Align.so: undefined symbol & symbol lookup error

daniel20091 has asked for the wisdom of the Perl Monks concerning the following question:

Hi All,

I am running a perl script on a web server. I am getting the error in the httpd error log file:

/usr/bin/perl: symbol lookup error: /usr/local/lib64/perl5/auto/Bio/Ex
+t/Align/Align.so: undefined symbol: bp_sw_read_Blast_file_CompMat, re
+ferer: http://XX/model_select.pl
[download]

I checked some of the forums and did this:

############################

cpanp -i /usr/local/lib64/perl5/auto/Bio/Ext/Align/Align.so
[ERROR] '/usr/local/lib64/perl5/auto/Bio/Ext/Align/Align.so' does not 
+contain an author part
[ERROR] Cannot find '/usr/local/lib64/perl5/auto/Bio/Ext/Align/Align.s
+o' in the module tree
No such module: /usr/local/lib64/perl5/auto/Bio/Ext/Align/Align.so
No modules found to operate on!
Nothing done
[download]

############################

I checked, "Align.so" exists in the path shown in the error message

Can someone please help me solve the problem. Thanks much, Dany

Comment on Align.so: undefined symbol & symbol lookup error Select or Download Code

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Re: Align.so: undefined symbol & symbol lookup error by Corion (Patriarch) on Sep 25, 2017 at 15:15 UTC
I checked some of the forums and did this: `cpanp -i /usr/local/lib64/perl5/auto/Bio/Ext/Align/Align.so` [download] Why did you do this and what did you want to achieve? If you want to install a module, it is easiest to name the module explicitly: `cpanp -i Bio::Ext::Align` [download] But it seems that you already have Bio::Ext::Align installed but it breaks on your system because of some symbols not getting found. Who did build that instance of Bio::Ext::Align and with what version of Perl did they build it (resp. against which version of the Blast libraries did they build it?).	[reply] [d/l] [select]

Replies are listed 'Best First'.

Re: Align.so: undefined symbol & symbol lookup error
by Corion (Patriarch) on Sep 25, 2017 at 15:15 UTC

I checked some of the forums and did this:
cpanp -i /usr/local/lib64/perl5/auto/Bio/Ext/Align/Align.so
[download]

Why did you do this and what did you want to achieve?

If you want to install a module, it is easiest to name the module explicitly:

cpanp -i Bio::Ext::Align
[download]

But it seems that you already have Bio::Ext::Align installed but it breaks on your system because of some symbols not getting found. Who did build that instance of Bio::Ext::Align and with what version of Perl did they build it (resp. against which version of the Blast libraries did they build it?).

[reply]
[d/l]
[select]