Package: Roleswitch

Version: 1.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Roleswitch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Roleswitch_1.21.0.tar.gz

StartedAt: 2019-04-05 03:32:32 -0400 (Fri, 05 Apr 2019)

EndedAt: 2019-04-05 03:35:08 -0400 (Fri, 05 Apr 2019)

EllapsedTime: 156.6 seconds

RetCode: 0

Status:  OK

CheckDir: Roleswitch.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:Roleswitch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Roleswitch_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Roleswitch.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Roleswitch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Roleswitch’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'pracma', 'reshape', 'plotrix', 'microRNA', 'biomaRt', 'Biostrings',
  'Biobase', 'DBI'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘Roleswitch’ 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
diagnosticPlot: no visible global function definition for ‘par’
diagnosticPlot: no visible global function definition for ‘axis’
diagnosticPlot: no visible global function definition for ‘plot’
getSeedMatrix: no visible global function definition for ‘data’
getTranscriptIDwithLongest3UTR: no visible global function definition
  for ‘aggregate’
roleswitch: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate axis data par plot
Consider adding
  importFrom("graphics", "axis", "par", "plot")
  importFrom("stats", "aggregate")
  importFrom("utils", "data")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getSeedMatrix 3.497  0.293  47.852
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Roleswitch.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 Roleswitch
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Roleswitch’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Roleswitch)

name	user	system	elapsed
Roleswitch-package	0.000	0.000	0.001
diagnosticPlot	0.044	0.001	0.045
getSeedMatrix	3.497	0.293	47.852
roleswitch	0.005	0.001	0.005
tcga_gbm_testdata	0.306	0.015	0.321