BioC 3.6: CHECK report for rexposome on tokay1

Package: rexposome

Version: 0.99.90

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_0.99.90.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_0.99.90.tar.gz

StartedAt: 2017-08-16 01:58:10 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:03:38 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 327.8 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_0.99.90.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_0.99.90.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/rexposome.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '0.99.90'
* 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  6.3Mb
  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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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      14.58   0.06   15.91
plotCorrelation-methods 12.46   0.02   12.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
plotCorrelation-methods 15.17   0.07   15.23
clustering-methods      11.45   0.02   11.47
* 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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'rexposome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rexposome' as rexposome_0.99.90.zip
* DONE (rexposome)

name	user	system	elapsed
classification-methods	0.01	0.02	0.03
clustering-methods	14.58	0.06	15.91
correlation-methods	4.01	0.01	4.03
ex_imp	0.03	0.00	0.03
expo	0.02	0.02	0.03
expo_c	0.01	0.00	0.01
expos-methods	0.05	0.00	0.05
exposureNames-methods	0.01	0.00	0.01
exwas-methods	0.55	0.00	0.55
familyNames-methods	0.03	0.00	0.03
highAndLow-methods	0.78	0.00	0.78
ilod-methods	0	0	0
imputation-methods	0	0	0
imputeLOD	0	0	0
loadExposome	0.02	0.01	0.03
loadImputed	0.01	0.00	0.02
me	0.00	0.02	0.01
mexwas-methods	0.77	0.00	0.77
ndim-methods	0.05	0.01	0.06
normalityTest-methods	0.11	0.03	0.14
pca-methods	0.32	0.02	0.34
phenotypeNames-methods	0.04	0.00	0.04
plotClassification-methods	0	0	0
plotCorrelation-methods	12.46	0.02	12.48
plotEXP-methods	0.63	0.01	0.64
plotEffect-methods	1.20	0.03	1.23
plotExwas-methods	0.49	0.02	0.50
plotFamily-methods	3.33	0.04	3.38
plotHistogram-methods	0.21	0.00	0.22
plotLOD-methods	1.08	0.00	1.08
plotMissings-methods	0.61	0.00	0.61
plotPCA-methods	1.24	0.00	1.23
plotPHE-methods	0.29	0.00	0.30
readExposome	0.06	0.00	0.07
standardize-methods	0.52	0.00	0.51
tableLOD-methods	0.33	0.00	0.33
tableMissings-methods	0.03	0.00	0.03
tef-methods	0.58	0.00	0.58
toES	0.09	0.00	0.09
trans-methods	0.06	0.00	0.07
volcano_plot	0.70	0.02	0.71

name	user	system	elapsed
classification-methods	0.02	0.00	0.01
clustering-methods	11.45	0.02	11.47
correlation-methods	4.90	0.00	4.91
ex_imp	0.05	0.00	0.04
expo	0.01	0.01	0.03
expo_c	0.02	0.00	0.02
expos-methods	0.05	0.02	0.06
exposureNames-methods	0.03	0.00	0.03
exwas-methods	0.67	0.02	0.69
familyNames-methods	0.02	0.00	0.02
highAndLow-methods	1.08	0.00	1.08
ilod-methods	0	0	0
imputation-methods	0	0	0
imputeLOD	0	0	0
loadExposome	0.12	0.00	0.12
loadImputed	0.02	0.00	0.02
me	0.02	0.00	0.02
mexwas-methods	0.54	0.01	0.56
ndim-methods	0.08	0.02	0.09
normalityTest-methods	0.52	0.00	0.52
pca-methods	0.39	0.00	0.39
phenotypeNames-methods	0.01	0.01	0.03
plotClassification-methods	0	0	0
plotCorrelation-methods	15.17	0.07	15.23
plotEXP-methods	0.79	0.01	0.80
plotEffect-methods	1.46	0.00	1.47
plotExwas-methods	0.60	0.00	0.59
plotFamily-methods	2.95	0.05	3.00
plotHistogram-methods	0.25	0.00	0.25
plotLOD-methods	1.19	0.00	1.19
plotMissings-methods	0.58	0.01	0.59
plotPCA-methods	1.37	0.02	1.40
plotPHE-methods	0.30	0.00	0.29
readExposome	0.09	0.00	0.10
standardize-methods	0.19	0.00	0.18
tableLOD-methods	0.31	0.00	0.32
tableMissings-methods	0.03	0.00	0.03
tef-methods	0.32	0.03	0.34
toES	0.09	0.02	0.11
trans-methods	0.08	0.01	0.09
volcano_plot	1.08	0.00	1.08