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CHECK report for marray on tokay2

This page was generated on 2019-10-16 12:19:20 -0400 (Wed, 16 Oct 2019).

Package 916/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
marray 1.62.0
Yee Hwa (Jean) Yang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/marray
Branch: RELEASE_3_9
Last Commit: c3f5485
Last Changed Date: 2019-05-02 11:53:02 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: marray
Version: 1.62.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:marray.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings marray_1.62.0.tar.gz
StartedAt: 2019-10-16 04:55:09 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:56:43 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 94.0 seconds
RetCode: 0
Status:  OK  
CheckDir: marray.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:marray.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings marray_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/marray.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.62.0'
* 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 'marray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    swirldata   5.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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' call to 'tkWidgets' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'limma'
  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:
  length.na log.na mean.na prod.na quantile.na scale.na sum.na
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
widget.marrayInfo : inputInfo: warning in assign(newname, newInfo, env
  = .GlobalEnv): partial argument match of 'env' to 'envir'
widget.marrayLayout : inputLayout: warning in assign(newname,
  newLayout, env = .GlobalEnv): partial argument match of 'env' to
  'envir'
widget.marrayRaw : inputRaw: warning in assign(newname, newRaw, env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
addLines: no visible global function definition for 'loess.control'
cor.na: no visible global function definition for 'cor'
findID: no visible binding for global variable 'gnames'
findID: no visible global function definition for 'phenoData'
htmlPage: no visible binding for global variable 'Gnames'
ma2D: no visible global function definition for 'loess.control'
ma2D: no visible binding for global variable 'na.omit'
ma2D: no visible global function definition for 'loess'
ma2D: no visible global function definition for 'predict'
maColorBar: no visible global function definition for 'heat.colors'
maColorBar: no visible global function definition for 'axis'
maColorBar: no visible global function definition for 'par'
maColorBar: no visible global function definition for 'box'
maCompNormA : : no visible global function definition for
  'ecdf'
maImage: no visible global function definition for 'rainbow'
maImage: no visible global function definition for 'layout'
maImage: no visible global function definition for 'par'
maImage.func: no visible global function definition for 'heat.colors'
maImage.func: no visible global function definition for 'axis'
maImage.func: no visible global function definition for 'contour'
maImage.func: no visible global function definition for 'box'
maImage.func: no visible global function definition for 'abline'
maLoess: no visible global function definition for 'loess.control'
maLoess: no visible binding for global variable 'na.omit'
maLoess: no visible global function definition for 'loess'
maLoess: no visible global function definition for 'predict'
maLoessLines: no visible global function definition for 'loess.control'
maLoessLines : : no visible binding for global variable
  'loess'
maLoessLines : : no visible global function definition for
  'quantile'
maLoessLines : : no visible global function definition for
  'predict'
maLowessLines : : no visible global function definition for
  'lowess'
maMAD: no visible global function definition for 'mad'
maMed: no visible global function definition for 'median'
maPalette: no visible global function definition for 'col2rgb'
maPalette: no visible global function definition for 'rgb'
maPlot: no visible global function definition for 'loess.control'
maPlot: no visible global function definition for 'abline'
maTop: no visible global function definition for 'quantile'
maTwoSamples: no visible global function definition for 'gpTools'
quantile.na: no visible global function definition for 'quantile'
read.Agilent: no visible binding for global variable 'read.table'
read.Galfile: no visible binding for global variable 'read.table'
read.marrayInfo: no visible global function definition for 'read.table'
read.marrayRaw: no visible global function definition for 'read.table'
scale.na: no visible global function definition for 'applyy'
table2html: no visible global function definition for 'browseURL'
var.na: no visible global function definition for 'var'
widget.TwoSamples: no visible binding for global variable 'fileBrowser'
widget.TwoSamples: no visible global function definition for
  'widgetRender'
widget.TwoSamples: no visible global function definition for
  'values.Widget'
widget.mapGeneInfo: no visible global function definition for
  'widgetRender'
widget.mapGeneInfo: no visible global function definition for
  'values.Widget'
widget.marrayInfo : inputInfo: no visible global function definition
  for 'tclvalue'
widget.marrayInfo : fileBrow: no visible global function definition for
  'tkdelete'
widget.marrayInfo : fileBrow: no visible global function definition for
  'fileBrowser'
widget.marrayInfo : fileBrow: no visible global function definition for
  'tkinsert'
widget.marrayInfo: no visible global function definition for
  'tktoplevel'
widget.marrayInfo: no visible global function definition for
  'tkwm.title'
widget.marrayInfo: no visible global function definition for 'tkframe'
widget.marrayInfo: no visible global function definition for 'tkpack'
widget.marrayInfo: no visible global function definition for 'tklabel'
widget.marrayInfo: no visible global function definition for 'tkentry'
widget.marrayInfo: no visible global function definition for 'tkbutton'
widget.marrayInfo: no visible global function definition for 'tkgrid'
widget.marrayInfo: no visible global function definition for
  'tkgrid.configure'
widget.marrayInfo : : no visible global function definition
  for 'tkdestroy'
widget.marrayLayout : inputLayout: no visible global function
  definition for 'tclvalue'
widget.marrayLayout : listColnames: no visible global function
  definition for 'tktoplevel'
widget.marrayLayout : listColnames: no visible global function
  definition for 'tkwm.title'
widget.marrayLayout : listColnames: no visible global function
  definition for 'tkframe'
widget.marrayLayout : listColnames: no visible global function
  definition for 'tkpack'
widget.marrayLayout : listColnames: no visible global function
  definition for 'tklabel'
widget.marrayLayout : listColnames: no visible global function
  definition for 'tkcheckbutton'
widget.marrayLayout : listColnames : getResults: no visible global
  function definition for 'tclvalue'
widget.marrayLayout : listColnames : getResults: no visible global
  function definition for 'tkdestroy'
widget.marrayLayout : listColnames: no visible global function
  definition for 'tkbutton'
widget.marrayLayout : fileBrow: no visible global function definition
  for 'tkdelete'
widget.marrayLayout : fileBrow: no visible global function definition
  for 'fileBrowser'
widget.marrayLayout : fileBrow: no visible global function definition
  for 'tkinsert'
widget.marrayLayout: no visible global function definition for
  'tktoplevel'
widget.marrayLayout: no visible global function definition for
  'tkwm.title'
widget.marrayLayout: no visible global function definition for
  'tkframe'
widget.marrayLayout: no visible global function definition for 'tkpack'
widget.marrayLayout: no visible global function definition for
  'tklabel'
widget.marrayLayout: no visible global function definition for
  'tkentry'
widget.marrayLayout: no visible global function definition for 'tkgrid'
widget.marrayLayout: no visible global function definition for
  'tkgrid.configure'
widget.marrayLayout: no visible global function definition for
  'tkconfigure'
widget.marrayLayout: no visible global function definition for
  'tkbutton'
widget.marrayLayout : : no visible global function
  definition for 'tclvalue'
widget.marrayLayout : : no visible global function
  definition for 'tkdestroy'
widget.marrayRaw : inputRaw: no visible global function definition for
  'tclvalue'
widget.marrayRaw : filesClick: no visible global function definition
  for 'fileBrowser'
widget.marrayRaw : browserToEntry: no visible global function
  definition for 'objectBrowser'
widget.marrayRaw : browserToEntry: no visible global function
  definition for 'tkdelete'
widget.marrayRaw : browserToEntry: no visible global function
  definition for 'tkinsert'
widget.marrayRaw: no visible global function definition for
  'tktoplevel'
widget.marrayRaw: no visible global function definition for
  'tkwm.title'
widget.marrayRaw: no visible global function definition for 'tkframe'
widget.marrayRaw: no visible global function definition for 'tkpack'
widget.marrayRaw: no visible global function definition for 'tkbutton'
widget.marrayRaw: no visible global function definition for 'tklabel'
widget.marrayRaw: no visible global function definition for 'tkentry'
widget.marrayRaw: no visible global function definition for 'tkgrid'
widget.marrayRaw: no visible global function definition for
  'tkgrid.configure'
widget.marrayRaw : : no visible global function definition
  for 'tkdestroy'
write.list: no visible global function definition for 'write.table'
write.marray: no visible global function definition for 'write.table'
write.xls: no visible binding for global variable 'write.table'
show,ShowLargeObject: no visible global function definition for
  'printHead'
Undefined global functions or variables:
  Gnames abline applyy axis box browseURL col2rgb contour cor ecdf
  fileBrowser gnames gpTools heat.colors layout loess loess.control
  lowess mad median na.omit objectBrowser par phenoData predict
  printHead quantile rainbow read.table rgb tclvalue tkbutton
  tkcheckbutton tkconfigure tkdelete tkdestroy tkentry tkframe tkgrid
  tkgrid.configure tkinsert tklabel tkpack tktoplevel tkwm.title
  values.Widget var widgetRender write.table
Consider adding
  importFrom("grDevices", "col2rgb", "heat.colors", "rainbow", "rgb")
  importFrom("graphics", "abline", "axis", "box", "contour", "layout",
             "par")
  importFrom("stats", "cor", "ecdf", "loess", "loess.control", "lowess",
             "mad", "median", "na.omit", "predict", "quantile", "var")
  importFrom("utils", "browseURL", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
maNormMain 9.27      0    9.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
maNormMain 7.16   0.02    7.18
* 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/marray.Rcheck/00check.log'
for details.



Installation output

marray.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/marray_1.62.0.tar.gz && rm -rf marray.buildbin-libdir && mkdir marray.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=marray.buildbin-libdir marray_1.62.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL marray_1.62.0.zip && rm marray_1.62.0.tar.gz marray_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 2821k  100 2821k    0     0  16.9M      0 --:--:-- --:--:-- --:--:-- 17.5M

install for i386

* installing *source* package 'marray' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'marray'
    finding HTML links ... done
    boxplot                                 html  
    bracketMethods                          html  
    cbind                                   html  
    checkTargetInfo                         html  
    coerce-methods                          html  
    dim                                     html  
    findID                                  html  
    htmlPage                                html  
    image                                   html  
    ma2D                                    html  
    maBoxplot                               html  
    maColorBar                              html  
    maCompCoord                             html  
    maCompInd                               html  
    maCompLayout                            html  
    maCompNormA                             html  
    maCompPlate                             html  
    maCoord2Ind                             html  
    maDefaultPar                            html  
    maDotsDefaults                          html  
    maDotsMatch                             html  
    maGenControls                           html  
    maGeneTable                             html  
    maImage                                 html  
    maImage.func                            html  
    maInd2Coord                             html  
    maLegendLines                           html  
    maLoess                                 html  
    maLoessLines                            html  
    maMAD                                   html  
    maMed                                   html  
    maNA                                    html  
    maNorm                                  html  
    maNorm2D                                html  
    maNormLoess                             html  
    maNormMAD                               html  
    maNormMain                              html  
    maNormMed                               html  
    maNormScale                             html  
    maNum2Logic                             html  
    maPalette                               html  
    maPlot                                  html  
    maPlot.func                             html  
    maSelectGnames                          html  
    maText                                  html  
    maTop                                   html  
    maTwoSamples                            html  
    mapGeneInfo                             html  
    marray-internal                         html  
    marrayInfo-class                        html  
    marrayLayout-class                      html  
    marrayNorm-class                        html  
    marrayRaw-class                         html  
    opVersionID                             html  
    plotMA                                  html  
    print-methods                           html  
    read.Galfile                            html  
    read.marrayInfo                         html  
    read.marrayLayout                       html  
    read.marrayRaw                          html  
    rm.na                                   html  
    showLargeObject                         html  
    stat.confband.text                      html  
    stat.gnames                             html  
    swirl                                   html  
    write.list                              html  
    write.marray                            html  
    write.xls                               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 'marray' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'marray' as marray_1.62.0.zip
* DONE (marray)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'marray' successfully unpacked and MD5 sums checked

Tests output


Example timings

marray.Rcheck/examples_i386/marray-Ex.timings

nameusersystemelapsed
boxplot0.250.030.28
checkTargetInfo0.110.000.11
dim0.020.000.02
findID0.080.000.07
htmlPage0.100.000.09
image0.070.000.08
ma2D000
maBoxplot000
maColorBar0.050.000.05
maCompCoord000
maCompInd000
maCompLayout0.020.000.01
maCompNormA000
maCompPlate000
maCoord2Ind000
maDefaultPar000
maDotsDefaults000
maDotsMatch000
maGenControls0.120.010.15
maGeneTable0.060.000.06
maImage0.520.030.54
maImage.func000
maInd2Coord000
maLegendLines000
maLoess000
maLoessLines000
maMAD000
maMed000
maNorm1.210.001.25
maNorm2D000
maNormLoess000
maNormMAD000
maNormMain9.270.009.26
maNormMed000
maNormScale0.120.000.13
maNum2Logic000
maPalette0.020.000.01
maPlot1.510.041.55
maPlot.func000
maSelectGnames000
maText000
maTop000
mapGeneInfo000
marrayInfo-class000
marrayLayout-class000
marrayNorm-class0.190.000.19
marrayRaw-class0.090.000.10
opVersionID000
plotMA1.590.001.59
read.Galfile0.050.000.22
read.marrayInfo0.050.000.05
read.marrayLayout0.110.000.10
read.marrayRaw1.980.003.30
rm.na000
stat.confband.text0.440.000.44
stat.gnames0.260.010.28
write.list0.110.030.14
write.marray0.070.000.06
write.xls0.070.020.10

marray.Rcheck/examples_x64/marray-Ex.timings

nameusersystemelapsed
boxplot0.190.010.20
checkTargetInfo0.060.000.06
dim000
findID0.080.000.07
htmlPage0.060.000.07
image0.090.000.09
ma2D000
maBoxplot000
maColorBar0.080.000.08
maCompCoord000
maCompInd0.020.000.01
maCompLayout000
maCompNormA000
maCompPlate000
maCoord2Ind000
maDefaultPar000
maDotsDefaults000
maDotsMatch000
maGenControls0.150.000.16
maGeneTable0.080.000.07
maImage0.460.060.52
maImage.func000
maInd2Coord000
maLegendLines000
maLoess000
maLoessLines000
maMAD000
maMed000
maNorm1.230.001.23
maNorm2D000
maNormLoess000
maNormMAD000
maNormMain7.160.027.18
maNormMed000
maNormScale0.140.010.15
maNum2Logic000
maPalette0.030.000.03
maPlot1.250.001.25
maPlot.func000
maSelectGnames0.010.000.02
maText000
maTop000
mapGeneInfo000
marrayInfo-class000
marrayLayout-class000
marrayNorm-class0.130.020.14
marrayRaw-class0.080.000.08
opVersionID0.010.000.01
plotMA1.520.001.52
read.Galfile0.030.000.03
read.marrayInfo0.050.000.05
read.marrayLayout0.060.000.06
read.marrayRaw1.170.011.19
rm.na000
stat.confband.text0.490.000.48
stat.gnames0.230.020.25
write.list0.110.000.11
write.marray0.090.000.10
write.xls0.080.000.07