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CHECK report for gprege on merida2

This page was generated on 2018-10-17 08:50:23 -0400 (Wed, 17 Oct 2018).

Package 641/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gprege 1.24.0
Alfredo Kalaitzis
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/gprege
Branch: RELEASE_3_7
Last Commit: 1495611
Last Changed Date: 2018-04-30 10:35:24 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gprege
Version: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2018-10-16 21:50:22 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:51:46 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 84.7 seconds
RetCode: 0
Status:  OK 
CheckDir: gprege.Rcheck
Warnings: 0

Command output

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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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/gprege.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.24.0’
* 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
exhaustivePlot 12.310  0.048  12.467
demTp63Gp1     11.526  0.068  11.652
gprege          9.478  0.034   9.555
* 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-3.7-bioc/meat/gprege.Rcheck/00check.log’
for details.



Installation output

gprege.Rcheck/00install.out

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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)

Tests output


Example timings

gprege.Rcheck/gprege-Ex.timings

nameusersystemelapsed
compareROC0.0560.0100.066
demTp63Gp111.526 0.06811.652
exhaustivePlot12.310 0.04812.467
gprege-package0.0000.0000.001
gprege9.4780.0349.555
rocStats0.5020.5081.011