Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:06:24 -0400 (Fri, 24 Sep 2021).

CHECK results for rexposome on tokay2

To the developers/maintainers of the rexposome package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rexposome.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1560/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rexposome 1.14.1  (landing page)
Xavier EscribĂ  Montagut
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/rexposome
git_branch: RELEASE_3_13
git_last_commit: 8a968e3
git_last_commit_date: 2021-07-12 06:24:53 -0400 (Mon, 12 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: rexposome
Version: 1.14.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rexposome.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rexposome_1.14.1.tar.gz
StartedAt: 2021-09-24 03:36:10 -0400 (Fri, 24 Sep 2021)
EndedAt: 2021-09-24 03:40:51 -0400 (Fri, 24 Sep 2021)
EllapsedTime: 281.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rexposome.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rexposome.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rexposome_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/rexposome.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.14.1'
* 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 ... WARNING
Found the following file with a non-portable file name:
  vignettes/rsconnect/documents/exposome_data_analysis.Rmd/rpubs.com/rpubs/Publish Document.dcf
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
Found the following non-portable file path:
  rexposome/vignettes/rsconnect/documents/exposome_data_analysis.Rmd/rpubs.com/rpubs/Publish Document.dcf

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'rexposome' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  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 ... WARNING
'::' or ':::' imports not declared from:
  'ggridges' 'missMDA' 'nnet'
* 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
invExWAS,ExposomeSet : <anonymous>: no visible global function
  definition for 'reformulate'
invExWAS,ExposomeSet : <anonymous>: no visible global function
  definition for 'terms'
invExWAS,ExposomeSet: no visible global function definition for
  'reformulate'
invExWAS,ExposomeSet: no visible global function definition for 'terms'
plotHistogram,ExposomeSet: no visible binding for global variable
  '..density..'
Undefined global functions or variables:
  ..density.. reformulate terms
Consider adding
  importFrom("stats", "reformulate", "terms")
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 LazyData ... 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 (user + system) or elapsed time > 5s
                         user system elapsed
clustering-methods      22.27   0.03    22.3
invExWAS-methods        12.20   0.10    12.3
plotCorrelation-methods 10.28   0.02    10.3
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
clustering-methods      17.71   0.02   17.72
invExWAS-methods        11.09   0.00   11.09
plotCorrelation-methods 10.02   0.08   10.09
* 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 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/rexposome.Rcheck/00check.log'
for details.



Installation output

rexposome.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/rexposome_1.14.1.tar.gz && rm -rf rexposome.buildbin-libdir && mkdir rexposome.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rexposome.buildbin-libdir rexposome_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL rexposome_1.14.1.zip && rm rexposome_1.14.1.tar.gz rexposome_1.14.1.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
 34 5994k   34 2085k    0     0  2610k      0  0:00:02 --:--:--  0:00:02 2610k
100 5994k  100 5994k    0     0  3635k      0  0:00:01  0:00:01 --:--:-- 3637k

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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/rexposome.buildbin-libdir/00LOCK-rexposome/00new/rexposome/help/exwas.html
    familyNames-methods                     html  
    highAndLow-methods                      html  
    ilod-methods                            html  
    imExposomeSet-class                     html  
    imputation-methods                      html  
    imputeLOD                               html  
    invExWAS-methods                        html  
    loadExposome                            html  
    loadExposome_plain                      html  
    loadImputed                             html  
    mExWAS-class                            html  
    me                                      html  
    mexwas-methods                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/rexposome.buildbin-libdir/00LOCK-rexposome/00new/rexposome/help/mexwas.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_1.14.1.zip
* DONE (rexposome)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'rexposome' successfully unpacked and MD5 sums checked

Tests output


Example timings

rexposome.Rcheck/examples_i386/rexposome-Ex.timings

nameusersystemelapsed
classification-methods0.010.000.01
clustering-methods22.27 0.0322.30
correlation-methods4.440.004.44
ex_imp0.030.000.03
expo0.030.000.03
expo_c0.020.000.02
expos-methods0.280.000.28
exposureNames-methods0.060.000.06
exwas-methods0.620.000.62
familyNames-methods0.080.000.08
highAndLow-methods1.410.001.41
ilod-methods000
imputation-methods000
imputeLOD000
invExWAS-methods12.2 0.112.3
loadExposome0.050.010.11
loadExposome_plain0.050.010.11
loadImputed0.030.000.03
me000
mexwas-methods1.230.021.25
ndim-methods0.070.000.06
normalityTest-methods0.340.010.36
pca-methods0.110.000.11
phenotypeNames-methods0.030.000.03
plotClassification-methods000
plotCorrelation-methods10.28 0.0210.30
plotEXP-methods0.300.010.31
plotEffect-methods0.730.020.75
plotExwas-methods0.430.000.42
plotFamily-methods2.650.052.74
plotHistogram-methods0.220.000.21
plotLOD-methods0.440.000.44
plotMissings-methods0.400.010.42
plotPCA-methods0.850.000.84
plotPHE-methods0.220.000.22
readExposome0.040.000.05
standardize-methods0.770.000.76
tableLOD-methods0.230.000.24
tableMissings-methods0.070.000.06
tef-methods0.400.000.41
toES0.130.000.12
trans-methods0.450.000.46
volcano_plot0.860.000.86

rexposome.Rcheck/examples_x64/rexposome-Ex.timings

nameusersystemelapsed
classification-methods0.000.010.01
clustering-methods17.71 0.0217.72
correlation-methods4.890.004.93
ex_imp0.030.000.04
expo0.030.000.03
expo_c0.000.020.01
expos-methods0.240.000.24
exposureNames-methods0.050.000.04
exwas-methods0.420.000.43
familyNames-methods0.010.000.01
highAndLow-methods1.190.001.19
ilod-methods000
imputation-methods000
imputeLOD000
invExWAS-methods11.09 0.0011.09
loadExposome0.040.000.03
loadExposome_plain0.040.000.03
loadImputed0.020.000.02
me000
mexwas-methods1.040.011.06
ndim-methods0.070.000.06
normalityTest-methods0.310.000.31
pca-methods0.080.000.08
phenotypeNames-methods0.010.000.02
plotClassification-methods000
plotCorrelation-methods10.02 0.0810.09
plotEXP-methods0.30.00.3
plotEffect-methods0.670.020.68
plotExwas-methods0.480.010.50
plotFamily-methods2.720.022.74
plotHistogram-methods0.190.000.19
plotLOD-methods0.370.000.37
plotMissings-methods0.330.000.33
plotPCA-methods0.80.00.8
plotPHE-methods0.190.010.20
readExposome0.030.000.03
standardize-methods0.640.000.64
tableLOD-methods0.170.020.19
tableMissings-methods0.030.010.05
tef-methods0.630.000.62
toES0.090.000.09
trans-methods0.260.000.27
volcano_plot0.660.000.66