Package: rexposome

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rexposome.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings rexposome_1.8.0.tar.gz

StartedAt: 2020-04-15 05:59:32 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:07:25 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 473.4 seconds

RetCode: 0

Status:  OK

CheckDir: rexposome.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rexposome.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings rexposome_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/rexposome.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.8.0'
* 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  6.1Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
clustering-methods      31.29   0.16   31.47
plotCorrelation-methods  9.43   0.11    9.53
correlation-methods      5.08   0.01    5.10
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
clustering-methods      20.72   0.03   20.77
plotCorrelation-methods  9.58   0.03    9.61
correlation-methods      5.21   0.01    5.22
volcano_plot             0.75   0.00   20.08
* 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-3.10-bioc/meat/rexposome.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/rexposome_1.8.0.tar.gz && rm -rf rexposome.buildbin-libdir && mkdir rexposome.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rexposome.buildbin-libdir rexposome_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL rexposome_1.8.0.zip && rm rexposome_1.8.0.tar.gz rexposome_1.8.0.zip
###
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  % 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 5210k  100 5210k    0     0  39.3M      0 --:--:-- --:--:-- --:--:-- 40.7M

install for i386

* installing *source* package 'rexposome' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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  
    extract-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 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 'rexposome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rexposome' as rexposome_1.8.0.zip
* DONE (rexposome)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'rexposome' successfully unpacked and MD5 sums checked