[Bioperl-l] bioperl-ext installation

Renxue Wang rwang at bccrc.ca
Mon Nov 28 14:20:00 EST 2005

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


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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