> On Oct 19, 2015, at 23:47, Areej S. Alsheikh <[email protected]> wrote:
>
> Hi,
>
> I'm trying to install bioperl on my Mac using fink.. The main issue I was
> having is that I'm not able to run a particular Bioperl script called:
> bp_genbank2gff3.pl <http://bp_genbank2gff3.pl/> as I keep getting the
> following error message:
> Can't locate YAML.pm in @INC (@INC contains: blib/lib
> /Users/Areej/bioperl-live /sw/lib/perl5/5.16.2/darwin-thread-multi-2level
> /sw/lib/perl5/5.16.2 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5
> /sw/lib/perl5/darwin /Library/Perl/5.16/darwin-thread-multi-2level
> /Library/Perl/5.16 /Network/Library/Perl/5.16/darwin-thread-multi-2level
> /Network/Library/Perl/5.16
> /Library/Perl/Updates/5.16.2/darwin-thread-multi-2level
> /Library/Perl/Updates/5.16.2
> /System/Library/Perl/5.16/darwin-thread-multi-2level
> /System/Library/Perl/5.16
> /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.16 .) at /usr/local/bin/bp_genbank2gff3.pl
> <http://bp_genbank2gff3.pl/> line 224.
> BEGIN failed--compilation aborted at /usr/local/bin/bp_genbank2gff3.pl
> <http://bp_genbank2gff3.pl/> line 224.
>
> So I rebuild bioperl using fink:
> fink rebuild bioperl-pm5162
>
> At the end of the build I see Failed: phase compiling .... (see title).
>
> The output display is attached in a text file. Thank you for your help.
>
> Areej
> <fink_run_rebuilding_bioperl.txt>———————————————————————————————————————
We prefer NOT to have attachments, because that makes threads on the list
archives harder to follow.
There is a message in the output that tells you exactly what the problem is and
what you are supposed to do:
Scanning binaries for incorrect dyld linking...
./blib/arch/auto/Tk/PNG/PNG.bundle uses
/usr/local/lib/libpng16.16.dylib
There are files installed in /usr/local on your computer that are
known to interfere with building some Fink packages. Try temporarily
renaming or moving /usr/local while Fink is compiling a package. See
http://fink.sourceforge.net/faq/comp-general.php#usr-local-libs for
more information.
--
Alexander Hansen, Ph.D.
Fink User Liaison
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