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BioC 3.5: CHECK report for made4 on toluca2

This page was generated on 2017-04-23 14:33:25 -0400 (Sun, 23 Apr 2017).

Package 738/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
made4 1.49.0
Aedin Culhane
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/made4
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: made4
Version: 1.49.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings made4_1.49.0.tar.gz
StartedAt: 2017-04-23 06:04:42 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 06:05:29 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 46.9 seconds
RetCode: 0
Status:  OK 
CheckDir: made4.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings made4_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/made4.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘made4/DESCRIPTION’ ... OK
* this is package ‘made4’ version ‘1.49.0’
* 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.


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
NCI600.0270.0020.029
array2ade40.8740.0321.117
bet.coinertia0.0010.0010.001
between.graph0.6450.0080.659
bga1.0650.0101.081
bga.jackknife2.3480.0162.405
bga.suppl0.7240.0090.741
cia0.3660.0060.376
commonMap0.0720.0010.073
comparelists0.0010.0000.001
do3d1.0980.0081.119
genes1d0.1950.0050.199
getcol0.0120.0010.013
graph1D0.0910.0020.093
heatplot4.2970.0704.441
html3D0.3350.0060.345
khan0.0130.0010.014
ord0.2980.0080.317
overview0.2310.0040.238
plotarrays0.3700.0040.386
plotgenes0.1480.0020.161
prettyDend0.2320.0040.261
randomiser0.0020.0000.003
s.var0.3360.0030.382
sumstats0.3290.0030.350
suppl0.6930.0050.715
topgenes0.1070.0030.111