Check results for 'stacomiR'

using R version 3.6.2 (2019-12-12)
using platform: x86_64-apple-darwin15.6.0 (64-bit)
using session charset: UTF-8
checking for file ‘stacomiR/DESCRIPTION’ ... OK
this is package ‘stacomiR’ version ‘0.5.4.3’
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 ... [28s/28s] OK
checking installed package size ... OK
checking package directory ... 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 R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... OK
checking whether the package can be loaded with stated dependencies ... OK
checking whether the package can be unloaded cleanly ... OK
checking whether the namespace can be loaded with stated dependencies ... OK
checking whether the namespace can be unloaded cleanly ... OK
checking loading without being on the library search path ... OK
checking dependencies in R code ... NOTE
No protocol specified

(R:99535): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
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checking S3 generic/method consistency ... WARNING
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(R:99545): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checking replacement functions ... WARNING
No protocol specified

(R:99555): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
checking foreign function calls ... NOTE
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(R:99565): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
checking R code for possible problems ... [30s/30s] NOTE
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(R:99593): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
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checking Rd files ... OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... WARNING
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(R:99625): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking for code/documentation mismatches ... WARNING
No protocol specified

(R:99635): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
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(R:99645): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
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(R:99655): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
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checking Rd \usage sections ... NOTE
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(R:99671): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... NOTE
  No protocol specified

  (R:99687): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
  No protocol specified
  Note: found 40588 marked UTF-8 strings
checking data for ASCII and uncompressed saves ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... ERROR
Running examples in ‘stacomiR-Ex.R’ failed
The error most likely occurred in:

> ### Name: report_mig_mult-class
> ### Title: Migration reports for multiple DC / species / stages
> ### Aliases: report_mig_mult-class report_mig_mult
> ### Keywords: classes
>
> ### ** Examples
>
> library(stacomiR)
>
> stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
> ## launches the application in the command line
> ## here an example of loading
> ## the following lines will only run if you have the program installed
> ## and the iav scheme available in the database
> ## this example generates the r_mig_mult dataset
> ## Not run:
> ##D stacomi(gr_interface=FALSE,
> ##D login_window=FALSE,
> ##D database_expected=TRUE)
> ##D r_mig_mult=new("report_mig_mult")
> ##D r_mig_mult=choice_c(r_mig_mult,
> ##D dc=c(5,6,12),
> ##D taxa=c("Anguilla anguilla"),
> ##D stage=c("AGG","AGJ","CIV"),datedebut="2011-01-01",datefin="2011-12-31")
> ##D r_mig_mult<-charge(r_mig_mult)
> ##D # launching charge will also load classes associated with the report
> ##D # e.g. report_ope, report_df, report_dc
> ##D r_mig_mult<-connect(r_mig_mult)
> ##D # calculations
> ##D r_mig_mult<-calcule(r_mig_mult,silent=TRUE)
> ##D
> ##D
> ## End(Not run)
>
> # Use this as example if you don't have a connexion to the database
> data("r_mig_mult")
> # The following re-create the object at the time of loading
> # All three classes were created by the charge and connect
> # method of report_mig_mult in the previous example
> data("r_mig_mult_ope")
> assign("report_ope",r_mig_mult_ope,envir=envir_stacomi)
> data("r_mig_mult_df")
> assign("report_df",r_mig_mult_df,envir=envir_stacomi)
> data("r_mig_mult_dc")
> assign("report_dc",r_mig_mult_dc,envir=envir_stacomi)
> # use the following to get the raw data loaded by the connect method
> # not shown there as the database and program might not be installed
>
> #Individual plot for all DC, taxa and stage where data present
> #Silent=TRUE to turn off messages
> # not run because of multiple graphical devices
>
> plot(r_mig_mult,plot.type="standard",silent=TRUE)
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
Warning in max(eff/1000, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... plot -> plot -> plot.default -> localWindow -> plot.window
Execution halted
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [7s/17s] ERROR
  Running ‘testthat.R’ [6s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  34: withOneRestart(expr, restarts[[1L]])
  35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  36: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() })
  37: FUN(X[[i]], ...)
  38: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  39: force(code)
  40: doWithOneRestart(return(expr), restart)
  41: withOneRestart(expr, restarts[[1L]])
  42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  43: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
  44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
  45: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
  46: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
  47: test_check("stacomiR")
  An irrecoverable exception occurred. R is aborting now ...
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... [0s/0s] NONE
‘stacomir.Rmd’using ‘UTF-8’... [0s/0s] OK
checking re-building of vignette outputs ... [9s/9s] OK
checking PDF version of manual ... OK
DONE
Status: 2 ERRORs, 4 WARNINGs, 5 NOTEs