It seems that the source package from github devtools::install_github("flr/FLAssess") also provides the binary. The build command doesn't find anything and tries to install the binary library, which contains a broken reference:

$ strings -a FLAssess.so | grep /home
/home/mosquia/R/x86_64-pc-linux-gnu-library/3.3/FLash/libs//FLash.so

Warning: namespace ‘FLAssess’ is not available and has been replaced
by .GlobalEnv when processing object ‘nhke’
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/FLAssess/libs/FLAssess.so':
/home/mosquia/R/x86_64-pc-linux-gnu-library/3.3/FLash/libs//FLash.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed

• removing ‘/usr/local/lib/R/site-library/FLAssess’
  Error: Command failed (1)

If the example in VPA.Rd is run, abundances are only calculated back to 2003 for all ages, and then the cohort starts disappearing.

I'm getting a cryptic error regarding possible dimension mis-match when combining the results of VPA with the original FLStock object.

> tmp <- VPA(stock, fratio = 1)
> stock <- stock + tmp
Error in !all.equal(dnx[c(-2, -6)], dny[c(-2, -6)]) : 
  invalid argument type

Any idea what the problem might be?