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BioC 3.1: CHECK report for made4 on moscato2

This page was generated on 2015-10-09 09:27:23 -0700 (Fri, 09 Oct 2015).

Package 543/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
made4 1.42.0
Aedin Culhane
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/made4
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: made4
Version: 1.42.0
Command: rm -rf made4.buildbin-libdir made4.Rcheck && mkdir made4.buildbin-libdir made4.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=made4.buildbin-libdir made4_1.42.0.tar.gz >made4.Rcheck\00install.out 2>&1 && cp made4.Rcheck\00install.out made4-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=made4.buildbin-libdir --install="check:made4-install.out" --force-multiarch --no-vignettes --timings made4_1.42.0.tar.gz
StartedAt: 2015-10-09 03:21:40 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:22:47 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 66.5 seconds
RetCode: 0
Status:  OK  
CheckDir: made4.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf made4.buildbin-libdir made4.Rcheck && mkdir made4.buildbin-libdir made4.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=made4.buildbin-libdir made4_1.42.0.tar.gz >made4.Rcheck\00install.out 2>&1 && cp made4.Rcheck\00install.out made4-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=made4.buildbin-libdir --install="check:made4-install.out" --force-multiarch --no-vignettes --timings made4_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/made4.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.42.0'
* 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 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
* 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'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [11s] OK
** running examples for arch 'x64' ... [14s] 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
  'E:/biocbld/bbs-3.1-bioc/meat/made4.Rcheck/00check.log'
for details.


made4.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'made4' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'made4' as made4_1.42.0.zip
* DONE (made4)

made4.Rcheck/examples_i386/made4-Ex.timings:

nameusersystemelapsed
NCI600.010.020.03
array2ade40.750.010.76
bet.coinertia000
between.graph0.300.020.32
bga0.340.020.37
bga.jackknife1.580.001.58
bga.suppl0.490.010.51
cia0.180.000.17
commonMap0.030.000.03
comparelists000
do3d0.420.000.43
genes1d0.110.000.10
getcol000
graph1D0.070.000.06
heatplot2.210.032.90
html3D0.250.000.32
khan0.020.000.01
ord0.20.00.2
overview0.200.000.21
plotarrays0.350.000.34
plotgenes0.140.000.14
prettyDend0.120.000.13
randomiser000
s.var0.260.000.27
sumstats0.260.000.27
suppl0.500.020.51
topgenes0.090.000.10

made4.Rcheck/examples_x64/made4-Ex.timings:

nameusersystemelapsed
NCI600.000.010.02
array2ade40.760.020.78
bet.coinertia000
between.graph0.380.000.37
bga0.470.010.49
bga.jackknife2.410.002.42
bga.suppl0.860.000.86
cia0.320.000.33
commonMap0.070.000.06
comparelists000
do3d0.790.000.80
genes1d0.250.000.24
getcol0.010.000.02
graph1D0.110.000.11
heatplot2.750.023.57
html3D0.360.010.37
khan0.010.000.02
ord0.270.000.26
overview0.150.000.16
plotarrays0.360.000.36
plotgenes0.160.000.15
prettyDend0.130.000.12
randomiser000
s.var0.320.000.31
sumstats0.310.000.31
suppl0.790.000.80
topgenes0.240.020.25