Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for made4 on tokay2

This page was generated on 2020-10-17 11:56:59 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE made4 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 973/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
made4 1.62.0
Aedin Culhane
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/made4
Branch: RELEASE_3_11
Last Commit: 2112e97
Last Changed Date: 2020-04-27 14:10:56 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: made4
Version: 1.62.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:made4.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings made4_1.62.0.tar.gz
StartedAt: 2020-10-17 05:36:20 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:39:35 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 195.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: made4.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:made4.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings made4_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/made4.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.62.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'ade4', 'RColorBrewer', 'gplots', 'scatterplot3d', 'Biobase',
  'SummarizedExperiment'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/made4/man/getdata.Rd:29: missing file link 'vsn'
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-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
Missing or unexported object: 'RColorBrewer::colorRampPalette'
* 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'
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'overview':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... ERROR
Running examples in 'made4-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: array2ade4
> ### Title: Converts microarray input data into a data frame suitable for
> ###   analysis in ADE4.
> ### Aliases: array2ade4
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(affy)
> data(geneData)
> class(geneData)
[1] "matrix" "array" 
> dim(geneData)
[1] 500  26
> dim(array2ade4(geneData))
Error in switch(class(arraydata), matrix = { : 
  EXPR must be a length 1 vector
Calls: array2ade4 -> getdata
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'made4-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: array2ade4
> ### Title: Converts microarray input data into a data frame suitable for
> ###   analysis in ADE4.
> ### Aliases: array2ade4
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(affy)
> data(geneData)
> class(geneData)
[1] "matrix" "array" 
> dim(geneData)
[1] 500  26
> dim(array2ade4(geneData))
Error in switch(class(arraydata), matrix = { : 
  EXPR must be a length 1 vector
Calls: array2ade4 -> getdata
Execution halted
* 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 ERRORs, 3 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/made4.Rcheck/00check.log'
for details.

Installation output

made4.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/made4_1.62.0.tar.gz && rm -rf made4.buildbin-libdir && mkdir made4.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=made4.buildbin-libdir made4_1.62.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL made4_1.62.0.zip && rm made4_1.62.0.tar.gz made4_1.62.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  344k  100  344k    0     0  5364k      0 --:--:-- --:--:-- --:--:-- 5940k

install for i386

* installing *source* package 'made4' ...
** using staged installation
** 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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/made4/man/getdata.Rd:29: missing file link 'vsn'
    graph1D                                 html  
    heatplot                                html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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-3.11-bioc/tmpdir/Rtmp8ezGqt/R.INSTALL1eb8460d5685/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'made4' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'made4' as made4_1.62.0.zip
* DONE (made4)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'made4' successfully unpacked and MD5 sums checked

Tests output

Example timings

made4.Rcheck/examples_i386/made4-Ex.timings

nameusersystemelapsed
NCI600.020.020.03

made4.Rcheck/examples_x64/made4-Ex.timings

nameusersystemelapsed
NCI600.000.020.02