[Bioc-devel] Perl version issue with building Rhtslib

[Martin Morgan]

Hi Dinakar -- your patch didn't make it through the mailing list; can 
you forward it to me directly? Thanks, Martin

On 03/17/2017 12:45 PM, Dinakar Kulkarni wrote:
> 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.
>


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