Package: ffpe

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ffpe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ffpe_1.31.0.tar.gz

StartedAt: 2020-01-16 04:24:48 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:33:10 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 502.4 seconds

RetCode: 0

Status:  OK

CheckDir: ffpe.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ffpe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ffpe_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ffpe.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ffpe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ffpe’ version ‘1.31.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ffpe’ 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 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 ... NOTE
CATplot: no visible global function definition for ‘abline’
sampleQC,matrix : makeplots: no visible global function definition for
  ‘cor’
sampleQC,matrix : makeplots: no visible global function definition for
  ‘median’
sampleQC,matrix : makeplots: no visible binding for global variable
  ‘median’
sampleQC,matrix : makeplots: no visible global function definition for
  ‘na.omit’
sampleQC,matrix : makeplots: no visible global function definition for
  ‘loess’
sampleQC,matrix : makeplots: no visible global function definition for
  ‘predict’
sampleQC,matrix : makeplots: no visible global function definition for
  ‘IQR’
sampleQC,matrix : makeplots: no visible global function definition for
  ‘abline’
sampleQC,matrix : makeplots: no visible global function definition for
  ‘legend’
sampleQC,matrix : makeplots: no visible global function definition for
  ‘lines’
sampleQC,matrix: no visible binding for global variable ‘IQR’
sampleQC,matrix: no visible global function definition for ‘na.omit’
sortedIqrPlot,matrix: no visible binding for global variable ‘quantile’
sortedIqrPlot,matrix: no visible global function definition for
  ‘segments’
sortedIqrPlot,matrix: no visible binding for global variable ‘IQR’
Undefined global functions or variables:
  IQR abline cor legend lines loess median na.omit predict quantile
  segments
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "segments")
  importFrom("stats", "IQR", "cor", "loess", "median", "na.omit",
             "predict", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
CATplot      6.990  0.639   7.632
ffpe-package 6.734  0.766   7.522
sampleQC     6.484  0.511   7.063
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ffpe.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ffpe
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ffpe’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package keeps a record of temporary installation path
* DONE (ffpe)

name	user	system	elapsed
CATplot	6.990	0.639	7.632
ffpe-package	6.734	0.766	7.522
sampleQC	6.484	0.511	7.063
sortedIqrPlot	1.428	0.268	1.696