server error with working directory

[EmmalineSheahan]

I was trying to analyze the simulations, but the code we added didn't show up in the output of the analyze_sim function, so I guess it didn't run, but when I tried to run it i found out their initial code jacks the working directory all up because of this in the analysis_workflow code:

#New parameter for taking into account which of us is running this code
if(Allen==1) {
  setwd('c:/documents and settings/hurlbert/species-energy-simulation')
  Rlib.location = "C:/program files/R/R-2.15.2/library"
  sim_dir = "C:/SENCoutput"
  analysis_dir = "//bioark.bio.unc.edu/hurlbertallen/manuscripts/cladevscommunity/analyses"
} else {
  setwd('C:/Users/steg815/Desktop/Stegen_PNNL/Spp-Energy-Niche-Conserv/species-energy-simulation')
  sim_dir = "C:/Users/steg815/Desktop/Stegen_PNNL/Spp-Energy-Niche-Conserv/sims.out.130204" #wherever all of your zipped output files are
  analysis_dir = "C:/Users/steg815/Desktop/Stegen_PNNL/Spp-Energy-Niche-Conserv/sims.out.130204" #wherever you want to store the results of these analyses
}

but now the server is freaking out, because it won't tell me what working directory I'm in, and it won't let me use setwd() to set a working directory

[dmcglinn]

Bummer - that's pretty unfortunate coding on their side. I'll take a look at the server and see what I can see.

[dmcglinn]

The file simulation/species-energy-simulation/raw_sim_output/log.txt suggests that the simulations did complete.

Starting sim 3465 , Thu Apr 12 00:21:35 2018 
Starting sim 3466 , Thu Apr 12 00:21:35 2018 
Starting sim 3467 , Thu Apr 12 00:21:35 2018 
Starting sim 3468 , Thu Apr 12 00:21:35 2018 
Starting sim 3469 , Thu Apr 12 00:21:35 2018 
Starting sim 3471 , Thu Apr 12 00:21:35 2018 
Starting sim 3470 , Thu Apr 12 00:21:35 2018 
Starting sim 3472 , Thu Apr 12 00:21:35 2018 
Starting sim 3474 , Thu Apr 12 00:21:35 2018 
Starting sim 3473 , Thu Apr 12 00:21:35 2018 
Finished sim 3468 , Thu Apr 12 00:44:10 2018 
Finished sim 3474 , Thu Apr 12 00:44:17 2018 
Finished sim 3469 , Thu Apr 12 00:44:26 2018 
Finished sim 3471 , Thu Apr 12 00:44:39 2018 
Finished sim 3467 , Thu Apr 12 00:44:41 2018 
Finished sim 3472 , Thu Apr 12 00:44:52 2018 
Finished sim 3465 , Thu Apr 12 00:44:57 2018 
Finished sim 3470 , Thu Apr 12 00:44:58 2018 
Finished sim 3466 , Thu Apr 12 00:45:00 2018 
Finished sim 3473 , Thu Apr 12 00:45:10 2018 

I had no problem with getwd() maybe just try again? Let me know if you still have trouble.

Dan