[R] R CMD methods and ggplot2 advice

[Thierry Onkelinx]

Dear Glenn,

Suppose this function

test <- function(df){
  ggplot(df, aes(x = gp, y = y)) + geom_point()
}

Then R CMD check will consider gp and y as global variables since they are
undefined. Because R CMD check cannot detect that gp and y will be
extracted from df by ggplot2.

Possible workarounds

# now gp and y are defined within the function. ggplot2 still looks for gp
and y in df.
test <- function(df){
  gp <- NULL
  y <- NULL
  ggplot(df, aes(x = gp, y = y)) + geom_point()
}

# now "gp" and "y" are strings and hence defined
test <- function(df){
  ggplot(df, aes_string(x = "gp", y = "y")) + geom_point()
}

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2015-05-26 2:24 GMT+02:00 Glenn Schultz <glennmschultz op me.com>:

> Hello All,
>
> I have two packages Bond Lab and the Companion to Investing in MBS.  Bond
> Lab clears the check and I am working on the on.load() to copy a needed
> directory per Duncan Murdoch's advise to make Bond Lab CRAN-able.  The
> companion passes with two notes.  The output is below:
>
> I get two notes (highlighted in red)
>
> Not sure on this one as I tried to declare methods but I get another note
> methods declared but not used.  The second note is related to ggplot2 they
> are variable passed to ggplot2 within a function.  I am not sure why they
> appear in the R CMD check.  If someone could point in the right direction
> to resolve these I would appreciate the advice.  These are my last
> remaining two issues to make the packages pass CRAN aside from the on.load()
>
> Best Regards,
> Glenn
>
> * checking dependencies in R code ... NOTE
> package ‘methods’ is used but not declared
>
>
> * checking R code for possible problems ... NOTE
> CreditEnhancement: no visible binding for global variable ‘Period’
> CreditEnhancement: no visible binding for global variable ‘Value’
> CreditEnhancement: no visible binding for global variable ‘Variable’
> CreditEnhancement: no visible binding for global variable ‘..density..’
> PassThrough.OAS: no visible binding for global variable ‘value’
> PassThrough.OAS: no visible binding for global variable ‘..density..’
> PassThroughCashFlow: no visible binding for global variable ‘Period’
> PassThroughCashFlow: no visible binding for global variable ‘value’
> PassThroughCashFlow: no visible binding for global variable ‘variable’
> PlotMtgKeyRates: no visible binding for global variable ‘Tenor’
> PlotMtgKeyRates: no visible binding for global variable ‘Duration’
> PlotTermStructure: no visible binding for global variable ‘value’
> PlotTermStructure: no visible binding for global variable ‘variable’
> REMICOAS: no visible binding for global variable ‘value’
> REMICOAS: no visible binding for global variable ‘..density..’
> TotalReturn: no visible binding for global variable ‘Scenario’
> TotalReturn: no visible binding for global variable ‘value’
> TotalReturn: no visible binding for global variable ‘variable’
> TwistScenario: no visible binding for global variable ‘Scenario’
> TwistScenario: no visible binding for global variable ‘Return’
> ValuationFramework: no visible binding for global variable ‘value’
> ValuationFramework: no visible binding for global variable ‘variable’
>
> ==> devtools::check()
>
> Updating Companion2IMBS documentation
> Loading Companion2IMBS
> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD build  \
>   '/Users/glennschultz/Companion to Investing in MBS' --no-resave-data  \
>   --no-manual
>
> * checking for file ‘/Users/glennschultz/Companion to Investing in
> MBS/DESCRIPTION’ ... OK
> * preparing ‘Companion2IMBS’:
> * checking DESCRIPTION meta-information ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> Removed empty directory ‘Companion2IMBS/inst’
> Removed empty directory ‘Companion2IMBS/test/testthat’
> Removed empty directory ‘Companion2IMBS/test’
> * building ‘Companion2IMBS_1.0.tar.gz’
>
> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD check  \
>
> '/var/folders/tv/sq6gmnvs13j8jrhkt87f_zmc0000gn/T//RtmpOabREs/Companion2IMBS_1.0.tar.gz'
>  \
>   --timings
>
> * using log directory ‘/Users/glennschultz/Companion2IMBS.Rcheck’
> * using R version 3.0.3 (2014-03-06)
> * using platform: x86_64-apple-darwin10.8.0 (64-bit)
> * using session charset: UTF-8
> * checking for file ‘Companion2IMBS/DESCRIPTION’ ... OK
> * checking extension type ... Package
> * this is package ‘Companion2IMBS’ version ‘1.0’
> * 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 ‘Companion2IMBS’ can be installed ... OK
> * checking installed package size ... 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 dependencies in R code ... NOTE
> package ‘methods’ is used but not declared
> See the information on DESCRIPTION files in the chapter ‘Creating R
> packages’ of the ‘Writing R Extensions’ manual.
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... NOTE
> CreditEnhancement: no visible binding for global variable ‘Period’
> CreditEnhancement: no visible binding for global variable ‘Value’
> CreditEnhancement: no visible binding for global variable ‘Variable’
> CreditEnhancement: no visible binding for global variable ‘..density..’
> PassThrough.OAS: no visible binding for global variable ‘value’
> PassThrough.OAS: no visible binding for global variable ‘..density..’
> PassThroughCashFlow: no visible binding for global variable ‘Period’
> PassThroughCashFlow: no visible binding for global variable ‘value’
> PassThroughCashFlow: no visible binding for global variable ‘variable’
> PlotMtgKeyRates: no visible binding for global variable ‘Tenor’
> PlotMtgKeyRates: no visible binding for global variable ‘Duration’
> PlotTermStructure: no visible binding for global variable ‘value’
> PlotTermStructure: no visible binding for global variable ‘variable’
> REMICOAS: no visible binding for global variable ‘value’
> REMICOAS: no visible binding for global variable ‘..density..’
> TotalReturn: no visible binding for global variable ‘Scenario’
> TotalReturn: no visible binding for global variable ‘value’
> TotalReturn: no visible binding for global variable ‘variable’
> TwistScenario: no visible binding for global variable ‘Scenario’
> TwistScenario: no visible binding for global variable ‘Return’
> ValuationFramework: no visible binding for global variable ‘value’
> ValuationFramework: no visible binding for global variable ‘variable’
> * 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 examples ... [60s/60s] OK
> Examples with CPU or elapsed time > 5s
>                     user system elapsed
> TwistScenario     18.827  1.037  19.872
> PassThrough.OAS   17.485  0.068  17.567
> CreditEnhancement 10.959  0.128  11.106
> PlotMtgKeyRates   10.081  0.421  10.506
> * checking PDF version of manual ... OK
> NOTE: There were 2 notes.
> See
>   ‘/Users/glennschultz/Companion2IMBS.Rcheck/00check.log’
> for details.
>
>
>
> R CMD check succeeded
>
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