Compilation Woes

[ghost]

Hello! I hope you are well -- I am unfamiliar with Perl, and having some trouble compiling SHAPEwarp on Ubuntu 18.04. When I run make I get this as the output: "/usr/bin/perl" -MFFI::Build::MM=cmd -e fbx_build

Which in itself I don't know is a good / bad thing. But when I run make test it fails, and I get this: t/basic.t .. Can't locate Core/Utils.pm in @ INC (you may need to install the Core::Utils module)

Which I'm pretty sure is not super great. So naturally (or naively) I tried to install Core::Utils in Perl (install Core::Utils), but it doesn't seem to be able to find it (which makes sense, I gather). I looked a little deeper into the error message from make test and saw this: BEGIN failed--compilation aborted at .../SHAPEwarp/blib/lib/SW/KmerLookup.pm line 4

Which looking at KmerLookup.pm line 4 reads: use Core::Utils, and I have officially gone full circle. When I run ./swKmerLookup with the input from issue #4 on the github I get a new error though: Can't locate Core/Mathematics.pm in @ INC (you may need to install the Core::Mathematics module) ... BEGIN failed--compilation aborted at ./swKmerLookup line 10

Which when looking at, seems to call: use Core::Mathematics

Which, similar to Core::Utils, doesn't seem to be a CPAN package / something I can locate.

I assume I'm missing something pretty basic here. I made sure to install all the prerequisites, and RNAFramework is in my PATH (and the PERL5LIB). The other issue on the github re: compilation errors says it took some messing around with Perl install to fix, but I figured I'd check here before I start blindly playing around with Perl stuffs.

Let me know if I can provide any other relevant information -- and thank you! Lucy

[dincarnato]

Dear Lucy,

please refer to the docs and the README. As stated there:

SHAPEwarp builds on top of the RNA Framework. To use SHAPEwarp, the lib/ folder of the RNA Framework must be added to the PERL5LIB environment variable:

export PERL5LIB=$PERL5LIB:/path/to/RNAFramework/lib

Hope this helps, Danny

[ghost]

Hi Danny,

Thank you for the quick reply! Like I mentioned, I have already linked RNAFramework/lib to my PERL5LIB. I tried recompiling RNAFrameworks, as well as all the other prerequisites, and still get the same error on make test.

I assume it is something wrong with either my RNAFrameworks, Perl, or some other missing prereq / mismatched compiler version or something. I'll go looking around their documentation to see if I messed something up / missed a prereq.

Thank you for the help! Lucy

[dincarnato]

You might have multiple Perl installs on your system

[ghost]

I couldn't really track the issue down. I ended up compiling SHAPEwarp successfully on a different machine following all the same steps. Something about the environment of the first machine might have been jumbling things up -- unsure.

Anyway, thank you -- I appreciate the fast replies. Lucy