Package: iCheck

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iCheck.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iCheck_1.16.0.tar.gz

StartedAt: 2020-04-15 03:06:19 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:11:32 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 313.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: iCheck.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iCheck.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iCheck_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/iCheck.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iCheck/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iCheck’ version ‘1.16.0’
* 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 ‘iCheck’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/iCheck.Rcheck/00install.out’ for details.
* 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 ... OK
* 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
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/iCheck.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 iCheck
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘iCheck’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
** 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’
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
** testing if installed package keeps a record of temporary installation path
* DONE (iCheck)

name	user	system	elapsed
LumiBatch2Table	0.108	0.003	0.112
R2PlotFunc	0.347	0.033	0.375
boxPlots	0.947	0.016	0.972
densityPlots	0.111	0.006	0.119
genSimData.BayesNormal	0.031	0.000	0.032
getPCAFunc	0.048	0.002	0.049
glmWrapper	0.534	0.036	0.572
lkhrWrapper	0.768	0.100	0.873
lmFitPaired	0.065	0.010	0.074
lmFitWrapper	0.072	0.004	0.077
pca2DPlot	0.096	0.002	0.101
pca3DPlot	0.048	0.002	0.050
plotCurves	0.038	0.001	0.039
plotQCCurves	0.081	0.002	0.083
plotSamplep95p05	0.060	0.001	0.062
quantilePlot	0.109	0.020	0.124
scatterPlots	0.122	0.009	0.131
sortExpressionSet	0.057	0.000	0.057