[R] R CMD methods and ggplot2 advice

[Glenn Schultz]

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