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CHECK report for OSAT on malbec1

This page was generated on 2019-04-16 11:49:36 -0400 (Tue, 16 Apr 2019).

Package 1104/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OSAT 1.30.0
Li Yan
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/OSAT
Branch: RELEASE_3_8
Last Commit: dc662ac
Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OSAT
Version: 1.30.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:OSAT.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings OSAT_1.30.0.tar.gz
StartedAt: 2019-04-16 01:55:12 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:55:41 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 29.0 seconds
RetCode: 0
Status:  OK 
CheckDir: OSAT.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:OSAT.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings OSAT_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/OSAT.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/OSAT.Rcheck/00check.log’
for details.



Installation output

OSAT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL OSAT
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output


Example timings

OSAT.Rcheck/OSAT-Ex.timings

nameusersystemelapsed
BeadChip-class0.0120.0000.012
BeadPlate-class0.0160.0000.015
MSAroboticPlate-class0.3720.0000.375
QC1.3360.0001.336
create.optimized.setup1.0880.0081.099
example.setup0.0480.0000.047
gContainer-class0.0160.0000.018
gExperimentSetup-class0.0520.0000.054
gSample-class0.0160.0000.015
gSlide-class0.0280.0000.027
get.experiment.setup1.2720.0001.274
multi.barplot0.0160.0000.015
multi.chisq.test0.0120.0040.017
optimal.block2.1840.0082.199
optimal.shuffle1.0640.0081.073