Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:08 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for rexposome on palomino3


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? 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 1628/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rexposome 1.18.2  (landing page)
Xavier EscribĂ  Montagut
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/rexposome
git_branch: RELEASE_3_15
git_last_commit: 653946b
git_last_commit_date: 2022-10-04 10:27:40 -0400 (Tue, 04 Oct 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: rexposome
Version: 1.18.2
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rexposome.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rexposome_1.18.2.tar.gz
StartedAt: 2022-10-19 03:25:39 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 03:28:51 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 191.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rexposome.Rcheck
Warnings: 5

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rexposome.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rexposome_1.18.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/rexposome.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rexposome/DESCRIPTION' ... OK
* this is package 'rexposome' version '1.18.2'
* 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  6.0Mb
  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
* 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' 'sandwich'
* 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 : <anonymous>: no visible global function
  definition for 'confint'
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.. confint reformulate terms
Consider adding
  importFrom("stats", "confint", "reformulate", "terms")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'extract':
  'extract-methods.Rd' 'get_robust_sd-methods.Rd'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'ExWAS':
Slots for class 'ExWAS'
  Code: comparison description effective formula robust.std.err
  Docs: comparison description effective formula

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'ExposomeSet'
  'robust'

Undocumented arguments in documentation object 'exwas'
  'robust'

Undocumented arguments in documentation object 'imExposomeSet'
  'robust'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
clustering-methods      18.33   0.08   18.58
invExWAS-methods        12.86   0.15   13.02
plotCorrelation-methods 10.17   0.11   10.28
correlation-methods      4.86   0.19    5.05
* 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 WARNINGs, 2 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/rexposome.Rcheck/00check.log'
for details.



Installation output

rexposome.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rexposome
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* 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
** 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
* DONE (rexposome)

Tests output


Example timings

rexposome.Rcheck/rexposome-Ex.timings

nameusersystemelapsed
classification-methods0.000.010.02
clustering-methods18.33 0.0818.58
correlation-methods4.860.195.05
ex_imp0.020.000.02
expo0.020.020.03
expo_c0.000.020.01
expos-methods0.330.000.33
exposureNames-methods0.040.000.04
exwas-methods0.360.020.38
familyNames-methods0.020.010.03
highAndLow-methods0.870.020.89
ilod-methods000
imputation-methods000
imputeLOD000
invExWAS-methods12.86 0.1513.02
loadExposome0.030.000.03
loadExposome_plain0.030.000.03
loadImputed0.020.020.03
me000
mexwas-methods0.950.010.97
ndim-methods0.060.000.07
normalityTest-methods0.290.000.28
pca-methods0.100.000.11
phenotypeNames-methods0.020.020.03
plotClassification-methods000
plotCorrelation-methods10.17 0.1110.28
plotEXP-methods0.220.000.22
plotEffect-methods0.950.000.95
plotExwas-methods0.410.010.42
plotFamily-methods2.310.052.36
plotHistogram-methods0.300.010.33
plotLOD-methods0.370.020.39
plotMissings-methods0.500.020.52
plotPCA-methods1.000.011.01
plotPHE-methods0.220.020.24
readExposome0.050.000.04
standardize-methods0.690.000.69
tableLOD-methods0.220.000.22
tableMissings-methods0.040.000.05
tef-methods0.320.000.31
toES0.120.000.13
trans-methods0.250.000.25
volcano_plot0.740.030.76