CRAN Package Check Results for Package incidence2

Last updated on 2021-04-22 08:48:20 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 5.28 103.50 108.78 OK
r-devel-linux-x86_64-debian-gcc 1.0.0 3.81 66.99 70.80 OK
r-devel-linux-x86_64-fedora-clang 1.0.0 128.30 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.0 109.77 NOTE
r-devel-windows-ix86+x86_64 1.0.0 11.00 114.00 125.00 OK
r-devel-windows-x86_64-gcc10-UCRT 1.0.0 NOTE
r-patched-linux-x86_64 1.0.0 8.30 84.78 93.08 OK
r-patched-solaris-x86 1.0.0 143.70 NOTE
r-release-linux-x86_64 1.0.0 4.92 85.82 90.74 OK
r-release-macos-x86_64 1.0.0 ERROR
r-release-windows-ix86+x86_64 1.0.0 11.00 108.00 119.00 OK
r-oldrel-macos-x86_64 1.0.0 ERROR
r-oldrel-windows-ix86+x86_64 1.0.0 18.00 82.00 100.00 ERROR

Check Details

Version: 1.0.0
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘graphics’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.0.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [3s/3s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
    
     `actual$count[103:106]`: 14 14 14 4
     `expected$count[102:105]`: 14 14 14 6
    
     [ FAIL 1 | WARN 0 | SKIP 35 | PASS 190 ]
     Deleting unused snapshots:
     * _snaps/plots/day.png
     * _snaps/plots/double.png
     * _snaps/plots/integer.png
     * _snaps/plots/month_grouped.png
     * _snaps/plots/multiday.png
     * _snaps/plots/quarterly_grouped.png
     * _snaps/plots/week_grouped.png
     Error: Test failures
     Execution halted
Flavor: r-release-macos-x86_64

Version: 1.0.0
Check: R code for possible problems
Result: NOTE
    int_cast: no visible global function definition for ‘deparse1’
    Undefined global functions or variables:
     deparse1
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.0
Check: examples
Result: ERROR
    Running examples in ‘incidence2-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: plot.incidence2
    > ### Title: Plotting functions
    > ### Aliases: plot.incidence2 facet_plot facet_plot.incidence2
    >
    > ### ** Examples
    >
    > if (requireNamespace("outbreaks", quietly = TRUE) && requireNamespace("ggplot2", quietly = TRUE)) {
    + withAutoprint({
    + data(ebola_sim_clean, package = "outbreaks")
    + dat <- ebola_sim_clean$linelist
    +
    + inci <- incidence(dat,
    + date_index = date_of_onset,
    + interval = 7,
    + groups = hospital)
    +
    + inci2 <- incidence(dat,
    + date_index = date_of_onset,
    + interval = 7,
    + groups = c(hospital, gender))
    +
    + plot(inci)
    + plot(inci, fill = hospital)
    + plot(inci, fill = hospital, stack = FALSE)
    +
    + facet_plot(inci)
    + facet_plot(inci2)
    + facet_plot(inci2, facets = gender)
    + facet_plot(inci2, facets = hospital, fill = gender)
    + })
    + }
    > data(ebola_sim_clean, package = "outbreaks")
    > dat <- ebola_sim_clean$linelist
    > inci <- incidence(dat, date_index = date_of_onset, interval = 7, groups = hospital)
    > inci2 <- incidence(dat, date_index = date_of_onset, interval = 7, groups = c(hospital,
    + gender))
    > plot(inci)
    Error in as.Date.numeric(value) : 'origin' must be supplied
    Calls: withAutoprint ... <Anonymous> -> f -> [<- -> [<-.Date -> as.Date -> as.Date.numeric
    Execution halted
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [14s/5s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     1. └─incidence2::incidence(...) test-incidence.R:556:2
     2. ├─base::do.call(min, args = c(x[date_index], na.rm = TRUE))
     3. └─base::Summary.factor(...)
    
     [ FAIL 6 | WARN 0 | SKIP 35 | PASS 185 ]
     Deleting unused snapshots:
     * _snaps/plots/day.png
     * _snaps/plots/double.png
     * _snaps/plots/integer.png
     * _snaps/plots/month_grouped.png
     * _snaps/plots/multiday.png
     * _snaps/plots/quarterly_grouped.png
     * _snaps/plots/week_grouped.png
     Error: Test failures
     Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘Introduction.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Quitting from lines 116-121 (Introduction.Rmd)
    Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
    'origin' must be supplied
    --- failed re-building ‘Introduction.Rmd’
    
    --- re-building ‘customizing_incidence_plots.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Quitting from lines 64-65 (customizing_incidence_plots.Rmd)
    Error: processing vignette 'customizing_incidence_plots.Rmd' failed with diagnostics:
    'origin' must be supplied
    --- failed re-building ‘customizing_incidence_plots.Rmd’
    
    --- re-building ‘handling_incidence_objects.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    --- finished re-building ‘handling_incidence_objects.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘Introduction.Rmd’ ‘customizing_incidence_plots.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 1.0.0
Check: tests
Result: ERROR
     Running 'testthat.R' [8s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(incidence2)
     >
     > test_check("incidence2")
    
     Attaching package: 'dplyr'
    
     The following object is masked from 'package:testthat':
    
     matches
    
     The following objects are masked from 'package:stats':
    
     filter, lag
    
     The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
     43 observations were removed.
     n greater than number of unique date groupings. Returning all rows.
     2087 missing observations were removed.
     2087 missing observations were removed.
     2087 missing observations were removed.
     2087 missing observations were removed.
     2087 missing observations were removed.
     == Skipped tests ===============================================================
     * On CRAN (28)
     * On Windows (7)
    
     == Failed tests ================================================================
     -- Failure (test-incidence.R:155:3): single week, with groups and without count work as expected --
     x$height (`actual`) not equal to `expected_heights` (`expected`).
    
     `actual` is an S3 object of class <factor>, an integer vector
     `expected` is a character vector ('short', 'tall', 'short', 'tall', 'short', ...)
     -- Failure (test-incidence.R:156:3): single week, with groups and without count work as expected --
     x$size (`actual`) not equal to `expected_sizes` (`expected`).
    
     `actual` is an S3 object of class <factor>, an integer vector
     `expected` is a character vector ('small', 'small', 'large', 'large', 'large', ...)
     -- Failure (test-incidence.R:192:3): single week, with groups and with count work as expected --
     x$height (`actual`) not equal to `expected_heights` (`expected`).
    
     `actual` is an S3 object of class <factor>, an integer vector
     `expected` is a character vector ('short', 'tall', 'short', 'tall', 'short', ...)
     -- Failure (test-incidence.R:193:3): single week, with groups and with count work as expected --
     x$size (`actual`) not equal to `expected_sizes` (`expected`).
    
     `actual` is an S3 object of class <factor>, an integer vector
     `expected` is a character vector ('small', 'small', 'large', 'large', 'large', ...)
     -- Error (test-incidence.R:556:3): character single week, no groupings and with count work as expected --
     Error: 'min' not meaningful for factors
     Backtrace:
     x
     1. \-incidence2::incidence(...) test-incidence.R:556:2
     2. +-base::do.call(min, args = c(x[date_index], na.rm = TRUE))
     3. \-base::Summary.factor(...)
    
     [ FAIL 5 | WARN 0 | SKIP 35 | PASS 186 ]
     Deleting unused snapshots:
     * _snaps/plots/day.png
     * _snaps/plots/double.png
     * _snaps/plots/integer.png
     * _snaps/plots/month_grouped.png
     * _snaps/plots/multiday.png
     * _snaps/plots/quarterly_grouped.png
     * _snaps/plots/week_grouped.png
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'Introduction.Rmd' using rmarkdown
    Quitting from lines 116-121 (Introduction.Rmd)
    Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
    'origin' must be supplied
    --- failed re-building 'Introduction.Rmd'
    
    --- re-building 'customizing_incidence_plots.Rmd' using rmarkdown
    Quitting from lines 64-65 (customizing_incidence_plots.Rmd)
    Error: processing vignette 'customizing_incidence_plots.Rmd' failed with diagnostics:
    'origin' must be supplied
    --- failed re-building 'customizing_incidence_plots.Rmd'
    
    --- re-building 'handling_incidence_objects.Rmd' using rmarkdown
    --- finished re-building 'handling_incidence_objects.Rmd'
    
    SUMMARY: processing the following files failed:
     'Introduction.Rmd' 'customizing_incidence_plots.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64