Problem running AliTV

[Daniel-Ze]

Hi, I'm encountering a problem trying to run AliTV and i can't figure out what the problem is.

Daniels-MBP:~ daniel$ perl /Users/daniel/Documents/GIT/AliTV/AliTV-perl-interface/bin/alitv.pl --project test advanced /Users/daniel/Sequenzen/test/test.yml `

Can't locate FindBin/Real.pm in @INC (you may need to install the FindBin::Real module)
(@INC contains: 
/Users/daniel/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level
/Users/daniel/anaconda3/lib/site_perl/5.26.2 
/Users/daniel/anaconda3/lib/5.26.2/darwin-thread-multi-2level 
/Users/daniel/anaconda3/lib/5.26.2 
.)
at /Users/daniel/Documents/GIT/AliTV/AliTV-perl-interface/bin/alitv.pl line 6.
BEGIN failed--compilation aborted at /Users/daniel/Documents/GIT/AliTV/AliTV-perl-interface/bin/alitv.pl line 6.

The mentioned module seems to be installed and up to date.

Daniels-MBP:~ daniel$ sudo cpanm install FindBin::Real
Password:
install is up to date. (0.01)
FindBin::Real is up to date. (1.05)

However if i try to find it's path it seems not to be working.

Daniels-MacBook-Pro:~ daniel$ perl -MFindBin::Real -e'print $_ . " => " . $INC{$_} . "\n" for keys %INC'
Can't locate FindBin/Real.pm in @INC (you may need to install the FindBin::Real module) 
(@INC contains: 
/Users/daniel/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level
/Users/daniel/anaconda3/lib/site_perl/5.26.2 
/Users/daniel/anaconda3/lib/5.26.2/darwin-thread-multi-2level 
/Users/daniel/anaconda3/lib/5.26.2 
.).
BEGIN failed--compilation aborted.

The installation of dependencies seems also to be fine.

Daniels-MacBook-Pro:AliTV-perl-interface daniel$ sudo cpanm -v --installdeps .
cpanm (App::cpanminus) 1.7044 on perl 5.018002 built for darwin-thread-multi-2level
Work directory is /Users/daniel/.cpanm/work/1535100358.27017
You have make /usr/bin/make
You have LWP 6.35
You have /usr/bin/tar: bsdtar 2.8.3 - libarchive 2.8.3
You have /usr/bin/unzip
--> Working on .
Entering /Users/daniel/Documents/GIT/AliTV/AliTV-perl-interface
Running Makefile.PL
Configuring /Users/daniel/Documents/GIT/AliTV/AliTV-perl-interface ... Generating a Unix-style Makefile
Writing Makefile for AliTV
Writing MYMETA.yml and MYMETA.json
OK
Checking dependencies from MYMETA.json ...
Checking if you have version 0.77 ... Yes (0.9902)
Checking if you have File::Copy 0 ... Yes (2.26)
Checking if you have File::Basename 0 ... Yes (2.84)
Checking if you have Bio::AlignIO 0 ... Yes (undef)
Checking if you have Storable 0 ... Yes (3.11)
Checking if you have FindBin::Real 0 ... Yes (1.05)
Checking if you have JSON 0 ... Yes (2.97001)
Checking if you have YAML 0 ... Yes (1.26)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have Test::Exception 0 ... Yes (0.43)
Checking if you have Bio::Root::Version 0 ... Yes (1.007002)
Checking if you have File::Path 0 ... Yes (2.09)
Checking if you have Bio::TreeIO 0 ... Yes (undef)
Checking if you have File::Which 0 ... Yes (1.22)
Checking if you have Test::Exit 0 ... Yes (0.11)
Checking if you have IPC::System::Simple 0 ... Yes (1.25)
Checking if you have Test::Warnings 0 ... Yes (0.026)
Checking if you have Hash::Merge 0 ... Yes (0.200)
Checking if you have Log::Log4perl 0.28 ... Yes (1.49)
Checking if you have Digest::MD5 0 ... Yes (2.52)
Checking if you have POSIX 0 ... Yes (1.32)
Checking if you have Bio::SeqIO 0 ... Yes (undef)
Checking if you have Bio::Tree::TreeI 0 ... Yes (undef)
Checking if you have Bio::Seq 0 ... Yes (undef)
Checking if you have File::Temp 0 ... Yes (0.2308)
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.34)
Checking if you have Bio::Tree::Node 0 ... Yes (undef)
<== Installed dependencies for .. Finishing.

I'm happy about every help that I can get concerning this topic!

Best regards Daniel

[Daniel-Ze]

Solved this problem but encountered a new one.

Solution for above: The MacOS Perl 5.18 path was not in INC

export PERL5LIB=PERL5LIB:/Library/Perl/5.18/

This solved the problem.

Sadly i encounter a new problem after solving this.

Segmentation fault: 11

This is the only error message that I get. Did somebody else encounter this?

Best regards Daniel

[Daniel-Ze]

This issue can be closed. The installation of Anaconda interfered with the Perl version of MacOS on more levels. Uninstallation of Anaconda solved the problem.

Best regards

[iimog]

Hey Daniel,

thanks for reporting and for the follow up. We'll keep in mind that Anaconda may interfere with the Perl version of MacOS in case someone else bumps into this. Feel free to open a new issue if you encounter another problem.

Best regards, Markus