CRAN Package Check Results for Package finalfit

Last updated on 2021-06-24 07:50:10 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.3 15.05 342.75 357.80 OK
r-devel-linux-x86_64-debian-gcc 1.0.3 12.43 251.59 264.02 OK
r-devel-linux-x86_64-fedora-clang 1.0.3 417.45 OK
r-devel-linux-x86_64-fedora-gcc 1.0.3 414.30 OK
r-devel-windows-x86_64 1.0.3 23.00 312.00 335.00 OK
r-devel-windows-x86_64-gcc10-UCRT 1.0.3 ERROR
r-patched-linux-x86_64 1.0.3 19.03 323.20 342.23 OK
r-patched-solaris-x86 1.0.3 559.80 NOTE
r-release-linux-x86_64 1.0.3 14.48 323.75 338.23 OK
r-release-macos-arm64 1.0.3 OK
r-release-macos-x86_64 1.0.3 OK
r-release-windows-ix86+x86_64 1.0.3 24.00 319.00 343.00 OK
r-oldrel-macos-x86_64 1.0.3 OK

Check Details

Version: 1.0.3
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'rstan', 'survminer'
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.3
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: 'survminer'
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.3
Check: examples
Result: ERROR
    Running examples in 'finalfit-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: surv_plot
    > ### Title: Plot survival curves with number-at-risk table
    > ### Aliases: surv_plot
    >
    > ### ** Examples
    >
    > library(finalfit)
    > library(dplyr)
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    >
    > # Survival plot
    > data(colon_s)
    > explanatory = c("perfor.factor")
    > dependent = "Surv(time, status)"
    > colon_s %>%
    + surv_plot(dependent, explanatory, xlab="Time (days)", pval=TRUE, legend="none")
    Error in loadNamespace(x) : there is no package called 'survminer'
    Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.3
Check: tests
Result: ERROR
     Running 'testthat.R'
    Running the tests in 'tests/testthat.R' failed.
    Last 13 lines of output:
     Backtrace:
     x
     1. +-testthat::expect_is(...) test_plots.R:23:8
     2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
     3. | \-rlang::eval_bare(expr, quo_get_env(quo))
     4. +-finalfit::surv_plot(colon_s, "Surv(time, status)", "age.factor")
     5. | \-base::do.call(survminer::ggsurvplot, args)
     6. \-base::loadNamespace(x)
     7. \-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     8. \-base:::withOneRestart(expr, restarts[[1L]])
     9. \-base:::doWithOneRestart(return(expr), restart)
    
     [ FAIL 1 | WARN 10 | SKIP 0 | PASS 130 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'all_tables_examples.Rmd' using rmarkdown
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(obstruct.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(extent.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, extent.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(obstruct.factor, extent.factor) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(age.factor, mort_5yr) :
     Chi-squared approximation may be incorrect
    Warning in chisq.test(obstruct.factor, mort_5yr) :
     Chi-squared approximation may be incorrect
    Note: dependent includes missing data. These are dropped.
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
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    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Setting levels: control = 0, case = 1
    Setting direction: controls < cases
    Setting levels: control = 0, case = 1
    Setting direction: controls < cases
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
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    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
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    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Setting levels: control = 0, case = 1
    Setting direction: controls < cases
    Waiting for profiling to be done...
    Setting levels: control = 0, case = 1
    Setting direction: controls < cases
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
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    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
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    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
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    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    boundary (singular) fit: see ?isSingular
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Note: dependent includes missing data. These are dropped.
    P-value for lmer is estimate assuming t-distribution is normal. Bootstrap for final publication.
    Note: dependent includes missing data. These are dropped.
    boundary (singular) fit: see ?isSingular
    P-value for lmer is estimate assuming t-distribution is normal. Bootstrap for final publication.
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
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    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Dependent variable is a survival object
    Loading required package: grid
    Loading required package: Matrix
    Loading required package: survival
    
    Attaching package: 'survey'
    
    The following object is masked from 'package:graphics':
    
     dotchart
    
    --- finished re-building 'all_tables_examples.Rmd'
    
    --- re-building 'bootstrap.Rmd' using rmarkdown
    --- finished re-building 'bootstrap.Rmd'
    
    --- re-building 'data_prep.Rmd' using rmarkdown
    --- finished re-building 'data_prep.Rmd'
    
    --- re-building 'export.Rmd' using rmarkdown
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Note: dependent includes missing data. These are dropped.
    Warning in chisq.test(extent.factor, differ.factor) :
     Chi-squared approximation may be incorrect
    Note: dependent includes missing data. These are dropped.
    Warning in chisq.test(extent.factor, differ.factor) :
     Chi-squared approximation may be incorrect
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    --- finished re-building 'export.Rmd'
    
    --- re-building 'finalfit.Rmd' using rmarkdown
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Warning in chisq.test(age.factor, perfor.factor) :
     Chi-squared approximation may be incorrect
    Note: dependent includes missing data. These are dropped.
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Setting levels: control = 0, case = 1
    Setting direction: controls < cases
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    --- finished re-building 'finalfit.Rmd'
    
    --- re-building 'missing.Rmd' using rmarkdown
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
    Attaching package: 'mice'
    
    The following object is masked from 'package:stats':
    
     filter
    
    The following objects are masked from 'package:base':
    
     cbind, rbind
    
    Note: Using an external vector in selections is ambiguous.
    i Use `all_of(dependent)` instead of `dependent` to silence this message.
    i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
    This message is displayed once per session.
    Note: Using an external vector in selections is ambiguous.
    i Use `all_of(explanatory)` instead of `explanatory` to silence this message.
    i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
    This message is displayed once per session.
    Setting levels: control = 0, case = 1
    Setting direction: controls < cases
    Setting levels: control = 0, case = 1
    Setting direction: controls < cases
    Setting levels: control = 0, case = 1
    Setting direction: controls < cases
    Setting levels: control = 0, case = 1
    Setting direction: controls < cases
    Note: dependent includes missing data. These are dropped.
    Warning: Removed 3 rows containing missing values (geom_errorbarh).
    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
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    Note: dependent includes missing data. These are dropped.
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    --- finished re-building 'missing.Rmd'
    
    --- re-building 'survival.Rmd' using rmarkdown
    Quitting from lines 153-158 (survival.Rmd)
    Error: processing vignette 'survival.Rmd' failed with diagnostics:
    there is no package called 'survminer'
    --- failed re-building 'survival.Rmd'
    
    SUMMARY: processing the following file failed:
     'survival.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 1.0.3
Check: installed package size
Result: NOTE
     installed size is 5.3Mb
     sub-directories of 1Mb or more:
     doc 4.5Mb
Flavor: r-patched-solaris-x86