Package: gprege

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gprege.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gprege_1.26.0.tar.gz

StartedAt: 2019-04-16 00:23:36 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:25:14 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 98.5 seconds

RetCode: 0

Status:  OK

CheckDir: gprege.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:gprege.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gprege_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/gprege.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gprege/DESCRIPTION’ ... OK
* this is package ‘gprege’ version ‘1.26.0’
* 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 ‘gprege’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
* 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 in Depends field not imported from: ‘gptk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compareROC: no visible global function definition for ‘par’
compareROC: no visible global function definition for ‘plot’
compareROC: no visible global function definition for ‘lines’
compareROC: no visible global function definition for ‘legend’
demTp63Gp1: no visible global function definition for ‘data’
demTp63Gp1: no visible binding for global variable ‘FullDellaGattaData’
demTp63Gp1: no visible binding for global variable
  ‘FragmentDellaGattaData’
demTp63Gp1: no visible binding for global variable ‘DGdat_p63’
demTp63Gp1: no visible binding for global variable ‘DGdat_p63_case1_GL’
demTp63Gp1: no visible binding for global variable ‘DGdat_p63_case2_GL’
demTp63Gp1: no visible binding for global variable ‘DGdat_p63_case3_GL’
demTp63Gp1: no visible global function definition for ‘graphics.off’
exhaustivePlot: no visible global function definition for ‘sd’
exhaustivePlot: no visible global function definition for ‘gpCreate’
exhaustivePlot: no visible global function definition for
  ‘gpExpandParam’
exhaustivePlot: no visible global function definition for
  ‘gpLogLikelihood’
exhaustivePlot: no visible global function definition for
  ‘filled.contour’
exhaustivePlot: no visible binding for global variable ‘gray.colors’
exhaustivePlot: no visible global function definition for ‘axis’
exhaustivePlot: no visible global function definition for ‘points’
exhaustivePlot: no visible global function definition for ‘dev.set’
exhaustivePlot: no visible global function definition for ‘gpPlot’
gprege: no visible global function definition for ‘gpOptions’
gprege: no visible global function definition for ‘sd’
gprege: no visible global function definition for ‘pdf’
gprege: no visible global function definition for ‘close.screen’
gprege: no visible global function definition for ‘split.screen’
gprege: no visible global function definition for ‘gpCreate’
gprege: no visible global function definition for ‘gpExpandParam’
gprege: no visible global function definition for ‘gpOptimise’
gprege: no visible global function definition for ‘gpExtractParam’
gprege: no visible global function definition for ‘gpLogLikelihood’
gprege: no visible global function definition for ‘screen’
gprege: no visible global function definition for ‘erase.screen’
gprege: no visible global function definition for ‘gpPlot’
gprege: no visible global function definition for ‘gpPosteriorMeanVar’
gprege: no visible global function definition for ‘rnorm’
gprege: no visible global function definition for ‘points’
gprege: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  DGdat_p63 DGdat_p63_case1_GL DGdat_p63_case2_GL DGdat_p63_case3_GL
  FragmentDellaGattaData FullDellaGattaData axis close.screen data
  dev.off dev.set erase.screen filled.contour gpCreate gpExpandParam
  gpExtractParam gpLogLikelihood gpOptimise gpOptions gpPlot
  gpPosteriorMeanVar graphics.off gray.colors legend lines par pdf plot
  points rnorm screen sd split.screen
Consider adding
  importFrom("grDevices", "dev.off", "dev.set", "graphics.off",
             "gray.colors", "pdf")
  importFrom("graphics", "axis", "close.screen", "erase.screen",
             "filled.contour", "legend", "lines", "par", "plot",
             "points", "screen", "split.screen")
  importFrom("stats", "rnorm", "sd")
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
demTp63Gp1     15.404  0.086  15.969
exhaustivePlot 14.979  0.068  15.335
gprege         10.875  0.024  11.032
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/gprege.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 gprege
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘gprege’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘gprege_quick.Rnw’ 
** testing if installed package can be loaded
* DONE (gprege)

name	user	system	elapsed
compareROC	0.066	0.011	0.078
demTp63Gp1	15.404	0.086	15.969
exhaustivePlot	14.979	0.068	15.335
gprege-package	0.000	0.000	0.001
gprege	10.875	0.024	11.032
rocStats	0.632	0.734	1.378