help interpreting and diagnosing errors in r4ss::SS_output()

[Brooke Lowman]

Hello,

I am working on getting an initial run of my assessment running with a subset of data sources. I have an (at least mostly) functional run (not converged on a solution, but it appears that the data are being read correctly, and output files are generated). When I attempt to read the outputs using r4ss::SS_outputs(), I get an error message: 

warning.sso file is missing the string 'N warnings'
Finished reading files
Error in 1:grep("fleet_name", tolower(names(fleetdefs))) :
  argument of length 0
In addition: Warning messages:
1: In SS_output(croaker_SS_dir) :
  Some stats skipped because the .cor file not found:C:/StockSynthesis/Croaker2026_MidAtl/BASE_MidAtl_2026/ss3.cor

2: In SS_output(croaker_SS_dir) : covar file contains the warning
     'Variances are 0.0 for first two elements, so do not write '
  input 'covar' changed to FALSE.

I have reviewed the echoinput.sso and Report.sso files and see that my fleet names show up as expected, so I'm struggling to understand the error message about argument of length 0 in grep(fleet_name, ...)

I am using stock synthesis v3.30.23.2

Any insight would be greatly appreciated. Thank you!

Brooke

[Kelli Johnson]

What version of r4ss are you using? The one on CRAN is outdated. Please install the GitHub version from r4ss/r4ss.

[Brooke Lowman]

Ah, yes, that fixed it. Thank you!