[Bioc-devel] Perl version issue with building Rhtslib

[Dinakar Kulkarni]

Hello,

The following error was generated while attempting to install the "Rhtslib"
package in R v3.3.2:

/usr/bin/perl: symbol lookup error: /perl-modules/5.18.2/1.142660/x86_64-
linux-2.6-rhel6/lib/perl5/x86_64-linux-thread-multi/auto/List/Util/Util.so:
undefined symbol: Perl_xs_apiversion_bootcheck

WARNING: 'autoconf' is missing on your system.

         You should only need it if you modified 'configure.ac',

         or m4 files included by it.

         The 'autoconf' program is part of the GNU Autoconf package:

         <http://www.gnu.org/software/autoconf/>

         It also requires GNU m4 and Perl in order to run:

         <http://www.gnu.org/software/m4/>

         <http://www.perl.org/>

make[1]: *** [configure] Error 127

make[1]: Leaving directory `/tmp/Rtmpn6FFZH/R.INSTALL671e
4ed4c86d/Rhtslib/src/htslib'

make: *** [htslib/libhts.la] Error 2

ERROR: compilation failed for package ‘Rhtslib’

On further investigation, I was able to determine that the default Perl
version on the OS (RHEL 6.6) was v5.10.1, so it turned out to be an
incompatibility issue.

I looked into the source for Rhtslib and see that it use these 3 Perl
scripts:

Rhtslib/src/htslib/test/compare_sam.pl
Rhtslib/src/htslib/test/test.pl
Rhtslib/src/htslib/test/test_view.pl

and they use the default env Perl. I believe that it would be better to
specify the Perl version within these scripts(i.e. use v5.18.2) for
compiling/building the package. I've attached suggested patch files here
for the same.

Thanks,
Dinakar.

-- 
Dinakar Kulkarni
Genentech, Inc.
kulkarni.dinakar at gene.com