BioC 3.5: CHECK report for made4 on veracruz2

Package: made4

Version: 1.50.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings made4_1.50.0.tar.gz

StartedAt: 2017-08-16 04:47:16 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:47:57 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 40.5 seconds

RetCode: 0

Status:  OK

CheckDir: made4.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings made4_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/made4.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 ‘made4/DESCRIPTION’ ... OK
* this is package ‘made4’ version ‘1.50.0’
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/made4.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
NCI60	0.019	0.002	0.021
array2ade4	0.691	0.025	1.018
bet.coinertia	0.000	0.000	0.001
between.graph	0.473	0.008	0.494
bga	0.803	0.010	0.852
bga.jackknife	1.660	0.013	1.711
bga.suppl	0.481	0.007	0.502
cia	0.253	0.005	0.265
commonMap	0.046	0.001	0.047
comparelists	0.001	0.000	0.002
do3d	0.746	0.006	0.774
genes1d	0.138	0.003	0.144
getcol	0.008	0.001	0.009
graph1D	0.057	0.001	0.059
heatplot	3.043	0.056	3.188
html3D	0.248	0.005	0.256
khan	0.011	0.001	0.012
ord	0.223	0.008	0.235
overview	0.166	0.004	0.173
plotarrays	0.258	0.003	0.266
plotgenes	0.124	0.002	0.129
prettyDend	0.153	0.005	0.161
randomiser	0.003	0.000	0.003
s.var	0.230	0.002	0.245
sumstats	0.257	0.003	0.264
suppl	0.440	0.006	0.455
topgenes	0.091	0.004	0.095