BioC 3.5: CHECK report for OSAT on veracruz2

Package: OSAT

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OSAT_1.24.0.tar.gz

StartedAt: 2017-10-18 06:59:11 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:59:42 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 31.7 seconds

RetCode: 0

Status:  OK

CheckDir: OSAT.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OSAT_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/OSAT.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.24.0’
* 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 ‘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 loading without being on the library search path ... 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 installed files from ‘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-3.5-bioc/meat/OSAT.Rcheck/00check.log’
for details.

* installing *source* package ‘OSAT’ ...
** R
** data
** inst
** preparing 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	0.040	0.002	0.041
BeadPlate-class	0.006	0.000	0.007
MSAroboticPlate-class	0.321	0.011	0.336
QC	1.239	0.013	1.320
create.optimized.setup	1.109	0.012	1.160
example.setup	0.037	0.004	0.045
gContainer-class	0.017	0.001	0.018
gExperimentSetup-class	0.058	0.002	0.061
gSample-class	0.013	0.001	0.015
gSlide-class	0.003	0.000	0.004
get.experiment.setup	1.095	0.009	1.148
multi.barplot	0.011	0.001	0.012
multi.chisq.test	0.023	0.001	0.024
optimal.block	1.663	0.014	1.775
optimal.shuffle	1.175	0.009	1.234