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BioC 3.6: CHECK report for facopy on veracruz1

This page was generated on 2017-08-16 13:46:13 -0400 (Wed, 16 Aug 2017).

Package 434/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
facopy 1.11.0
David Mosen-Ansorena
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/facopy
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: facopy
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings facopy_1.11.0.tar.gz
StartedAt: 2017-08-16 02:54:47 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:57:39 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 172.5 seconds
RetCode: 0
Status:  OK 
CheckDir: facopy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings facopy_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/facopy.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘facopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘facopy’ version ‘1.11.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘cgdsr’ ‘coin’ ‘ggplot2’ ‘gridExtra’ ‘facopy.annot’ ‘grid’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘facopy’ 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 ... NOTE
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.aggregateInt: no visible global function definition for ‘data’
.checkFullModel: no visible global function definition for ‘formula’
.enrichment: no visible global function definition for ‘phyper’
.enrichment: no visible global function definition for ‘p.adjust’
.enrichment: no visible global function definition for ‘write.table’
.enrichment: no visible global function definition for ‘data’
.enrichment: no visible global function definition for ‘pdf’
.enrichment: no visible global function definition for ‘dev.off’
.enrichment : <anonymous>: no visible global function definition for
  ‘heat.colors’
.facopyPlotInt: no visible global function definition for ‘data’
.getFacopyAnnot: no visible global function definition for ‘data’
.graphPathway: no visible global function definition for ‘mtext’
.makeArmsInt: no visible global function definition for ‘data’
.makeCor : <anonymous>: no visible global function definition for ‘lm’
.plotArm: no visible global function definition for ‘data’
.plotVicinityInt: no visible global function definition for ‘par’
.plotVicinityInt : makeAb: no visible global function definition for
  ‘abline’
.plotVicinityInt: no visible global function definition for ‘layout’
.plotVicinityInt: no visible global function definition for ‘plot.new’
.plotVicinityInt: no visible global function definition for
  ‘plot.window’
.plotVicinityInt: no visible global function definition for ‘grid’
.plotVicinityInt: no visible global function definition for ‘quantile’
.plotVicinityInt: no visible global function definition for ‘rect’
.plotVicinityInt: no visible global function definition for ‘title’
.plotVicinityInt: no visible global function definition for ‘axis’
.plotVicinityInt: no visible global function definition for ‘mtext’
.plotVicinityInt: no visible global function definition for ‘legend’
.plotVicinityInt: no visible global function definition for ‘image’
.readFromGAP: no visible global function definition for ‘read.table’
.readFromInt: no visible global function definition for ‘read.delim’
.refcols: no visible global function definition for ‘colorRampPalette’
addFeatures: no visible global function definition for ‘read.table’
addVariables: no visible global function definition for ‘read.table’
alterationSummary: no visible global function definition for
  ‘write.table’
calculateCor: no visible global function definition for ‘read.table’
facopy : doMultinom: no visible global function definition for
  ‘formula’
facopy : doMultinom: no visible global function definition for ‘anova’
facopy: no visible global function definition for ‘formula’
facopy: no visible global function definition for ‘glm’
facopy: no visible global function definition for ‘binomial’
facopy: no visible global function definition for ‘anova’
facopyEnrichment: no visible global function definition for ‘data’
plotPCA: no visible global function definition for ‘points’
plotPCA: no visible global function definition for ‘legend’
plotPCA: no visible global function definition for ‘image’
plotPCA: no visible global function definition for ‘quantile’
variableCor: no visible global function definition for ‘combn’
variableCor: no visible global function definition for ‘chisq.test’
variableCor: no visible global function definition for ‘fisher.test’
variableCor: no visible global function definition for ‘cor.test’
variableCor: no visible global function definition for ‘oneway.test’
variableCor: no visible global function definition for ‘kruskal.test’
variableCor: no visible global function definition for ‘write.table’
variableSummary : wilcoxtest: no visible global function definition for
  ‘wilcox.test’
variableSummary : cortest: no visible global function definition for
  ‘cor.test’
variableSummary: no visible global function definition for ‘combn’
variableSummary: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  abline anova axis binomial chisq.test colorRampPalette combn cor.test
  data dev.off fisher.test formula glm grid heat.colors image
  kruskal.test layout legend lm mtext oneway.test p.adjust par pdf
  phyper plot.new plot.window points quantile read.delim read.table
  rect title wilcox.test write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "heat.colors",
             "pdf")
  importFrom("graphics", "abline", "axis", "grid", "image", "layout",
             "legend", "mtext", "par", "plot.new", "plot.window",
             "points", "rect", "title")
  importFrom("stats", "anova", "binomial", "chisq.test", "cor.test",
             "fisher.test", "formula", "glm", "kruskal.test", "lm",
             "oneway.test", "p.adjust", "phyper", "quantile",
             "wilcox.test")
  importFrom("utils", "combn", "data", "read.delim", "read.table",
             "write.table")
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
Examples with CPU or elapsed time > 5s
            user system elapsed
facopyPlot 9.399  0.028   9.736
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/facopy.Rcheck/00check.log’
for details.


facopy.Rcheck/00install.out:

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

facopy.Rcheck/facopy-Ex.timings:

nameusersystemelapsed
addFeatures1.8920.0131.908
addVariables0.0540.0070.061
alterationSummary0.5800.0160.597
calculateCor1.1590.0394.778
facopy1.8070.0101.860
facopyEnrichment0.0310.0030.035
facopyInfo-class0.0020.0000.001
facopyPlot9.3990.0289.736
getFacopyInfo0.0170.0010.020
myCalls0.0250.0040.030
myStudy0.0390.0050.044
myVariables0.0030.0040.007
plotBar0.4120.0130.443
plotHist1.7590.0311.866
plotPCA0.1310.0080.150
plotZoom0.2300.0090.249
preview0.6740.0260.721
readCNData0.0010.0000.000
variableCor0.0990.0040.104
variableSummary0.1570.0050.166