"negative length vectors are not allowed" error message when using R studio

Hello,

I have been using R and R studio since quite a few years, however, I am a "user" rather than a developer. I do not create packages, but do write my own scripts.
For work I am using packages developed by FLR project (a fisheries science suite of statistical methods etc)- and there have previously been small issues, but we managed to resolve them all.
Now I seem to have an issue with R studio:
I run a function (FLXSA(stk1, idx1, xsa.control)) which performs complicated calculations on two object (stk1 and idx1) to create a new object.
I can run the code once and it will perform the task. However, in my script I do have to use the function multiple times, and I get the error message
Error in lapply(assess@index, FLQuant) : **
** negative length vectors are not allowed

I tried to run it with the reprex render function, and it will perform the task without error messages- so I cannot even show you how it looks,
I can run the script under "plain" R (outside R studio) without an issue (but this is very inconvenient).
The function will work the first time when I open R-studio, but when I try to run it again the error occurs.
I can clear the environment and it might work once, but this does not help as I have too run the function repeatedly throughout the session.

Any suggestions? I am really at a loss here...
Thanks!

Hi, and welcome!

It looks like you're dealing with an S4 object (assess@index), which is tricky anyway, but your lapply call works in 3 of 4 cases, excluding only RStudio second calls.

As this is not reproducible in a reprex, debugging is hard, of course.

Can you produce a prototype function with data example that demonstrates this behavior for testing? sessionInfo() would also be helpful, since FLXSA produces complex return objects

library(FLXSA)
#> Loading required package: FLCore
#> Loading required package: lattice
#> Loading required package: iterators
#> FLCore (Version 2.6.14, packaged: 2019-11-18 21:54:10 UTC)
#> Loading required package: FLAssess
data(ple4)
data(ple4.indices)

res <- FLXSA(ple4, ple4.indices)
str(res)
#> Formal class 'FLXSA' [package "FLXSA"] with 24 slots
#>   ..@ survivors  :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1:10, 1:62, 1, 1, 1, 1] 461236 256258 335129 196400 123106 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr [1:10] "1" "2" "3" "4" ...
#>   .. .. .. .. ..$ year  : chr [1:62] "1957" "1958" "1959" "1960" ...
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr "1000"
#>   ..@ se.int     :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 0.1462 0.0997 0.084 0.0779 0.0773 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. ..$ year  : chr "2018"
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr ""
#>   ..@ se.ext     :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 0.1144 0.0706 0.0714 0.0517 0.0411 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. ..$ year  : chr "2018"
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr ""
#>   ..@ n.fshk     :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1, 1, 1, 1, 1, 1] NA
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr "all"
#>   .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr "NA"
#>   ..@ n.nshk     :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1, 1, 1, 1, 1, 1] NA
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr "all"
#>   .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr "NA"
#>   ..@ var.fshk   :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1, 1, 1, 1, 1, 1] NA
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr "all"
#>   .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr "NA"
#>   ..@ var.nshk   :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1, 1, 1, 1, 1, 1] NA
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr "all"
#>   .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr "NA"
#>   ..@ q.hat      :Formal class 'FLQuants' [package "FLCore"] with 4 slots
#>   .. .. ..@ .Data:List of 6
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 0 0 0 0 0 0 0 0 0
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 0.000168 0.000167 0.000182 0.000212 0.000261 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:7, 1, 1, 1, 1, 1] 0.017123 0.004378 0.002124 0.00109 0.000689 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:7] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 0.0954 0.0709 0.0632 0.0636 0.0646 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 0.00405 0.0115 0.01848 0.0235 0.02607 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:8, 1, 1, 1, 1, 1] 0.00175 0.01082 0.01962 0.02623 0.03163 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:8] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. ..@ names: chr [1:6] "BTS-Isis-early" "BTS-Combined (ISIS and TRIDENS)" "SNS" "BTS-Combined (all)" ...
#>   .. .. ..@ desc : chr(0) 
#>   .. .. ..@ lock : logi FALSE
#>   ..@ q2.hat     :Formal class 'FLQuants' [package "FLCore"] with 4 slots
#>   .. .. ..@ .Data:List of 6
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 1 1 1 1 1 1 1 1 1
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 1 1 1 1 1 1 1 1 1
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:7, 1, 1, 1, 1, 1] 1 1 1 1 1 1 1
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:7] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 1 1 1 1 1 1 1 1 1
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1, 1, 1, 1, 1] 1 1 1 1 1 1 1 1 1
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:8, 1, 1, 1, 1, 1] 1 1 1 1 1 1 1 1
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:8] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr ""
#>   .. .. ..@ names: chr [1:6] "BTS-Isis-early" "BTS-Combined (ISIS and TRIDENS)" "SNS" "BTS-Combined (all)" ...
#>   .. .. ..@ desc : chr(0) 
#>   .. .. ..@ lock : logi FALSE
#>   ..@ diagnostics:'data.frame':  1044 obs. of  6 variables:
#>   .. ..$ w     : num [1:1044] 4 4 4 4 4 4 4 4 4 4 ...
#>   .. ..$ nhat  : num [1:1044] 9.59 9.74 9.62 9.15 9.49 ...
#>   .. ..$ yrcls : num [1:1044] 1948 1949 1950 1951 1952 ...
#>   .. ..$ age   : num [1:1044] 9 9 9 9 9 9 9 9 9 9 ...
#>   .. ..$ year  : num [1:1044] 1957 1958 1959 1960 1961 ...
#>   .. ..$ source: chr [1:1044] "fshk" "fshk" "fshk" "fshk" ...
#>   ..@ control    :Formal class 'FLXSA.control' [package "FLXSA"] with 14 slots
#>   .. .. ..@ tol     : num 4e-06
#>   .. .. ..@ maxit   : int 30
#>   .. .. ..@ min.nse : num 0.3
#>   .. .. ..@ fse     : num 0.5
#>   .. .. ..@ rage    : int 0
#>   .. .. ..@ qage    : int 9
#>   .. .. ..@ shk.n   : logi TRUE
#>   .. .. ..@ shk.f   : logi TRUE
#>   .. .. ..@ shk.yrs : int 5
#>   .. .. ..@ shk.ages: int 5
#>   .. .. ..@ window  : int 100
#>   .. .. ..@ tsrange : num 20
#>   .. .. ..@ tspower : num 3
#>   .. .. ..@ vpa     : logi FALSE
#>   ..@ catch.n    :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1, 1, 1, 1, 1, 1] NA
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr "all"
#>   .. .. .. .. ..$ year  : chr "1"
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr "NA"
#>   ..@ stock.n    :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1:10, 1:61, 1, 1, 1, 1] 461236 256258 335129 196400 123106 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr [1:10] "1" "2" "3" "4" ...
#>   .. .. .. .. ..$ year  : chr [1:61] "1957" "1958" "1959" "1960" ...
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr "1000"
#>   ..@ harvest    :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. ..@ .Data: num [1:10, 1:61, 1, 1, 1, 1] 0.102 0.18 0.286 0.361 0.318 ...
#>   .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. ..$ age   : chr [1:10] "1" "2" "3" "4" ...
#>   .. .. .. .. ..$ year  : chr [1:61] "1957" "1958" "1959" "1960" ...
#>   .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. ..$ iter  : chr "1"
#>   .. .. ..@ units: chr "f"
#>   ..@ index.name : chr [1:6] "BTS-Isis-early" "BTS-Combined (ISIS and TRIDENS)" "SNS" "BTS-Combined (all)" ...
#>   ..@ index.range:List of 6
#>   .. ..$ : Named num [1:7] 1 9 9 1985 1995 ...
#>   .. .. ..- attr(*, "names")= chr [1:7] "min" "max" "plusgroup" "minyear" ...
#>   .. ..$ : Named num [1:7] 1 9 9 1996 2017 ...
#>   .. .. ..- attr(*, "names")= chr [1:7] "min" "max" "plusgroup" "minyear" ...
#>   .. ..$ : Named num [1:7] 1 7 7 1970 2017 ...
#>   .. .. ..- attr(*, "names")= chr [1:7] "min" "max" "plusgroup" "minyear" ...
#>   .. ..$ : Named num [1:7] 1 10 1 1996 2017 ...
#>   .. .. ..- attr(*, "names")= chr [1:7] "min" "max" "plusgroup" "minyear" ...
#>   .. ..$ : Named num [1:7] 1 10 1 1996 2017 ...
#>   .. .. ..- attr(*, "names")= chr [1:7] "min" "max" "plusgroup" "minyear" ...
#>   .. ..$ : Named num [1:7] 1 8 8 2007 2017 ...
#>   .. .. ..- attr(*, "names")= chr [1:7] "min" "max" "plusgroup" "minyear" ...
#>   ..@ index      :Formal class 'FLQuants' [package "FLCore"] with 4 slots
#>   .. .. ..@ .Data:List of 6
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1:11, 1, 1, 1, 1] 183.86 255.04 57.37 18.25 2.13 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr [1:11] "1985" "1986" "1987" "1988" ...
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr "NA"
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1:22, 1, 1, 1, 1] 169.55 143.2 24.08 7.71 5.48 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr [1:22] "1996" "1997" "1998" "1999" ...
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr "NA"
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:7, 1:48, 1, 1, 1, 1] 11562 13240 4665 1071 239 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:7] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr [1:48] "1970" "1971" "1972" "1973" ...
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr "NA"
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1:22, 1, 1, 1, 1] 29541 33155 9189 3140 2397 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr [1:22] "1996" "1997" "1998" "1999" ...
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ season: chr "all"
#>   .. .. .. .. .. .. .. ..$ area  : chr "unique"
#>   .. .. .. .. .. .. .. ..$ iter  : chr "1"
#>   .. .. .. .. .. ..@ units: chr "NA"
#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1:22, 1, 1, 1, 1] 738 2342 2140 928 789 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
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#>   .. .. .. .. .. .. .. ..$ year  : chr [1:22] "1996" "1997" "1998" "1999" ...
#>   .. .. .. .. .. .. .. ..$ unit  : chr "unique"
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#>   .. .. .. .. .. ..@ units: chr ""
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#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
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#>   .. .. ..@ lock : logi FALSE
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#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1:22, 1, 1, 1, 1] 1009465 856677 132389 36307 21007 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr [1:22] "1996" "1997" "1998" "1999" ...
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#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:7, 1:48, 1, 1, 1, 1] 686889 3037348 2201170 983796 347748 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:7] "1" "2" "3" "4" ...
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#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr [1:22] "1996" "1997" "1998" "1999" ...
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#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:9, 1:22, 1, 1, 1, 1] 182848 206007 117955 40407 31068 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
#>   .. .. .. .. .. .. .. ..$ age   : chr [1:9] "1" "2" "3" "4" ...
#>   .. .. .. .. .. .. .. ..$ year  : chr [1:22] "1996" "1997" "1998" "1999" ...
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#>   .. .. .. ..$ :Formal class 'FLQuant' [package "FLCore"] with 2 slots
#>   .. .. .. .. .. ..@ .Data: num [1:8, 1:11, 1, 1, 1, 1] 1323346 532141 316668 246172 66366 ...
#>   .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 6
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#>   .. .. ..@ desc : chr(0) 
#>   .. .. ..@ lock : logi FALSE
#>   ..@ call       : chr [1:3] ".local" "stock" "indices"
#>   ..@ name       : chr ""
#>   ..@ desc       : chr "FLXSA run: "
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#>   .. ..- attr(*, "names")= chr [1:7] "min" "max" "plusgroup" "minyear" ...

Created on 2020-01-11 by the reprex package (v0.3.0)

Hello, Thanks for trying to help me.
Indeed the sample you chose is probably quite a nice bit of code, it is from the FLR tutorial and indeed that's where I first experienced the issue (when I tried to run the repeated FLXSA in testing values for fse.
Here is a shot and my session info.
I am also adding a screenshot, as to show the error message... not sure that will help. Before running the script that produced the error message at the bottom, I actually cleaned the environment, including any hidden files.

I am an R user, I m not very good in doing any manipulations on R-studio... indeed due to the setup at my work I have no administration rights whatsoever and cannot use github.

library(FLash)

#> FLCore (Version 2.6.13, packaged: 2019-04-03 16:07:10 UTC)
library(FLAssess)
library(FLa4a)

#> This is FLa4a 1.6.7. For overview type 'help(package="FLa4a")'
library(FLXSA)
library(ggplotFL)

data(ple4)
data(ple4.indices)

xsa.control <- FLXSA.control(maxit = 50, fse = 2.5)
ple4.xsa    <- FLXSA(ple4, ple4.indices, xsa.control)
ple4.new  <- ple4 + ple4.xsa

Created on 2020-01-13 by the reprex package (v0.3.0)

Session info

devtools::session_info()
#> - Session info ----------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.6.1 (2019-07-05)
#>  os       Windows 10 x64              
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  English_United Kingdom.1252 
#>  ctype    English_United Kingdom.1252 
#>  tz       Europe/London               
#>  date     2020-01-13                  
#> 
#> - Packages --------------------------------------------------------------
#>  package     * version    date       lib source        
#>  ADGofTest     0.3        2011-12-28 [1] CRAN (R 3.6.0)
#>  assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.1)
#>  backports     1.1.4      2019-04-10 [1] CRAN (R 3.6.0)
#>  callr         3.3.2      2019-09-22 [1] CRAN (R 3.6.1)
#>  cli           1.1.0      2019-03-19 [1] CRAN (R 3.6.1)
#>  coda        * 0.19-3     2019-07-05 [1] CRAN (R 3.6.1)
#>  colorspace    1.4-1      2019-03-18 [1] CRAN (R 3.6.1)
#>  copula      * 0.999-19.1 2019-04-22 [1] CRAN (R 3.6.1)
#>  crayon        1.3.4      2017-09-16 [1] CRAN (R 3.6.1)
#>  desc          1.2.0      2018-05-01 [1] CRAN (R 3.6.1)
#>  devtools      2.2.1      2019-09-24 [1] CRAN (R 3.6.1)
#>  digest        0.6.20     2019-07-04 [1] CRAN (R 3.6.1)
#>  dplyr         0.8.3      2019-07-04 [1] CRAN (R 3.6.1)
#>  ellipsis      0.3.0      2019-09-20 [1] CRAN (R 3.6.1)
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.1)
#>  FLa4a       * 1.6.7      2019-04-03 [1] local         
#>  FLash       * 2.5.11     2018-11-09 [1] local         
#>  FLAssess    * 2.6.3      2019-02-25 [1] local         
#>  FLCore      * 2.6.13     2019-04-03 [1] flr (R 3.5.3) 
#>  FLXSA       * 2.6.2      2018-07-19 [1] local         
#>  fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.1)
#>  ggplot2     * 3.2.0      2019-06-16 [1] CRAN (R 3.6.0)
#>  ggplotFL    * 2.6.6      2019-04-03 [1] local         
#>  glue          1.3.1      2019-03-12 [1] CRAN (R 3.6.1)
#>  gridExtra     2.3        2017-09-09 [1] CRAN (R 3.6.1)
#>  gsl           2.1-6      2019-03-25 [1] CRAN (R 3.6.0)
#>  gtable        0.3.0      2019-03-25 [1] CRAN (R 3.6.1)
#>  highr         0.8        2019-03-20 [1] CRAN (R 3.6.1)
#>  htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.1)
#>  iterators   * 1.0.12     2019-07-26 [1] CRAN (R 3.6.1)
#>  knitr         1.23       2019-05-18 [1] CRAN (R 3.6.1)
#>  lattice     * 0.20-38    2018-11-04 [2] CRAN (R 3.6.1)
#>  lazyeval      0.2.2      2019-03-15 [1] CRAN (R 3.6.1)
#>  magrittr      1.5        2014-11-22 [1] CRAN (R 3.6.1)
#>  MASS          7.3-51.4   2019-03-31 [2] CRAN (R 3.6.1)
#>  Matrix        1.2-17     2019-03-22 [2] CRAN (R 3.6.1)
#>  memoise       1.1.0      2017-04-21 [1] CRAN (R 3.6.1)
#>  mgcv          1.8-28     2019-03-21 [2] CRAN (R 3.6.1)
#>  munsell       0.5.0      2018-06-12 [1] CRAN (R 3.6.1)
#>  mvtnorm       1.0-11     2019-06-19 [1] CRAN (R 3.6.0)
#>  nlme          3.1-140    2019-05-12 [2] CRAN (R 3.6.1)
#>  numDeriv      2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.0)
#>  pcaPP         1.9-73     2018-01-14 [1] CRAN (R 3.6.0)
#>  pillar        1.4.2      2019-06-29 [1] CRAN (R 3.6.1)
#>  pkgbuild      1.0.6      2019-10-09 [1] CRAN (R 3.6.1)
#>  pkgconfig     2.0.2      2018-08-16 [1] CRAN (R 3.6.1)
#>  pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.6.1)
#>  prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.6.1)
#>  processx      3.4.1      2019-07-18 [1] CRAN (R 3.6.1)
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