Xavier Escribà Montagut
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/rexposome |
| Branch: RELEASE_3_12 |
| Last Commit: c47928c |
| Last Changed Date: 2021-03-11 05:00:56 -0400 (Thu, 11 Mar 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:12 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the rexposome package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1508/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rexposome 1.12.4 (landing page) Xavier Escribà Montagut
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: rexposome |
| Version: 1.12.4 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rexposome.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings rexposome_1.12.4.tar.gz |
| StartedAt: 2021-05-06 06:07:30 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:12:47 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 317.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rexposome.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rexposome.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings rexposome_1.12.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/rexposome.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.12.4'
* 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 6.2Mb
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 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 26.44 0.11 26.55
invExWAS-methods 12.43 0.04 12.49
plotCorrelation-methods 11.14 0.03 11.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clustering-methods 24.61 0.06 24.88
invExWAS-methods 14.08 0.15 14.22
plotCorrelation-methods 10.96 0.03 11.00
correlation-methods 6.96 0.02 6.97
* 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-3.12-bioc/meat/rexposome.Rcheck/00check.log'
for details.
rexposome.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/rexposome_1.12.4.tar.gz && rm -rf rexposome.buildbin-libdir && mkdir rexposome.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rexposome.buildbin-libdir rexposome_1.12.4.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL rexposome_1.12.4.zip && rm rexposome_1.12.4.tar.gz rexposome_1.12.4.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 5994k 100 5994k 0 0 72.0M 0 --:--:-- --:--:-- --:--:-- 73.1M
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
invExWAS-methods html
loadExposome html
loadExposome_plain 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_1.12.4.zip
* DONE (rexposome)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'rexposome' successfully unpacked and MD5 sums checked
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rexposome.Rcheck/examples_i386/rexposome-Ex.timings
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rexposome.Rcheck/examples_x64/rexposome-Ex.timings
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