Errors when reproducing on Ubuntu 13.10

[ethanwhite]

After fixing the first round of issues this morning I've run into some more. Here's the full output including the error messages:

ethan@natasha:~/mete-spatial (master)$ Rscript ddr_run_all.R 
[1] "Analysis Begin"
[1] "Downloading datasets, ..."
Loading required package: methods
Loading required package: bitops
[1] "Oosting_Trees_1998.txt was downloaded and written to ./data/raw_data/Oosting_Trees_1998.txt"
[1] "FERP07data.csv was downloaded and written to ./data/raw_data/FERP07data.csv"
[1] "Downloading datasets, complete!"
[1] "Finding and exporting site names, ..."
[1] "Finding and exporting site names, complete!"
[1] "Filtering and cleaning empirical data, ..."
[1] "Filtering and cleaning empirical data, complete!"
[1] "Creating site x species matrices, ..."
[1] "Creating site x species matrices, complete!"
[1] "Computing empirical SAD, ..."
[1] "Computing empirical SAD, complete!"
[1] "Exporting empirical data summaries, ..."
[1] "Exporting empirical data summaries, complete!"
[1] "Submitting jobs to simulate empirical communities under METE, ..."
[1] "Submitting jobs to simulate empirical communities under METE, complete!"
[1] "Submitting jobs to compute the empirical DDRs, ..."
[1] "Submitting jobs to compute the empirical DDRs, complete!"
[1] "Submitting jobs to compute the METE simulated DDRs, ..."
[1] "Submitting jobs to compute the METE simulated DDRs, complete!"
[1] "Aggregating and exporting the empirical DDR results, ..."
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: getResults -> load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file './sorensen/sorensen_ucsc_bisect_abu_indivRPM.Rdata', probable reason 'No such file or directory'
Execution halted
[1] "Aggregating and exporting the simulated DDR results, ..."
[1] "Aggregating and exporting the simulated DDR results, complete!"
[1] "Comparing empirical and METE DDR, ..."
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file './sorensen/empirSorBin_bisect.Rdata', probable reason 'No such file or directory'
Execution halted
[1] "Generating figures, ..."
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file './sorensen/empirSorAbu_bisect.Rdata', probable reason 'No such file or directory'
Execution halted
[1] "Figures are stored in the directory ./figs/"
[1] "Analysis Complete"
   user  system elapsed 
300.711  32.572 346.521 

[ethanwhite]

Closing the duplicate.