BioC 3.0: CHECK report for made4 on oaxaca

Package: made4

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch made4_1.40.0.tar.gz

StartedAt: 2015-04-10 00:54:32 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:55:18 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 45.9 seconds

RetCode: 0

Status:  OK

CheckDir: made4.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch made4_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/made4.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.40.0’
* 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 ... [2s/2s] 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’
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’
do3d: no visible global function definition for ‘scatterplot3d’
dudi.rwcoa: no visible global function definition for ‘dudi.coa’
getdata: no visible global function definition for ‘exprs’
heatplot : cols.gentleman: no visible global function definition for
  ‘brewer.pal’
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 ‘exprs’
plot.bga: no visible global function definition for ‘scatterutil.eigen’
plot.ord: no visible global function definition for ‘scatterutil.eigen’
s.groups: no visible global function definition for ‘scatterutil.base’
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.match.col: no visible global function definition for
  ‘scatterutil.base’
s.match.col: no visible global function definition for
  ‘scatterutil.eti’
s.var: no visible global function definition for ‘scatterutil.base’
s.var: no visible global function definition for ‘scatterutil.eti’
suppl : suppl.coord: no visible global function definition for ‘suprow’
* 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 ... [12s/13s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.028	0.003	0.030
array2ade4	1.145	0.035	1.223
bet.coinertia	0.001	0.000	0.001
between.graph	0.438	0.009	0.470
bga	0.513	0.009	0.533
bga.jackknife	2.448	0.005	2.488
bga.suppl	0.692	0.010	0.772
cia	0.235	0.005	0.240
commonMap	0.034	0.001	0.036
comparelists	0.002	0.000	0.001
do3d	0.600	0.007	0.620
genes1d	0.136	0.004	0.143
getcol	0.014	0.002	0.016
graph1D	0.092	0.001	0.093
heatplot	2.133	0.038	2.198
html3D	0.332	0.006	0.339
khan	0.014	0.001	0.015
ord	0.186	0.004	0.227
overview	0.170	0.004	0.176
plotarrays	0.466	0.007	0.620
plotgenes	0.156	0.002	0.158
prettyDend	0.131	0.004	0.144
randomiser	0.003	0.001	0.004
s.var	0.423	0.003	0.427
sumstats	0.353	0.003	0.552
suppl	0.731	0.006	0.747
topgenes	0.109	0.003	0.112