CRAN Package Check Results for Package stacomiR

Last updated on 2020-03-07 09:48:51 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.5.4.2	30.54	303.56	334.10	WARN
r-devel-linux-x86_64-debian-gcc	0.5.4.2	26.06	228.66	254.72	WARN
r-devel-linux-x86_64-fedora-clang	0.5.4.2			414.58	WARN
r-devel-linux-x86_64-fedora-gcc	0.5.4.2			383.72	WARN
r-devel-windows-ix86+x86_64	0.5.4.2	79.00	444.00	523.00	NOTE
r-devel-windows-ix86+x86_64-gcc8	0.5.4.2	65.00	346.00	411.00	NOTE
r-patched-linux-x86_64	0.5.4.2	28.60	277.44	306.04	WARN
r-patched-solaris-x86	0.5.4.2			577.10	WARN
r-release-linux-x86_64	0.5.4.2	26.52	275.69	302.21	WARN
r-release-windows-ix86+x86_64	0.5.4.2	50.00	296.00	346.00	WARN
r-release-osx-x86_64	0.5.4.2				ERROR
r-oldrel-windows-ix86+x86_64	0.5.4.2	39.00	276.00	315.00	OK
r-oldrel-osx-x86_64	0.5.4.2				ERROR

Check Details

Version: 0.5.4.2
Check: Rd \usage sections
Result: WARN
    Documented arguments not in \usage in documentation object 'plot,report_sample_char,missing-method':
     '...'

    Functions with \usage entries need to have the appropriate \alias
    entries, and all their arguments documented.
    The \usage entries must correspond to syntactically valid R code.
    See chapter 'Writing R documentation files' in the 'Writing R
    Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64

Version: 0.5.4.2
Check: package vignettes
Result: NOTE
Package vignette with placeholder title 'Vignette Title':
'stacomir.Rmd'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 0.5.4.2
Check: data for non-ASCII characters
Result: NOTE
Note: found 40588 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 0.5.4.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘stacomir.Rmd’ using rmarkdown
    Quitting from lines 281-303 (stacomir.Rmd)
    Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
    round(sum(datasub$value, na.rm = TRUE), 2) and round(sum(datasub2$value, na.rm = TRUE), 2) are not equal:
     Mean relative difference: 0.000996741
    --- failed re-building ‘stacomir.Rmd’

    SUMMARY: processing the following file failed:
     ‘stacomir.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.5.4.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘stacomir.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 281-303 (stacomir.Rmd)
    Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
    round(sum(datasub$value, na.rm = TRUE), 2) and round(sum(datasub2$value, na.rm = TRUE), 2) are not equal:
     Mean relative difference: 0.000996741
    --- failed re-building ‘stacomir.Rmd’

    SUMMARY: processing the following file failed:
     ‘stacomir.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.5.4.2
Check: dependencies in R code
Result: NOTE
    No protocol specified

    (R:72891): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
Flavor: r-release-osx-x86_64

Version: 0.5.4.2
Check: S3 generic/method consistency
Result: WARN
    No protocol specified

    (R:72901): 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.
Flavor: r-release-osx-x86_64

Version: 0.5.4.2
Check: replacement functions
Result: WARN
    No protocol specified

    (R:72911): 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’.
Flavor: r-release-osx-x86_64

Version: 0.5.4.2
Check: foreign function calls
Result: NOTE
    No protocol specified

    (R:72921): 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.
Flavor: r-release-osx-x86_64

Version: 0.5.4.2
Check: R code for possible problems
Result: NOTE
    No protocol specified

    (R:72949): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
Flavor: r-release-osx-x86_64

Version: 0.5.4.2
Check: for missing documentation entries
Result: WARN
    No protocol specified

    (R:72981): 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.
Flavor: r-release-osx-x86_64

Version: 0.5.4.2
Check: for code/documentation mismatches
Result: WARN
    No protocol specified

    (R:72991): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
    No protocol specified

    (R:73001): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
    No protocol specified

    (R:73011): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
Flavor: r-release-osx-x86_64

Version: 0.5.4.2
Check: Rd \usage sections
Result: NOTE
    No protocol specified

    (R:73027): 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.
Flavor: r-release-osx-x86_64

Version: 0.5.4.2
Check: data for non-ASCII characters
Result: NOTE
     No protocol specified

     (R:73043): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     No protocol specified
     Note: found 40588 marked UTF-8 strings
Flavor: r-release-osx-x86_64

Version: 0.5.4.2
Check: examples
Result: 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
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: tests
Result: ERROR
     Running ‘testthat.R’ [6s/7s]
    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 ...
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: dependencies in R code
Result: NOTE
    No protocol specified

    (R:45677): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
Flavor: r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: S3 generic/method consistency
Result: WARN
    No protocol specified

    (R:45684): 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.
Flavor: r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: replacement functions
Result: WARN
    No protocol specified

    (R:45691): 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’.
Flavor: r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: foreign function calls
Result: NOTE
    No protocol specified

    (R:45698): 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.
Flavor: r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: R code for possible problems
Result: NOTE
    No protocol specified

    (R:45717): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
Flavor: r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: for missing documentation entries
Result: WARN
    No protocol specified

    (R:45740): 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.
Flavor: r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: for code/documentation mismatches
Result: WARN
    No protocol specified

    (R:45747): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
    No protocol specified

    (R:45754): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
    No protocol specified

    (R:45761): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
    No protocol specified
Flavor: r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: Rd \usage sections
Result: NOTE
    No protocol specified

    (R:45771): 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.
Flavor: r-oldrel-osx-x86_64

Version: 0.5.4.2
Check: data for non-ASCII characters
Result: NOTE
     No protocol specified

     (R:45784): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     No protocol specified
     Note: found 40588 marked UTF-8 strings
Flavor: r-oldrel-osx-x86_64