[BiO BB] bioperl-ext installation

Renxue Wang rwang at bccrc.ca
Mon Nov 28 14:25:43 EST 2005

Hi, There,

I am trying to install bioperl-ext package on my Redhat 9.0, but the hit
a lot of problems. I followed the instructions of README and some points
in some web postings, but it did not go through. I thought someone might
have some better ideas on what is going on there and what I should do.
Would you let me know if you do? I attach the error messages below. 

Thanks a lot, 


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
make[2]: *** [read.o] Error 1
make[2]: Leaving directory
A problem was encountered while attempting to compile and install your
C code. The command that failed was:
The build directory was:
To debug the problem, cd to the build directory, and inspect the output
 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
# 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 /usr/lib/perl5/site_perl
/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
STACK Bio::Tools::pSW::new
STACK toplevel ./align.pl:11
[root at VLING010 melan_simu4th]#

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