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CHECK report for PROPER on veracruz1

This page was generated on 2018-04-12 13:40:00 -0400 (Thu, 12 Apr 2018).

Package 1075/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PROPER 1.10.0
Hao Wu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/PROPER
Branch: RELEASE_3_6
Last Commit: 78025ac
Last Changed Date: 2017-10-30 12:40:47 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PROPER
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PROPER_1.10.0.tar.gz
StartedAt: 2018-04-12 07:55:24 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 07:56:18 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 54.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: PROPER.Rcheck
Warnings: 2

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PROPER_1.10.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PROPER.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PROPER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PROPER’ version ‘1.10.0’
* 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 ‘PROPER’ 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 ... WARNING
'library' or 'require' call not declared from: ‘edgeR’
'library' or 'require' call to ‘edgeR’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RNAseq.SimOptions.2grp: no visible global function definition for
  ‘data’
RNAseq.SimOptions.2grp: no visible binding for global variable ‘cheung’
add.axis1: no visible global function definition for ‘axis’
add.axis1: no visible global function definition for ‘text’
comparePower: no visible global function definition for ‘p.adjust’
estParam: no visible global function definition for ‘exprs’
getDisp1: no visible global function definition for ‘median’
lfc.alt: no visible global function definition for ‘rnorm’
lfc.null: no visible global function definition for ‘rnorm’
plotAll: no visible global function definition for ‘par’
plotAll: no visible global function definition for ‘mtext’
plotFDR: no visible global function definition for ‘matplot’
plotFDR: no visible global function definition for ‘mtext’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘box’
plotFDR: no visible global function definition for ‘grid’
plotFDR: no visible global function definition for ‘legend’
plotFDcost : <anonymous>: no visible global function definition for
  ‘sd’
plotFDcost: no visible global function definition for ‘matplot’
plotFDcost: no visible global function definition for ‘arrows’
plotFDcost: no visible global function definition for ‘mtext’
plotFDcost: no visible global function definition for ‘axis’
plotFDcost: no visible global function definition for ‘box’
plotFDcost: no visible global function definition for ‘grid’
plotFDcost: no visible global function definition for ‘legend’
plotPower: no visible binding for global variable ‘sd’
plotPower: no visible global function definition for ‘matplot’
plotPower: no visible global function definition for ‘arrows’
plotPower: no visible global function definition for ‘mtext’
plotPower: no visible global function definition for ‘legend’
plotPower: no visible global function definition for ‘grid’
plotPower: no visible global function definition for ‘axis’
plotPower: no visible global function definition for ‘box’
plotPowerAlpha: no visible binding for global variable ‘sd’
plotPowerAlpha: no visible global function definition for ‘matplot’
plotPowerAlpha: no visible global function definition for ‘arrows’
plotPowerAlpha: no visible global function definition for ‘mtext’
plotPowerAlpha: no visible global function definition for ‘axis’
plotPowerAlpha: no visible global function definition for ‘box’
plotPowerAlpha: no visible global function definition for ‘grid’
plotPowerAlpha: no visible global function definition for ‘abline’
plotPowerAlpha: no visible global function definition for ‘legend’
plotPowerFD: no visible binding for global variable ‘sd’
plotPowerFD: no visible global function definition for ‘matplot’
plotPowerFD: no visible global function definition for ‘arrows’
plotPowerFD: no visible global function definition for ‘mtext’
plotPowerFD: no visible global function definition for ‘axis’
plotPowerFD: no visible global function definition for ‘box’
plotPowerFD: no visible global function definition for ‘grid’
plotPowerFD: no visible global function definition for ‘legend’
plotPowerHist: no visible global function definition for ‘axis’
plotPowerTD: no visible binding for global variable ‘sd’
plotPowerTD: no visible global function definition for ‘matplot’
plotPowerTD: no visible global function definition for ‘arrows’
plotPowerTD: no visible global function definition for ‘mtext’
plotPowerTD: no visible global function definition for ‘axis’
plotPowerTD: no visible global function definition for ‘box’
plotPowerTD: no visible global function definition for ‘grid’
plotPowerTD: no visible global function definition for ‘legend’
rnegbinom: no visible global function definition for ‘rpois’
rnegbinom: no visible global function definition for ‘rgamma’
run.DESeq: no visible global function definition for ‘newCountDataSet’
run.DESeq: no visible global function definition for
  ‘estimateSizeFactors’
run.DESeq: no visible global function definition for
  ‘estimateDispersions’
run.DESeq: no visible global function definition for ‘nbinomTest’
run.DSS: no visible global function definition for ‘newSeqCountSet’
run.DSS: no visible global function definition for ‘estNormFactors’
run.DSS: no visible global function definition for ‘estDispersion’
run.DSS: no visible global function definition for ‘waldTest’
runSims: no visible global function definition for ‘median’
setBaselineExpr.seqDepth: no visible global function definition for
  ‘data’
table2hist: no visible global function definition for ‘hist’
table2hist: no visible global function definition for ‘rnorm’
table2hist: no visible global function definition for ‘plot’
table2hist: no visible global function definition for ‘axis’
table2hist: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline arrows axis box cheung data estDispersion estNormFactors
  estimateDispersions estimateSizeFactors exprs grid hist legend
  matplot median mtext nbinomTest newCountDataSet newSeqCountSet
  p.adjust par plot rgamma rnorm rpois sd text waldTest
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "grid",
             "hist", "legend", "matplot", "mtext", "par", "plot", "text")
  importFrom("stats", "median", "p.adjust", "rgamma", "rnorm", "rpois",
             "sd")
  importFrom("utils", "data")
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 ... WARNING
Codoc mismatches from documentation object 'estParam':
estParam
  Code: function(X, type = 1)
  Docs: function(X, type = c(1, 2))
  Mismatches in argument default values:
    Name: 'type' Code: 1 Docs: c(1, 2)

* 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
Examples with CPU or elapsed time > 5s
          user system elapsed
runSims 18.609  0.937  19.885
* 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 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/PROPER.Rcheck/00check.log’
for details.



Installation output

PROPER.Rcheck/00install.out

* installing *source* package ‘PROPER’ ...
** 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 (PROPER)

Tests output


Example timings

PROPER.Rcheck/PROPER-Ex.timings

nameusersystemelapsed
RNAseq.SimOptions.2grp0.6080.0220.647
comparePower0.0020.0010.003
estParam0.0010.0000.001
plotPowerHist0.0010.0000.002
plots0.0010.0000.002
power.seqDepth0.0010.0000.001
runSims18.609 0.93719.885
simRNAseq0.2750.0180.299
summaryPower0.0010.0000.000