The program did not
work with my alignment script using Bio::Tools::pSW. Seems some
components (here "blosum62.bla") was not installed properly.

 

[root at VLING010 melan_simu4th]# ./align.pl test.ORTH test

Warning Error

        Could not open blosum62.bla as a filename for read Blast matrix

 

------------- EXCEPTION  -------------

MSG: blosum62.bla cannot be read as a BLAST comparison matrix file

STACK Bio::Tools::pSW::matrix
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/pSW.pm:360

STACK Bio::Tools::pSW::new
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/pSW.pm:155

STACK toplevel ./align.pl:11

 

--------------------------------------

[root at VLING010 melan_simu4th]#