> On Oct 19, 2015, at 23:47, Areej S. Alsheikh <areej.alshe...@gmail.com> 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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