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CHECK report for pcot2 on malbec2

This page was generated on 2018-10-17 08:21:47 -0400 (Wed, 17 Oct 2018).

Package 1073/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcot2 1.48.0
Sarah Song
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/pcot2
Branch: RELEASE_3_7
Last Commit: 34dcf7a
Last Changed Date: 2018-04-30 10:35:05 -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: pcot2
Version: 1.48.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pcot2.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pcot2_1.48.0.tar.gz
StartedAt: 2018-10-16 02:37:29 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:38:09 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 40.9 seconds
RetCode: 0
Status:  OK 
CheckDir: pcot2.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pcot2.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pcot2_1.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/pcot2.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcot2/DESCRIPTION’ ... OK
* this is package ‘pcot2’ version ‘1.48.0’
* 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 ‘pcot2’ 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 ... NOTE
'library' or 'require' call to ‘amap’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Cor: no visible global function definition for ‘var’
Cor: no visible global function definition for ‘cov2cor’
aveProbe: no visible binding for global variable ‘median’
corplot: no visible global function definition for ‘hclust’
corplot2: no visible global function definition for ‘cor’
corplot2: no visible global function definition for ‘layout’
corplot2: no visible global function definition for ‘par’
corplot2: no visible global function definition for ‘hclust’
corplot2: no visible global function definition for ‘image’
corplot2: no visible global function definition for ‘title’
corplot2: no visible global function definition for ‘box’
corplot2: no visible global function definition for ‘axis’
corplot2: no visible global function definition for ‘plot.new’
geneLocator: no visible global function definition for ‘plot.new’
geneLocator: no visible global function definition for ‘par’
geneLocator: no visible global function definition for ‘image’
geneLocator: no visible global function definition for ‘title’
geneLocator: no visible global function definition for ‘axis’
geneLocator: no visible global function definition for ‘locator’
pco: no visible global function definition for ‘cmdscale’
pcot2: no visible global function definition for ‘p.adjust’
plotCor: no visible global function definition for ‘par’
plotCor: no visible global function definition for ‘layout’
plotCor: no visible global function definition for ‘image’
plotCor: no visible global function definition for ‘title’
plotCor: no visible global function definition for ‘box’
plotCor: no visible global function definition for ‘axis’
rb: no visible global function definition for ‘rgb’
rg: no visible global function definition for ‘rgb’
rg: no visible global function definition for ‘dnorm’
t2: no visible global function definition for ‘var’
t2: no visible global function definition for ‘pf’
t2.unequ: no visible global function definition for ‘var’
wb: no visible global function definition for ‘rgb’
wb: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  axis box cmdscale cor cov2cor dnorm hclust image layout locator
  median p.adjust par pf plot.new rgb title var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "box", "image", "layout", "locator",
             "par", "plot.new", "title")
  importFrom("stats", "cmdscale", "cor", "cov2cor", "dnorm", "hclust",
             "median", "p.adjust", "pf", "var")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
pcot2    9.176  0.472  11.980
aveProbe 5.848  0.208   6.061
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/pcot2.Rcheck/00check.log’
for details.



Installation output

pcot2.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL pcot2
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘pcot2’ ...
** R
** 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 (pcot2)

Tests output


Example timings

pcot2.Rcheck/pcot2-Ex.timings

nameusersystemelapsed
aveProbe5.8480.2086.061
corplot0.4320.0160.451
corplot20.4960.0080.514
getImat0.2960.0000.295
pcot2 9.176 0.47211.980