Package: facopy

Version: 1.13.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:facopy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings facopy_1.13.0.tar.gz

StartedAt: 2018-03-04 23:35:23 -0500 (Sun, 04 Mar 2018)

EndedAt: 2018-03-04 23:37:34 -0500 (Sun, 04 Mar 2018)

EllapsedTime: 131.0 seconds

RetCode: 0

Status:  OK

CheckDir: facopy.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:facopy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings facopy_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/facopy.Rcheck’
* using R Under development (unstable) (2018-01-28 r74177)
* using platform: x86_64-pc-linux-gnu (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 ‘1.13.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
facopyPlot 5.82  0.016   5.844
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/facopy.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
addFeatures	2.492	0.076	2.580
addVariables	0.068	0.004	0.070
alterationSummary	0.852	0.008	0.865
calculateCor	1.172	0.004	3.349
facopy	1.656	0.004	1.663
facopyEnrichment	0.036	0.000	0.034
facopyInfo-class	0.000	0.000	0.001
facopyPlot	5.820	0.016	5.844
getFacopyInfo	0.004	0.000	0.020
myCalls	0.028	0.000	0.028
myStudy	0.036	0.000	0.036
myVariables	0.000	0.004	0.003
plotBar	0.320	0.004	0.325
plotHist	0.968	0.004	0.995
plotPCA	0.18	0.00	0.18
plotZoom	0.216	0.004	0.220
preview	0.888	0.016	0.904
readCNData	0.004	0.000	0.001
variableCor	0.072	0.000	0.072
variableSummary	0.152	0.000	0.150