search

christianparobek / skeleSim

Null models, performance testing, and power estimation with population simulations
3 stars 6 forks source link

Cannot find fsc executable #51

Closed christianparobek closed 8 years ago

christianparobek commented 8 years ago

Not sure if this is a bug or a system problem, but it's something I've all of a sudden started encountering. When I run any given sim it doesn't produce a results-containing Rdata file. So I worked through the script.R file and when I ran the ssClass <- runSim(ssClass) command I got back this:

sh: 1: fsc252: not found
Error in fastsimcoal(pop.info = fscPopInfo(pop.size = sc@pop.size, sample.size = sc@sample.size,  : 
  fastsimcoal exited with error 127

When I tab out which fsc on my system it returns which fsc25221, which makes me think I still have fsc installed, just that skeleSim is looking for fsc252 instead. Oddly, in the GUI, under "Select fastsimcoal executable", fsc25221 is the default. I've tried tracking this down using ui.R as a starting point, but no luck.

Thoughts?

stranda commented 8 years ago

can you look at the current ssClass tab in the GUI and see what fsc version is actually listed in the fastsimcoal.exec slot? Also, see if you can change it with the pulldown.

On Thu, Apr 21, 2016 at 1:27 PM, Christian Parobek <notifications@github.com

wrote:

Not sure if this is a bug or a system problem, but it's something I've all of a sudden started encountering. When I run any given sim it doesn't produce a results-containing Rdata file. So I worked through the script.R file and when I ran the ssClass <- runSim(ssClass) command I got back this:

sh: 1: fsc252: not found Error in fastsimcoal(pop.info = fscPopInfo(pop.size = sc@pop.size, sample.size = sc@sample.size, : fastsimcoal exited with error 127

When I tab out which fsc on my system it returns which fsc25221, which makes me think I still have fsc installed, just that skeleSim is looking for fsc252 instead. Oddly, in the GUI, under "Select fastsimcoal executable", fsc25221 is the default. I've tried tracking this down using ui.R as a starting point, but no luck.

Thoughts?

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/51

Allan Strand, Biology http://linum.cofc.edu College of Charleston Ph. (843) 953-9189 Charleston, SC 29424 Fax (843) 953-9199

christianparobek commented 8 years ago

Ah, interesting find! Wow this is super weird. Even though it said fsc25221 in the dropdown menu, it said fsc252 in the ssClass. Then when I erased and retyped fsc25221 in the dropdown menu, it now populates as fsc25221 in the ssClass object.

Maybe this is just my computer being flaky. I suppose we can keep this in mind, but works for now!

Thanks!

christianparobek commented 8 years ago

I'm reopening this because this has still been giving me problems (though I haven't tried in last 24 hours) and because I just found a clue...

In the fsc.classes.R file, I found this: fastsimcoal.exec = "fsc252".

Is there a reason that it says fsc252 rather than fsc25221? If not, perhaps changing this would help solve the problem?

stranda commented 8 years ago

I'll take another look at this.

thierrygosselin commented 8 years ago

Not sure if it's normal behaviour.

Currently on macOS you need to have fastsimcoal binary, currently fsc25221 in /usr/local/bin otherwise if it's just in the PATH (e.g. through .bash_profile) it just won't show in the FastSimCoal Params tab.

EricArcher commented 8 years ago

The installation vignette has been updated to indicate that the fastsimcoal binary needs to be in /usr/local/bin. I need to work on this with the system call in strataG to make it operate from folders in the PATH as desired.