Multiple platform build/check report for BioC 3.6 - CHECK report for rexposome on tokay1

Package: rexposome

Version: 1.0.0

Command: rm -rf rexposome.buildbin-libdir rexposome.Rcheck && mkdir rexposome.buildbin-libdir rexposome.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rexposome.buildbin-libdir rexposome_1.0.0.tar.gz >rexposome.Rcheck\00install.out 2>&1 && cp rexposome.Rcheck\00install.out rexposome-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=rexposome.buildbin-libdir --install="check:rexposome-install.out" --force-multiarch --no-vignettes --timings rexposome_1.0.0.tar.gz

StartedAt: 2018-04-12 02:36:36 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:42:06 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 329.5 seconds

RetCode: 0

Status: OK

CheckDir: rexposome.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf rexposome.buildbin-libdir rexposome.Rcheck && mkdir rexposome.buildbin-libdir rexposome.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rexposome.buildbin-libdir rexposome_1.0.0.tar.gz >rexposome.Rcheck\00install.out 2>&1 && cp rexposome.Rcheck\00install.out rexposome-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=rexposome.buildbin-libdir --install="check:rexposome-install.out" --force-multiarch --no-vignettes --timings rexposome_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/rexposome.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rexposome/DESCRIPTION' ... OK
* this is package 'rexposome' version '1.0.0'
* package encoding: UTF-8
* 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 'rexposome' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    doc       2.7Mb
    extdata   2.2Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
imputeLOD: multiple local function definitions for 'faux' with
  different formal arguments
plotHistogram,ExposomeSet: no visible binding for global variable
  '..density..'
Undefined global functions or variables:
  ..density..
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
clustering-methods      27.59   0.03   27.62
plotCorrelation-methods 15.55   0.00   15.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
clustering-methods      20.93   0.05   20.97
plotCorrelation-methods 14.35   0.03   14.38
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/rexposome.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'rexposome' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'rexposome'
    finding HTML links ... done
    ExWAS-class                             html  
    ExposomeClust-class                     html  
    ExposomeCorr-class                      html  
    finding level-2 HTML links ... done

    ExposomePCA-class                       html  
    ExposomeSet-class                       html  
    classification-methods                  html  
    clustering-methods                      html  
    correlation-methods                     html  
    ex_imp                                  html  
    expo                                    html  
    expo_c                                  html  
    expos-methods                           html  
    exposureNames-methods                   html  
    exwas-methods                           html  
    familyNames-methods                     html  
    highAndLow-methods                      html  
    ilod-methods                            html  
    imExposomeSet-class                     html  
    imputation-methods                      html  
    imputeLOD                               html  
    loadExposome                            html  
    loadImputed                             html  
    mExWAS-class                            html  
    me                                      html  
    mexwas-methods                          html  
    ndim-methods                            html  
    normalityTest-methods                   html  
    pca-methods                             html  
    phenotypeNames-methods                  html  
    plot3PCA-methods                        html  
    plotClassification-methods              html  
    plotCorrelation-methods                 html  
    plotEXP-methods                         html  
    plotEffect-methods                      html  
    plotExwas-methods                       html  
    plotFamily-methods                      html  
    plotHistogram-methods                   html  
    plotLOD-methods                         html  
    plotMissings-methods                    html  
    plotPCA-methods                         html  
    plotPHE-methods                         html  
    plotVolcano-methods                     html  
    readExposome                            html  
    rexposome                               html  
    standardize-methods                     html  
    tableLOD-methods                        html  
    tableMissings-methods                   html  
    tef-methods                             html  
    toES                                    html  
    trans-methods                           html  
    volcano_plot                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'rexposome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rexposome' as rexposome_1.0.0.zip
* DONE (rexposome)
In R CMD INSTALL
In R CMD INSTALL

name	user	system	elapsed
classification-methods	0.24	0.00	0.24
clustering-methods	27.59	0.03	27.62
correlation-methods	3.7	0.0	3.7
ex_imp	0.09	0.00	0.10
expo	0.03	0.00	0.03
expo_c	0.02	0.00	0.01
expos-methods	0.05	0.00	0.05
exposureNames-methods	0.03	0.00	0.03
exwas-methods	0.57	0.02	0.58
familyNames-methods	0.28	0.00	0.28
highAndLow-methods	0.94	0.00	0.93
ilod-methods	0	0	0
imputation-methods	0	0	0
imputeLOD	0	0	0
loadExposome	0.10	0.00	0.11
loadImputed	0.02	0.00	0.02
me	0	0	0
mexwas-methods	0.55	0.01	0.56
ndim-methods	0.07	0.00	0.06
normalityTest-methods	0.09	0.03	0.12
pca-methods	0.33	0.00	0.33
phenotypeNames-methods	0.03	0.02	0.05
plotClassification-methods	0	0	0
plotCorrelation-methods	15.55	0.00	15.55
plotEXP-methods	0.64	0.00	0.64
plotEffect-methods	1.43	0.00	1.43
plotExwas-methods	0.53	0.00	0.53
plotFamily-methods	3.38	0.03	3.41
plotHistogram-methods	0.23	0.00	0.23
plotLOD-methods	0.75	0.00	0.75
plotMissings-methods	0.84	0.00	0.85
plotPCA-methods	1.19	0.00	1.19
plotPHE-methods	0.28	0.02	0.30
readExposome	0.06	0.01	0.07
standardize-methods	0.17	0.02	0.19
tableLOD-methods	0.56	0.00	0.56
tableMissings-methods	0.02	0.00	0.02
tef-methods	0.48	0.01	0.50
toES	0.09	0.00	0.09
trans-methods	0.07	0.00	0.06
volcano_plot	0.64	0.00	0.64

name	user	system	elapsed
classification-methods	0.31	0.02	0.33
clustering-methods	20.93	0.05	20.97
correlation-methods	4.31	0.00	4.32
ex_imp	0.07	0.00	0.06
expo	0.01	0.00	0.02
expo_c	0.02	0.00	0.02
expos-methods	0.04	0.02	0.06
exposureNames-methods	0	0	0
exwas-methods	0.58	0.01	0.60
familyNames-methods	0.01	0.02	0.03
highAndLow-methods	0.91	0.01	0.92
ilod-methods	0	0	0
imputation-methods	0	0	0
imputeLOD	0	0	0
loadExposome	0.07	0.00	0.07
loadImputed	0.43	0.00	0.43
me	0.00	0.02	0.01
mexwas-methods	0.59	0.00	0.60
ndim-methods	0.06	0.00	0.06
normalityTest-methods	0.10	0.00	0.09
pca-methods	0.42	0.00	0.42
phenotypeNames-methods	0.03	0.00	0.03
plotClassification-methods	0	0	0
plotCorrelation-methods	14.35	0.03	14.38
plotEXP-methods	0.72	0.00	0.72
plotEffect-methods	1.49	0.02	1.50
plotExwas-methods	0.86	0.01	0.87
plotFamily-methods	3.28	0.02	3.30
plotHistogram-methods	0.20	0.03	0.24
plotLOD-methods	0.80	0.01	0.81
plotMissings-methods	0.65	0.00	0.65
plotPCA-methods	1.47	0.00	1.47
plotPHE-methods	0.74	0.00	0.74
readExposome	0.07	0.00	0.08
standardize-methods	0.16	0.00	0.16
tableLOD-methods	0.28	0.00	0.28
tableMissings-methods	0.04	0.00	0.05
tef-methods	0.33	0.00	0.32
toES	0.11	0.00	0.11
trans-methods	0.08	0.00	0.08
volcano_plot	0.75	0.00	0.75

CHECK report for rexposome on tokay1

Summary

Command output

Installation output

Tests output

Example timings