Package: OSAT

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OSAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OSAT_1.30.0.tar.gz

StartedAt: 2019-04-16 01:44:11 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:44:47 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 36.7 seconds

RetCode: 0

Status:  OK

CheckDir: OSAT.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:OSAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OSAT_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/OSAT.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 ‘OSAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OSAT’ version ‘1.30.0’
* 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 ‘OSAT’ 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
assign.sample.to.container: no visible global function definition for
  ‘head’
barplot.gExperimentSetup: no visible global function definition for
  ‘layout’
barplot.gExperimentSetup: no visible global function definition for
  ‘barplot’
barplot.gExperimentSetup: no visible global function definition for
  ‘gray’
barplot.gExperimentSetup: no visible global function definition for
  ‘points’
barplot.gExperimentSetup: no visible global function definition for
  ‘mtext’
multi.barplot: no visible global function definition for ‘layout’
multi.barplot: no visible global function definition for ‘barplot’
multi.barplot: no visible global function definition for ‘gray’
multi.barplot: no visible global function definition for ‘mtext’
show,gAssembly: no visible global function definition for ‘head’
show,gAssembly: no visible global function definition for ‘tail’
show,gContainer: no visible global function definition for ‘head’
show,gContainer: no visible global function definition for ‘tail’
show,gExperimentSetup: no visible global function definition for ‘head’
show,gExperimentSetup: no visible global function definition for ‘tail’
show,gPlate: no visible global function definition for ‘head’
show,gPlate: no visible global function definition for ‘tail’
show,gSample: no visible global function definition for ‘head’
show,gSample: no visible global function definition for ‘tail’
Undefined global functions or variables:
  barplot gray head layout mtext points tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "barplot", "layout", "mtext", "points")
  importFrom("utils", "head", "tail")
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
* 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-3.8-bioc/meat/OSAT.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 OSAT
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘OSAT’ ...
** 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 (OSAT)

name	user	system	elapsed
BeadChip-class	0.016	0.002	0.018
BeadPlate-class	0.006	0.000	0.006
MSAroboticPlate-class	0.349	0.017	0.370
QC	1.577	0.048	1.648
create.optimized.setup	1.444	0.018	1.500
example.setup	0.036	0.004	0.040
gContainer-class	0.014	0.001	0.015
gExperimentSetup-class	0.049	0.001	0.050
gSample-class	0.012	0.000	0.012
gSlide-class	0.040	0.001	0.040
get.experiment.setup	1.542	0.016	1.568
multi.barplot	0.014	0.001	0.015
multi.chisq.test	0.016	0.002	0.025
optimal.block	2.649	0.018	2.736
optimal.shuffle	1.514	0.029	1.565