- using R Under development (unstable) (2025-09-14 r88831)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.7 (3+b2)
Debian flang-new version 19.1.7 (3+b2)
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
- checking for file ‘stacomiR/DESCRIPTION’ ... OK
- this is package ‘stacomiR’ version ‘0.6.1’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [2s/4s] OK
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘stacomiR’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [5s/8s] OK
- checking whether the package can be loaded with stated dependencies ... [6s/9s] OK
- checking whether the package can be unloaded cleanly ... [6s/9s] OK
- checking whether the namespace can be loaded with stated dependencies ... [5s/7s] OK
- checking whether the namespace can be unloaded cleanly ... [6s/8s] OK
- checking loading without being on the library search path ... [6s/9s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [44s/58s] OK
- checking Rd files ... [2s/3s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [6s/8s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [19s/25s] ERROR
Running examples in ‘stacomiR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: report_silver_eel-class
> ### Title: Class "report_silver_eel"
> ### Aliases: report_silver_eel-class report_silver_eel
> ### Keywords: classes
>
> ### ** Examples
>
> # launching stacomi without selecting the scheme or interface
> stacomi( database_expected=FALSE)
> # the following script will load data from the two Anguillere monitored in the Somme
>
> # If you have a working database
> # the following line of code will create the r_silver dataset
> # from the "fd80." schema in the database
> ## Not run:
> ##D stacomi(database_expected=TRUE, sch="fd80.") # overrides the default option sch = 'iav'
> ##D # prompt for user and password, you can set these in the options,
> ##D # including dbname and host
> ##D if (interactive()){
> ##D if (!exists("user")){
> ##D user <- readline(prompt="Enter user: ")
> ##D password <- readline(prompt="Enter password: ")
> ##D }
> ##D }
> ##D options(
> ##D stacomiR.dbname = "bd_contmig_nat",
> ##D stacomiR.host ="localhost",
> ##D stacomiR.port = "5432",
> ##D stacomiR.user = user,
> ##D stacomiR.user = password
> ##D )
> ##D
> ##D #create an instance of the class
> ##D r_silver<-new("report_silver_eel")
> ##D r_silver<-choice_c(r_silver,
> ##D dc=c(2,6),
> ##D horodatedebut="2010-09-01",
> ##D horodatefin="2016-10-04",
> ##D silent=FALSE)
> ##D r_silver<-connect(r_silver)
> ## End(Not run)
>
> # load the dataset generated by previous lines
> data("r_silver")
> # the calculation will fill the slot calcdata
> r_silver<-calcule(r_silver)
> # stages are in r_silver@calcdata[["6"]][,"stage"]
> #look at data structure using str(r_silver@calcdata[["6"]])
>
> # standard plot as drawn by Laurent Beaulaton (Analyse des donnees d'argenture acquises en France)
> # showing Durif's stage according to size and eye diameter
> plot(r_silver, plot.type=1)
>
> # number per month or year and Durif's stage (year if number of dc >1)
> plot(r_silver, plot.type="2")
>
> # plot showing fulton's coefficient, and size weight graphs
> # inspired from Acou et al., 2009
> # Differential Production and Condition Indices of Premigrant
> # Eels in Two Small Atlantic Coastal Catchments
> # of France
> plot(r_silver, plot.type="3")
Error in loadNamespace(x) : there is no package called ‘MASS’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [45s/59s] OK
Running ‘testthat.R’ [45s/59s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [8s/11s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from stacomir.Rmd:349-366 [silver]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'MASS'
---
Backtrace:
▆
1. ├─base::plot(r_silver, plot.type = "3")
2. ├─stacomiR::plot(r_silver, plot.type = "3")
3. │ └─stacomiR (local) .local(x, ...)
4. └─base::loadNamespace(x)
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
there is no package called 'MASS'
--- failed re-building ‘stacomir.Rmd’
SUMMARY: processing the following file failed:
‘stacomir.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [17s/22s] OK
- checking HTML version of manual ... [7s/14s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs