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CHECK report for made4 on tokay1

This page was generated on 2019-04-13 11:19:34 -0400 (Sat, 13 Apr 2019).

Package 864/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
made4 1.56.0
Aedin Culhane
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/made4
Branch: RELEASE_3_8
Last Commit: 175c6c9
Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: made4
Version: 1.56.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:made4.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings made4_1.56.0.tar.gz
StartedAt: 2019-04-13 03:29:09 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:30:54 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 105.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: made4.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:made4.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings made4_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/made4.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'made4/DESCRIPTION' ... OK
* this is package 'made4' version '1.56.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'made4' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/array2ade4.Rd:15: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/array2ade4.Rd:30: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bet.coinertia.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bet.coinertia.Rd:21: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.Rd:16: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.jackknife.Rd:37: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.suppl.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.suppl.Rd:19: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.suppl.Rd:45: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.suppl.Rd:63: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/cia.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/cia.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/getdata.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/getdata.Rd:25: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/getdata.Rd:29: missing file link 'vsn'
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/heatplot.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/ord.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/overview.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/plotarrays.Rd:45: file link 's.groups' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/plotarrays.Rd:46: file link 's.match.col' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/prettyDend.Rd:11: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/s.var.Rd:65: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/s.var.Rd:65: file link 'plot.cia' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/suppl.Rd:17: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/suppl.Rd:38: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/suppl.Rd:47: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/made4.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
Missing link or links in documentation object 'getdata.Rd':
  '[vsn:vsn]{vsn}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/made4.Rcheck/00check.log'
for details.

Installation output

made4.Rcheck/00install.out

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### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/made4_1.56.0.tar.gz && rm -rf made4.buildbin-libdir && mkdir made4.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=made4.buildbin-libdir made4_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL made4_1.56.0.zip && rm made4_1.56.0.tar.gz made4_1.56.0.zip
###
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install for i386

* installing *source* package 'made4' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'made4'
    finding HTML links ... done
    NCI60                                   html  
    array2ade4                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/array2ade4.Rd:15: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/array2ade4.Rd:30: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    bet.coinertia                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bet.coinertia.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bet.coinertia.Rd:21: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    between.graph                           html  
    bga                                     html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.Rd:16: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    bga.jackknife                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.jackknife.Rd:37: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
    bga.suppl                               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.suppl.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.suppl.Rd:19: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.suppl.Rd:45: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/bga.suppl.Rd:63: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
    checkfac                                html  
    chime3D                                 html  
    cia                                     html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/cia.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/cia.Rd:20: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    commonMap                               html  
    comparelists                            html  
    do3d                                    html  
    dudi.rwcoa                              html  
    forrwcoa                                html  
    genes                                   html  
    genes1d                                 html  
    getcol                                  html  
    getdata                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/getdata.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/getdata.Rd:25: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/getdata.Rd:29: missing file link 'vsn'
    graph1D                                 html  
    heatplot                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/heatplot.Rd:14: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    html3D                                  html  
    jmol3D                                  html  
    khan                                    html  
    ord                                     html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/ord.Rd:13: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    overview                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/overview.Rd:10: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    plotarrays                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/plotarrays.Rd:45: file link 's.groups' in package 'made4' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/plotarrays.Rd:46: file link 's.match.col' in package 'made4' does not exist and so has been treated as a topic
    plotgenes                               html  
    prettyDend                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/prettyDend.Rd:11: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    randomiser                              html  
    s.var                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/s.var.Rd:65: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/s.var.Rd:65: file link 'plot.cia' in package 'made4' does not exist and so has been treated as a topic
    sumstats                                html  
    suppl                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/suppl.Rd:17: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/suppl.Rd:38: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGiJkEo/R.INSTALL13ec21021f3a/made4/man/suppl.Rd:47: file link 'plot.bga' in package 'made4' does not exist and so has been treated as a topic
    topgenes                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'made4' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'made4' as made4_1.56.0.zip
* DONE (made4)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'made4' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

made4.Rcheck/examples_i386/made4-Ex.timings

nameusersystemelapsed
NCI600.010.000.01
array2ade40.570.020.58
bet.coinertia000
between.graph0.200.010.22
bga0.300.020.31
bga.jackknife1.470.001.47
bga.suppl0.320.000.33
cia0.130.010.14
commonMap0.010.000.01
comparelists000
do3d0.290.040.32
genes1d0.060.000.06
getcol0.010.000.01
graph1D0.070.000.07
heatplot1.810.071.89
html3D0.190.000.19
khan0.010.000.01
ord0.190.020.20
overview0.110.020.13
plotarrays0.230.000.23
plotgenes0.110.010.13
prettyDend0.080.000.08
randomiser000
s.var0.180.000.19
sumstats0.190.000.19
suppl0.380.000.37
topgenes0.070.000.08

made4.Rcheck/examples_x64/made4-Ex.timings

nameusersystemelapsed
NCI600.000.020.01
array2ade40.610.030.64
bet.coinertia000
between.graph0.250.000.25
bga0.320.000.33
bga.jackknife1.830.001.83
bga.suppl0.380.000.37
cia0.150.000.16
commonMap0.030.000.03
comparelists000
do3d0.350.000.34
genes1d0.080.000.08
getcol0.010.000.02
graph1D0.050.000.04
heatplot1.890.061.96
html3D0.200.020.21
khan0.020.000.02
ord0.220.000.21
overview0.140.000.14
plotarrays0.220.030.25
plotgenes0.110.010.13
prettyDend0.090.000.09
randomiser000
s.var0.220.020.24
sumstats0.220.000.22
suppl0.440.000.43
topgenes0.060.020.08