cran checks

[tdhock]

this issue will be to discuss how to fix issues in R CMD check --as-cran

[tdhock]

@faizan-khan-iit here is what the check for ggplot2Animint looks like on my system.

• can you change the Maintainer to yourself?
• there are some ggplot2 dependecies -- loadNamespace or requireNamespace -- can you please remove them?
• what about structure(list() instead of NULL?

thocking@silene:~/R$ R CMD check --as-cran ggplot2Animint_2.1.0.99.tar.gz 
* using log directory ‘/home/thocking/R/ggplot2Animint.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘ggplot2Animint/DESCRIPTION’ ... OK
* this is package ‘ggplot2Animint’ version ‘2.1.0.99’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Hadley Wickham <hadley@rstudio.com>’

New submission
* 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 ‘ggplot2Animint’ can be installed ... 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘ggplot2’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... 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 ... WARNING
'::' or ':::' import not declared from: ‘ggplot2’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
** found \donttest examples: check also with --run-donttest
* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘ggplot2’
* checking tests ...
  Running ‘testthat.R’ [14s/14s]
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In structure(NULL, class = "waiver") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
  2: In structure(NULL, class = "waiver") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
  3: In structure(NULL, class = "waiver") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
  4: In structure(NULL, class = "waiver") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
  Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘ggplot2’
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 2 NOTEs
See
  ‘/home/thocking/R/ggplot2Animint.Rcheck/00check.log’
for details.

thocking@silene:~/R$ 

[faizan-khan-iit]

@tdhock I have made some relevant changes to the code. Could you please try again? The examples and tests still fail in the R CMD check though.

As for this warning

 1: In structure(NULL, class = "waiver") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.

I believe I already made those changes before (see here). Could you verify this on your system? Cause I am not getting this warning anymore.. My output for R CMD checks:

* checking for file 'C:\Users\Faizan\Downloads\git\ggplot\ggplot2/DESCRIPTION' ... OK
* preparing 'ggplot2Animint':
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'ggplot2Animint_2.1.0.99.tar.gz'

Setting env vars ---------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE
Checking ggplot2Animint --------------------------------------------------------
"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD check  \
  "C:\Users\Faizan\AppData\Local\Temp\RtmpUHBWCI/ggplot2Animint_2.1.0.99.tar.gz"  \
  --as-cran --timings --no-manual 

* using log directory 'C:/Users/Faizan/Downloads/git/ggplot/ggplot2Animint.Rcheck'
* using R version 3.4.0 (2017-04-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'ggplot2Animint/DESCRIPTION' ... OK
* this is package 'ggplot2Animint' version '2.1.0.99'
* 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 whether package 'ggplot2Animint' can be installed ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
 WARNING
'qpdf' is needed for checks on size reduction of PDFs
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'ggplot2Animint-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_summary_bin
> ### Title: Summarise y values at unique/binned x x.
> ### Aliases: stat_summary_bin stat_summary
> 
> ### ** Examples
> 
> d <- ggplot(mtcars, aes(cyl, mpg)) + geom_point()
> d + stat_summary(fun.data = "mean_cl_boot", colour = "red", size = 2)
> 
> # You can supply individual functions to summarise the value at
> # each x:
> d + stat_summary(fun.y = "median", colour = "red", size = 2, geom = "point")
Error: ScalesList was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
** found \donttest examples: check also with --run-donttest
* checking for unstated dependencies in 'tests' ... WARNING
'library' or 'require' call not declared from: 'ggplot2'
* checking tests ...
  Running 'testthat.R' [20s]
Warning message:
running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 1 
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 622 SKIPPED: 0 FAILED: 53
  1. Failure: geom_boxplot range includes all outliers (@test-boxplot.r#11) 
  2. Failure: geom_boxplot range includes all outliers (@test-boxplot.r#12) 
  3. Failure: stringsAsFactors doesn't affect results (@test-data.r#22) 
  4. Failure: stringsAsFactors doesn't affect results (@test-data.r#23) 
  5. Failure: stringsAsFactors doesn't affect results (@test-data.r#24) 
  6. Failure: stringsAsFactors doesn't affect results (@test-data.r#25) 
  7. Error: facets with free scales scale independently (@test-facet-.r#22) 
  8. Error: shrink parameter affects scaling (@test-facet-.r#44) 
  9. Error: labeller() dispatches labellers (@test-facet-labels.r#87) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: 2 ERRORs, 2 WARNINGs

See
  'C:/Users/Faizan/Downloads/git/ggplot/ggplot2Animint.Rcheck/00check.log'
for details.

checking examples ... ERROR
Running examples in 'ggplot2Animint-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_summary_bin
> ### Title: Summarise y values at unique/binned x x.
> ### Aliases: stat_summary_bin stat_summary
> 
> ### ** Examples
> 
> d <- ggplot(mtcars, aes(cyl, mpg)) + geom_point()
> d + stat_summary(fun.data = "mean_cl_boot", colour = "red", size = 2)
> 
> # You can supply individual functions to summarise the value at
> # each x:
> d + stat_summary(fun.y = "median", colour = "red", size = 2, geom = "point")
Error: ScalesList was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
** found \donttest examples: check also with --run-donttest

checking tests ... ERROR
  Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 622 SKIPPED: 0 FAILED: 53
  1. Failure: geom_boxplot range includes all outliers (@test-boxplot.r#11) 
  2. Failure: geom_boxplot range includes all outliers (@test-boxplot.r#12) 
  3. Failure: stringsAsFactors doesn't affect results (@test-data.r#22) 
  4. Failure: stringsAsFactors doesn't affect results (@test-data.r#23) 
  5. Failure: stringsAsFactors doesn't affect results (@test-data.r#24) 
  6. Failure: stringsAsFactors doesn't affect results (@test-data.r#25) 
  7. Error: facets with free scales scale independently (@test-facet-.r#22) 
  8. Error: shrink parameter affects scaling (@test-facet-.r#44) 
  9. Error: labeller() dispatches labellers (@test-facet-labels.r#87) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted

checking for unstated dependencies in 'tests' ... WARNING
'library' or 'require' call not declared from: 'ggplot2'
R CMD check results
2 errors | 1 warning  | 0 notes

R CMD check succeeded

I guess some warnings might be because I am using a Windows machine. Still most errors are, as expected, in tests and examples...

[tdhock]

also you may want to turn on travis for this repo, with the standard r cran checks

[tdhock]

still have list() NULL problems

thocking@silene:~/R$ R CMD build ggplot2-faizan && R CMD check --as-cran ggplot2Animint_2.1.0.99.tar.gz 
* checking for file ‘ggplot2-faizan/DESCRIPTION’ ... OK
* preparing ‘ggplot2Animint’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘ggplot2Animint_2.1.0.99.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'

* using log directory ‘/home/thocking/R/ggplot2Animint.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘ggplot2Animint/DESCRIPTION’ ... OK
* this is package ‘ggplot2Animint’ version ‘2.1.0.99’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Faizan Khan <faizan.khan.iitbhu@gmail.com>’

New submission
* 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 ‘ggplot2Animint’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives no person with name and author role
* 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 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 ... OK
* checking Rd files ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
** found \donttest examples: check also with --run-donttest
* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘ggplot2’
* checking tests ...
  Running ‘testthat.R’ [14s/14s]
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In structure(NULL, class = "waiver") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
  2: In structure(NULL, class = "waiver") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
  3: In structure(NULL, class = "waiver") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
  4: In structure(NULL, class = "waiver") :
    Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
    Consider 'structure(list(), *)' instead.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/thocking/R/ggplot2Animint.Rcheck/00check.log’
for details.

thocking@silene:~/R$ 

[tdhock]

this line probably means you need to remove some library(ggplot2) from the testing code

* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘ggplot2’

[tdhock]

need to change ggplot2 to ggplot2Animint in testthat.R!

[tdhock]

also in these files:

grep -nH -e ggplot2 *.r
test-function-args.r:10:  ggplot2_ns <- asNamespace("ggplot2")
test-function-args.r:11:  objs <- ls(ggplot2_ns)
test-function-args.r:24:    geom_fun    <- ggplot2_ns[[geom_fun_name]]
test-function-args.r:43:  ggplot2_ns <- asNamespace("ggplot2")
test-function-args.r:44:  objs <- ls(ggplot2_ns)
test-function-args.r:56:    stat_fun         <- ggplot2_ns[[stat_fun_name]]
test-scales.r:136:  scale_x_continuous <- function(...) ggplot2::scale_x_continuous("1")
test-scales.r:141:    scale_x_continuous <- function(...) ggplot2::scale_x_continuous("2")
test-scales.r:157:    ggplot2::scale_colour_hue)
test-scales.r:166:  # from the ggplot2 namespace
test-scales.r:168:    ggplot2::scale_colour_hue)

[faizan-khan-iit]

@tdhock I will try and replicate your output on my Linux system tomorrow if possible. Because I don't think we should still have that warning. Do you also get that warning while using the newer syntax in animint2 code that you mentioned here?

[tdhock]

no warning for the animint2 code,

thocking@silene:~/R$ R --no-save < animint2-test.R

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ggplot2Animint)
> ## Example 1
> mtcars$cyl <- as.factor(mtcars$cyl)
> # New syntax
> p2 <- ggplot() + geom_point(aes(x=hp,
+                                 y=disp),
+                             showSelected = c("cyl", "am"), 
+                             data = mtcars)
> animint2::animint2dir(list(p2=p2), "~/test_animint2_initial2")
> devtools::session_info()
Session info -------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 system   x86_64, linux-gnu           
 ui       X11                         
 language en_CA:en                    
 collate  en_CA.UTF-8                 
 tz       America/Montreal            
 date     2017-08-01                  

Packages -----------------------------------------------------------------------
 package        * version     date       source                          
 animint2         2017.06.13  2017-08-01 local                           
 assertthat       0.2.0       2017-04-11 cran (@0.2.0)                   
 colorspace       1.2-6       2015-03-11 CRAN (R 3.2.3)                  
 devtools         1.12.0.9000 2016-08-12 Github (hadley/devtools@565ac15)
 digest           0.6.12      2017-01-27 cran (@0.6.12)                  
 ggplot2Animint * 2.1.0.99    2017-08-01 local                           
 gtable           0.2.0       2016-02-26 CRAN (R 3.2.3)                  
 labeling         0.3         2014-08-23 CRAN (R 3.2.3)                  
 lazyeval         0.2.0       2016-06-12 CRAN (R 3.3.3)                  
 memoise          1.0.0       2016-01-29 CRAN (R 3.2.3)                  
 munsell          0.4.3       2016-02-13 CRAN (R 3.2.3)                  
 plyr             1.8.4       2016-06-08 CRAN (R 3.2.3)                  
 Rcpp             0.12.7      2016-09-05 cran (@0.12.7)                  
 RJSONIO          1.3-1       2016-08-03 local                           
 scales           0.4.1       2016-11-09 CRAN (R 3.3.2)                  
 tibble           1.2         2016-08-26 CRAN (R 3.3.1)                  
 withr            1.0.2       2016-06-20 CRAN (R 3.2.3)                  
> 
thocking@silene:~/R$ 

[vivekktiwari]

my check() output on animint2 :

Major Issue I am facing is on RSelenium package not being available for R v3.4.4 or R v3.5.0

> install.packages("RSelenium")
Installing package into ‘C:/Users/Hp/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘RSelenium’ is not available (for R version 3.5.0)

Same for when done in R v3.4.4

Output:

 check()
Updating animint2 documentation
Loading animint2
Setting env vars --------------------------------------------------------
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building animint2 -------------------------------------------------------
"C:/PROGRA~1/R/R-35~1.0/bin/x64/R" --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD build  \
  "C:\Users\Hp\Desktop\GProject\animint2" --no-resave-data --no-manual 

* checking for file 'C:\Users\Hp\Desktop\GProject\animint2/DESCRIPTION' ... OK
* preparing 'animint2':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'animint2_2017.08.24.tar.gz'

Setting env vars --------------------------------------------------------
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE
Checking animint2 -------------------------------------------------------
"C:/PROGRA~1/R/R-35~1.0/bin/x64/R" --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD check  \
  "C:\Users\Hp\AppData\Local\Temp\RtmpGwKG83/animint2_2017.08.24.tar.gz"  \
  --as-cran --timings --no-manual 

* using log directory 'C:/Users/Hp/AppData/Local/Temp/RtmpGwKG83/animint2.Rcheck'
* using R version 3.5.0 (2018-04-23)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'animint2/DESCRIPTION' ... OK
* this is package 'animint2' version '2017.08.24'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'RSelenium'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for .dll and .exe files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'animint2' can be installed ... OK
* checking package 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 ... WARNING
'::' or ':::' imports not declared from:
  'RJSONIO' 'hexbin'
':::' call which should be '::': 'ggplot2Animint:::zeroGrob'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'ggplot2Animint:::guides_geom' 'ggplot2Animint:::guides_merge'
  'ggplot2Animint:::guides_train' 'ggplot2Animint:::plot_theme'
  'ggplot2Animint:::stairstep'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
animint2dir: no visible global function definition for 'browseURL'
animint2gist: no visible global function definition for 'browseURL'
getCommonChunk: no visible global function definition for 'na.omit'
getLegendList: no visible global function definition for 'str'
html_dependency_animint: no visible global function definition for
  'packageVersion'
html_dependency_plotJSON: no visible global function definition for
  'packageVersion'
html_dependency_shinyAnimint: no visible global function definition for
  'packageVersion'
parsePlot: no visible global function definition for 'setNames'
saveChunks: no visible global function definition for 'write.table'
saveChunks: no visible global function definition for 'str'
saveLayer : <anonymous>: no visible binding for global variable 'xminv'
saveLayer : <anonymous>: no visible binding for global variable 'y'
saveLayer : <anonymous>: no visible binding for global variable 'xmaxv'
saveLayer: no visible global function definition for 'head'
saveLayer: no visible global function definition for 'tail'
saveLayer: no visible global function definition for 'write.table'
saveLayer : bad.chunk: no visible binding for global variable
  'chunks.for'
saveLayer: no visible global function definition for 'na.omit'
split.x: no visible global function definition for 'na.omit'
split.x: no visible global function definition for 'str'
stop_binary: no visible binding for global variable 'pJS'
stop_binary: no visible binding for global variable 'remDr'
tests_init: no visible binding for '<<-' assignment to 'pJS'
tests_init: no visible binding for '<<-' assignment to 'remDr'
tests_init: no visible binding for global variable 'remDr'
toRGB: no visible global function definition for 'col2rgb'
toRGB: no visible global function definition for 'rgb'
Undefined global functions or variables:
  browseURL chunks.for col2rgb head na.omit pJS packageVersion remDr
  rgb setNames str tail write.table xmaxv xminv y
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "browseURL", "head", "packageVersion", "str",
             "tail", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'animint2dir.Rd':
  'ggplot2'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'ChromHMMiterations' 'FluView' 'FunctionalPruning' 'PeakConsistency'
  'TestROC' 'UStornadoes' 'VariantModels' 'WorldBank' 'breakpoints'
  'change' 'climate' 'compare' 'generation.loci' 'intreg' 'malaria'
  'mixtureKNN' 'pirates' 'prior' 'prostateLasso' 'vervet' 'worldPop'
Undocumented data sets:
  'ChromHMMiterations' 'FluView' 'FunctionalPruning' 'PeakConsistency'
  'TestROC' 'UStornadoes' 'VariantModels' 'WorldBank' 'breakpoints'
  'change' 'climate' 'compare' 'generation.loci' 'intreg' 'malaria'
  'mixtureKNN' 'pirates' 'prior' 'prostateLasso' 'vervet' 'worldPop'
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 ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'geom_tallrect'
  'na.rm' 'show.legend' 'inherit.aes'

Undocumented arguments in documentation object 'geom_widerect'
  'na.rm' 'show.legend' 'inherit.aes'

Undocumented arguments in documentation object 'getCommonChunk'
  'chunk.vars'

Undocumented arguments in documentation object 'parsePlot'
  'plot' 'plot.name'

Undocumented arguments in documentation object 'saveLayer'
  'layer_name' 'ggplot' 'built' 'AnimationInfo'
Documented arguments not in \usage in documentation object 'saveLayer':
  'geom_num'

Undocumented arguments in documentation object 'setPlotSizes'
  'AllPlotsInfo'

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.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'animint2-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: animint2dir
> ### Title: Compile and render an animint in a local directory
> ### Aliases: animint2dir animint
> 
> ### ** Examples
> 
> ## Make a Gapminder plot (aka Google motion chart), which is actually
> ## just a scatterplot with size and color that moves over time.
> library(animint2)
> data(WorldBank)
> gapminder <-
+   list(title="Linked scatterplot and time series",
+        ts=ggplot()+
+        make_tallrect(WorldBank, "year")+
+        geom_line(aes(year, life.expectancy, group=country, color=region),
+                  clickSelects="country",
+                  data=WorldBank, size=4, alpha=3/5),
+        time=list(variable="year",ms=3000),
+        duration=list(year=1000),
+        scatter=ggplot()+
+        geom_point(aes(fertility.rate, life.expectancy,
+                       key=country, colour=region, size=population),
+                   showSelected="year",
+                   clickSelects="country",
+                   data=WorldBank)+
+        geom_text(aes(fertility.rate, life.expectancy, label=country),
+                  showSelected=c("country", "year"),
+                  data=WorldBank)+
+        make_text(WorldBank, 5, 80, "year")+
+        scale_size_animint(pixel.range=c(2,20), breaks=10^(4:9)))
> animint2dir(gapminder, "WorldBank-viz")
Warning in issueSelectorWarnings(meta$geoms, meta$selector.aes, meta$duration) :
  to ensure that smooth transitions are interpretable, aes(key) should be specifed for geoms with showSelected=year, problem: geom4_text_scatter
Warning in issueSelectorWarnings(meta$geoms, meta$selector.aes, meta$duration) :
  to ensure that smooth transitions are interpretable, aes(key) should be specifed for geoms with showSelected=year, problem: geom5_text_scatter
Error in loadNamespace(name) : there is no package called 'RJSONIO'
Calls: animint2dir ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("animint2")
  Loading required package: ggplot2Animint
  > library("RSelenium")
  Error in library("RSelenium") : there is no package called 'RSelenium'
  Execution halted
* DONE

Status: 2 ERRORs, 4 WARNINGs, 2 NOTEs
See
  'C:/Users/Hp/AppData/Local/Temp/RtmpGwKG83/animint2.Rcheck/00check.log'
for details.

R CMD check results
2 errors | 4 warnings | 2 notes
checking examples ... ERROR
Running examples in 'animint2-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: animint2dir
> ### Title: Compile and render an animint in a local directory
> ### Aliases: animint2dir animint
> 
> ### ** Examples
... 23 lines ...
+                  data=WorldBank)+
+        make_text(WorldBank, 5, 80, "year")+
+        scale_size_animint(pixel.range=c(2,20), breaks=10^(4:9)))
> animint2dir(gapminder, "WorldBank-viz")
Warning in issueSelectorWarnings(meta$geoms, meta$selector.aes, meta$duration) :
  to ensure that smooth transitions are interpretable, aes(key) should be specifed for geoms with showSelected=year, problem: geom4_text_scatter
Warning in issueSelectorWarnings(meta$geoms, meta$selector.aes, meta$duration) :
  to ensure that smooth transitions are interpretable, aes(key) should be specifed for geoms with showSelected=year, problem: geom5_text_scatter
Error in loadNamespace(name) : there is no package called 'RJSONIO'
Calls: animint2dir ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("animint2")
  Loading required package: ggplot2Animint
  > library("RSelenium")
  Error in library("RSelenium") : there is no package called 'RSelenium'
  Execution halted

checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  'RJSONIO' 'hexbin'
':::' call which should be '::': 'ggplot2Animint:::zeroGrob'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'ggplot2Animint:::guides_geom' 'ggplot2Animint:::guides_merge'
  'ggplot2Animint:::guides_train' 'ggplot2Animint:::plot_theme'
  'ggplot2Animint:::stairstep'
  See the note in ?`:::` about the use of this operator.

checking Rd cross-references ... WARNING
Missing link or links in documentation object 'animint2dir.Rd':
  'ggplot2'

See section 'Cross-references' in the 'Writing R Extensions' manual.


checking for missing documentation entries ... WARNING
Undocumented code objects:
  'ChromHMMiterations' 'FluView' 'FunctionalPruning' 'PeakConsistency'
  'TestROC' 'UStornadoes' 'VariantModels' 'WorldBank' 'breakpoints'
  'change' 'climate' 'compare' 'generation.loci' 'intreg' 'malaria'
  'mixtureKNN' 'pirates' 'prior' 'prostateLasso' 'vervet' 'worldPop'
Undocumented data sets:
  'ChromHMMiterations' 'FluView' 'FunctionalPruning' 'PeakConsistency'
  'TestROC' 'UStornadoes' 'VariantModels' 'WorldBank' 'breakpoints'
  'change' 'climate' 'compare' 'generation.loci' 'intreg' 'malaria'
  'mixtureKNN' 'pirates' 'prior' 'prostateLasso' 'vervet' 'worldPop'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.

checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'geom_tallrect'
  'na.rm' 'show.legend' 'inherit.aes'

Undocumented arguments in documentation object 'geom_widerect'
  'na.rm' 'show.legend' 'inherit.aes'

Undocumented arguments in documentation object 'getCommonChunk'
  'chunk.vars'

... 6 lines ...
Documented arguments not in \usage in documentation object 'saveLayer':
  'geom_num'

Undocumented arguments in documentation object 'setPlotSizes'
  'AllPlotsInfo'

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.

checking package dependencies ... NOTE
Package suggested but not available for checking: 'RSelenium'

checking R code for possible problems ... NOTE
animint2dir: no visible global function definition for 'browseURL'
animint2gist: no visible global function definition for 'browseURL'
getCommonChunk: no visible global function definition for 'na.omit'
getLegendList: no visible global function definition for 'str'
html_dependency_animint: no visible global function definition for
  'packageVersion'
html_dependency_plotJSON: no visible global function definition for
  'packageVersion'
html_dependency_shinyAnimint: no visible global function definition for
... 21 lines ...
toRGB: no visible global function definition for 'col2rgb'
toRGB: no visible global function definition for 'rgb'
Undefined global functions or variables:
  browseURL chunks.for col2rgb head na.omit pJS packageVersion remDr
  rgb setNames str tail write.table xmaxv xminv y
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "browseURL", "head", "packageVersion", "str",
             "tail", "write.table")
to your NAMESPACE file.