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BioC 3.4: CHECK report for made4 on zin1

This page was generated on 2016-09-21 03:35:52 -0700 (Wed, 21 Sep 2016).

Package 678/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
made4 1.47.0
Aedin Culhane
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/made4
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: made4
Version: 1.47.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings made4_1.47.0.tar.gz
StartedAt: 2016-09-20 08:46:35 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:47:03 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 27.5 seconds
RetCode: 0
Status:  OK 
CheckDir: made4.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings made4_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/made4.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘made4/DESCRIPTION’ ... OK
* this is package ‘made4’ version ‘1.47.0’
* 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 ‘made4’ 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' calls to packages already attached by Depends:
  ‘RColorBrewer’ ‘gplots’ ‘scatterplot3d’
  Please remove these calls from your code.
'library' or 'require' call to ‘affy’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘ade4’ ‘gplots’ ‘scatterplot3d’
  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
plot.bga: warning in s.var(dudi.bga$bet$ls, xax = axis1, yax = axis2,
  col = as.vector(factor(dudi.bga$fac, labels = arraycol)), ...):
  partial argument match of 'col' to 'colpoints'
plot.ord: warning in s.var(dudi.ord$co, xax = axis1, yax = axis2, col =
  cols.array, label = arraylabels, ...): partial argument match of
  'col' to 'colpoints'
plot.ord: warning in plotgenes(dudi.ord$li, genelabels = genelabels,
  nlab = nlab, col = genecol, axis1 = axis1, axis2 = axis2, ...):
  partial argument match of 'col' to 'colpoints'
bet.coinertia: no visible global function definition for ‘dudi.nsc’
bet.coinertia: no visible global function definition for ‘bca’
bet.coinertia: no visible global function definition for ‘coinertia’
bet.coinertia: no visible global function definition for ‘dudi.pca’
between.graph: no visible global function definition for ‘par’
between.graph: no visible global function definition for ‘points’
between.graph: no visible global function definition for ‘text’
between.graph: no visible global function definition for ‘abline’
between.graph: no visible binding for global variable ‘segments’
bga: no visible global function definition for ‘bca’
cia: no visible global function definition for ‘dudi.nsc’
cia: no visible global function definition for ‘coinertia’
cia: no visible global function definition for ‘dudi.coa’
commonMap: no visible global function definition for ‘plot.new’
commonMap: no visible global function definition for ‘par’
commonMap: no visible global function definition for ‘points’
commonMap: no visible global function definition for ‘abline’
commonMap: no visible global function definition for ‘segments’
do3d: no visible global function definition for ‘scatterplot3d’
dudi.rwcoa: no visible global function definition for ‘dudi.coa’
getcol: no visible global function definition for ‘par’
getcol: no visible global function definition for ‘image’
getdata: no visible global function definition for ‘exprs’
graph1D: no visible global function definition for ‘plot.new’
graph1D: no visible global function definition for ‘par’
graph1D: no visible global function definition for ‘points’
graph1D: no visible global function definition for ‘text’
graph1D: no visible global function definition for ‘abline’
heatplot : distEisen: no visible global function definition for ‘cor’
heatplot : distEisen: no visible global function definition for
  ‘as.dist’
heatplot : cols: no visible global function definition for ‘col2rgb’
heatplot : cols: no visible global function definition for ‘rgb’
heatplot : cols.gentleman: no visible global function definition for
  ‘colorRampPalette’
heatplot : cols.gentleman: no visible global function definition for
  ‘brewer.pal’
heatplot : distf: no visible global function definition for ‘dist’
heatplot: no visible global function definition for ‘as.dendrogram’
heatplot: no visible global function definition for ‘hclust’
heatplot: no visible global function definition for ‘heatmap.2’
ord: no visible global function definition for ‘dudi.coa’
ord: no visible global function definition for ‘dudi.pca’
ord: no visible global function definition for ‘dudi.nsc’
overview: no visible global function definition for ‘layout’
overview : distEisen: no visible global function definition for ‘cor’
overview : distEisen: no visible global function definition for
  ‘as.dist’
overview : colhc: no visible global function definition for ‘par’
overview : colhc: no visible global function definition for ‘image’
overview: no visible global function definition for ‘exprs’
overview: no visible global function definition for ‘hclust’
overview: no visible global function definition for ‘plot’
overview: no visible global function definition for ‘par’
plot.bga: no visible global function definition for ‘par’
plot.bga: no visible global function definition for ‘title’
plot.bga: no visible global function definition for ‘scatterutil.eigen’
plot.cia: no visible global function definition for ‘layout’
plot.ord: no visible global function definition for ‘par’
plot.ord: no visible global function definition for ‘scatterutil.eigen’
plot.suppl: no visible global function definition for ‘par’
prettyDend: no visible global function definition for ‘layout’
prettyDend : distEisen: no visible global function definition for ‘cor’
prettyDend : distEisen: no visible global function definition for
  ‘as.dist’
prettyDend : colhc: no visible global function definition for ‘par’
prettyDend : colhc: no visible global function definition for ‘image’
prettyDend : colhc: no visible global function definition for ‘mtext’
prettyDend: no visible global function definition for ‘hclust’
prettyDend: no visible global function definition for ‘plot’
rotate3d: no visible global function definition for ‘par’
rotate3d: no visible global function definition for ‘dev.copy’
rotate3d: no visible binding for global variable ‘pdf’
rotate3d: no visible global function definition for ‘dev.off’
rotate3d: no visible global function definition for ‘dev.cur’
s.groups: no visible global function definition for ‘par’
s.groups: no visible global function definition for ‘scatterutil.base’
s.groups: no visible global function definition for ‘points’
s.groups: no visible global function definition for ‘scatterutil.star’
s.groups: no visible global function definition for
  ‘scatterutil.ellipse’
s.groups: no visible global function definition for ‘scatterutil.eti’
s.groups: no visible global function definition for ‘box’
s.match.col : arrow1: no visible global function definition for
  ‘segments’
s.match.col : arrow1: no visible global function definition for
  ‘strheight’
s.match.col : arrow1: no visible global function definition for ‘par’
s.match.col : arrow1: no visible global function definition for
  ‘arrows’
s.match.col: no visible global function definition for ‘par’
s.match.col: no visible global function definition for
  ‘scatterutil.base’
s.match.col: no visible global function definition for ‘points’
s.match.col: no visible global function definition for
  ‘scatterutil.eti’
s.match.col: no visible global function definition for ‘box’
s.var: no visible global function definition for ‘par’
s.var: no visible global function definition for ‘scatterutil.base’
s.var : fun: no visible global function definition for ‘segments’
s.var : fun: no visible global function definition for ‘par’
s.var: no visible global function definition for ‘scatterutil.eti’
s.var: no visible global function definition for ‘points’
s.var: no visible global function definition for ‘box’
suppl : suppl.coord: no visible global function definition for ‘suprow’
suppl : threshold : calc.threshold: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  abline arrows as.dendrogram as.dist bca box brewer.pal coinertia
  col2rgb colorRampPalette cor dev.copy dev.cur dev.off dist dudi.coa
  dudi.nsc dudi.pca exprs hclust heatmap.2 image layout mtext par pdf
  plot plot.new points rgb scatterplot3d scatterutil.base
  scatterutil.eigen scatterutil.ellipse scatterutil.eti
  scatterutil.star sd segments strheight suprow text title
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.copy",
             "dev.cur", "dev.off", "pdf", "rgb")
  importFrom("graphics", "abline", "arrows", "box", "image", "layout",
             "mtext", "par", "plot", "plot.new", "points", "segments",
             "strheight", "text", "title")
  importFrom("stats", "as.dendrogram", "as.dist", "cor", "dist",
             "hclust", "sd")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: array2ade4.Rd:38: Dropping empty section \references
prepare_Rd: between.graph.Rd:40-42: Dropping empty section \value
prepare_Rd: between.graph.Rd:47: Dropping empty section \note
prepare_Rd: checkfac.Rd:15-16: Dropping empty section \details
prepare_Rd: checkfac.Rd:22: Dropping empty section \note
prepare_Rd: checkfac.Rd:23: Dropping empty section \seealso
prepare_Rd: checkfac.Rd:24-25: Dropping empty section \examples
prepare_Rd: chime3D.Rd:56: Dropping empty section \seealso
prepare_Rd: chime3D.Rd:57-59: Dropping empty section \examples
prepare_Rd: cia.Rd:106: Dropping empty section \note
prepare_Rd: commonMap.Rd:29-30: Dropping empty section \value
prepare_Rd: commonMap.Rd:31: Dropping empty section \references
prepare_Rd: do3d.Rd:73: Dropping empty section \note
prepare_Rd: do3d.Rd:71: Dropping empty section \references
prepare_Rd: dudi.rwcoa.Rd:39-41: Dropping empty section \examples
prepare_Rd: forrwcoa.Rd:38-40: Dropping empty section \examples
prepare_Rd: genes.Rd:28: Dropping empty section \value
prepare_Rd: genes.Rd:32-33: Dropping empty section \examples
prepare_Rd: genes1d.Rd:34: Dropping empty section \references
prepare_Rd: getdata.Rd:36: Dropping empty section \examples
prepare_Rd: graph1D.Rd:33-34: Dropping empty section \details
prepare_Rd: graph1D.Rd:35-37: Dropping empty section \value
prepare_Rd: graph1D.Rd:40: Dropping empty section \note
prepare_Rd: graph1D.Rd:38: Dropping empty section \references
prepare_Rd: html3D.Rd:74: Dropping empty section \seealso
prepare_Rd: jmol3D.Rd:37: Dropping empty section \seealso
prepare_Rd: jmol3D.Rd:38-39: Dropping empty section \examples
prepare_Rd: ord.Rd:93: Dropping empty section \references
prepare_Rd: overview.Rd:26: Dropping empty section \value
prepare_Rd: overview.Rd:29: Dropping empty section \note
prepare_Rd: overview.Rd:27: Dropping empty section \references
prepare_Rd: prettyDend.Rd:27: Dropping empty section \value
prepare_Rd: prettyDend.Rd:30: Dropping empty section \note
prepare_Rd: prettyDend.Rd:28: Dropping empty section \references
prepare_Rd: sumstats.Rd:52: Dropping empty section \note
prepare_Rd: sumstats.Rd:50: Dropping empty section \references
prepare_Rd: sumstats.Rd:56: Dropping empty section \seealso
prepare_Rd: topgenes.Rd:40: Dropping empty section \note
prepare_Rd: topgenes.Rd:38: Dropping empty section \references
* 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
* 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-3.4-bioc/meat/made4.Rcheck/00check.log’
for details.


made4.Rcheck/00install.out:

* installing *source* package ‘made4’ ...
** 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 (made4)

made4.Rcheck/made4-Ex.timings:

nameusersystemelapsed
NCI600.0160.0000.017
array2ade40.5200.0160.779
bet.coinertia000
between.graph0.3000.0000.299
bga0.3640.0040.368
bga.jackknife1.4080.0041.410
bga.suppl0.4040.0000.405
cia0.1440.0000.142
commonMap0.0200.0000.022
comparelists0.0000.0000.001
do3d0.3440.0000.344
genes1d0.1360.0000.136
getcol0.0120.0000.010
graph1D0.0640.0000.064
heatplot1.9120.0201.930
html3D0.2640.0000.262
khan0.0080.0000.010
ord0.1880.0080.199
overview0.1200.0000.121
plotarrays0.2560.0000.255
plotgenes0.1520.0000.154
prettyDend0.0800.0000.079
randomiser0.0000.0000.002
s.var0.2240.0000.232
sumstats0.2200.0040.227
suppl0.4760.0000.478
topgenes0.0760.0040.080