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CHECK report for made4 on malbec2

This page was generated on 2019-10-16 11:55:36 -0400 (Wed, 16 Oct 2019).

Package 903/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
made4 1.58.0
Aedin Culhane
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/made4
Branch: RELEASE_3_9
Last Commit: 11083d1
Last Changed Date: 2019-05-02 11:53:03 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: made4
Version: 1.58.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:made4.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings made4_1.58.0.tar.gz
StartedAt: 2019-10-16 02:49:10 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:49:51 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 41.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: made4.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:made4.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings made4_1.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/made4.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘made4/DESCRIPTION’ ... OK
* this is package ‘made4’ version ‘1.58.0’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.bga plot.cia plot.ord plot.suppl print.comparelists
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ... 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/made4.Rcheck/00check.log’
for details.



Installation output

made4.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL made4
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘made4’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (made4)

Tests output


Example timings

made4.Rcheck/made4-Ex.timings

nameusersystemelapsed
NCI600.0220.0040.025
array2ade40.8630.0361.138
bet.coinertia0.0010.0000.000
between.graph0.4160.0120.427
bga0.4300.0040.434
bga.jackknife2.2890.0082.297
bga.suppl0.6010.0000.601
cia0.2050.0080.213
commonMap0.0310.0000.031
comparelists0.0010.0000.001
do3d0.4330.0080.441
genes1d0.1240.0040.128
getcol0.0140.0000.014
graph1D0.0890.0000.089
heatplot2.1650.0282.193
html3D0.1780.0040.182
khan0.010.000.01
ord0.1640.0040.168
overview0.120.000.12
plotarrays0.2070.0000.207
plotgenes0.0870.0000.087
prettyDend0.0850.0000.085
randomiser0.0010.0000.001
s.var0.1890.0000.189
sumstats0.1830.0000.183
suppl0.3570.0040.361
topgenes0.0670.0000.067