| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:28 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1592/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rexposome 1.17.1 (landing page) Xavier Escribà Montagut
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: rexposome |
| Version: 1.17.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rexposome.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rexposome_1.17.1.tar.gz |
| StartedAt: 2022-03-17 20:03:19 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:05:47 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 148.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rexposome.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rexposome.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rexposome_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/rexposome.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.17.1'
* 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 6.4Mb
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'
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clustering-methods 14.78 0.08 14.86
plotCorrelation-methods 8.54 0.07 8.59
invExWAS-methods 8.37 0.03 8.41
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/rexposome.Rcheck/00check.log'
for details.
rexposome.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rexposome
###
##############################################################################
##############################################################################
* installing to library 'D:/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
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: D:/biocbuild/bbs-3.15-bioc/R/library/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: D:/biocbuild/bbs-3.15-bioc/R/library/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
* DONE (rexposome)
Making 'packages.html' ... done
rexposome.Rcheck/rexposome-Ex.timings
| name | user | system | elapsed | |
| classification-methods | 0.00 | 0.02 | 0.01 | |
| clustering-methods | 14.78 | 0.08 | 14.86 | |
| correlation-methods | 3.20 | 0.15 | 3.36 | |
| ex_imp | 0.00 | 0.02 | 0.02 | |
| expo | 0.01 | 0.01 | 0.03 | |
| expo_c | 0.02 | 0.00 | 0.02 | |
| expos-methods | 0.2 | 0.0 | 0.2 | |
| exposureNames-methods | 0.02 | 0.00 | 0.02 | |
| exwas-methods | 0.33 | 0.02 | 0.34 | |
| familyNames-methods | 0.01 | 0.02 | 0.03 | |
| highAndLow-methods | 0.72 | 0.01 | 0.73 | |
| ilod-methods | 0 | 0 | 0 | |
| imputation-methods | 0 | 0 | 0 | |
| imputeLOD | 0 | 0 | 0 | |
| invExWAS-methods | 8.37 | 0.03 | 8.41 | |
| loadExposome | 0.03 | 0.00 | 0.03 | |
| loadExposome_plain | 0.03 | 0.00 | 0.03 | |
| loadImputed | 0.01 | 0.00 | 0.02 | |
| me | 0 | 0 | 0 | |
| mexwas-methods | 1.04 | 0.00 | 1.03 | |
| ndim-methods | 0.06 | 0.02 | 0.08 | |
| normalityTest-methods | 0.30 | 0.04 | 0.34 | |
| pca-methods | 0.09 | 0.00 | 0.10 | |
| phenotypeNames-methods | 0.01 | 0.00 | 0.02 | |
| plotClassification-methods | 0 | 0 | 0 | |
| plotCorrelation-methods | 8.54 | 0.07 | 8.59 | |
| plotEXP-methods | 0.28 | 0.00 | 0.28 | |
| plotEffect-methods | 0.72 | 0.00 | 0.72 | |
| plotExwas-methods | 0.56 | 0.01 | 0.58 | |
| plotFamily-methods | 2.31 | 0.00 | 2.31 | |
| plotHistogram-methods | 0.33 | 0.00 | 0.33 | |
| plotLOD-methods | 0.42 | 0.00 | 0.42 | |
| plotMissings-methods | 0.30 | 0.02 | 0.31 | |
| plotPCA-methods | 1.01 | 0.01 | 1.04 | |
| plotPHE-methods | 0.16 | 0.00 | 0.15 | |
| readExposome | 0.03 | 0.00 | 0.03 | |
| standardize-methods | 0.56 | 0.00 | 0.57 | |
| tableLOD-methods | 0.18 | 0.00 | 0.17 | |
| tableMissings-methods | 0.01 | 0.00 | 0.02 | |
| tef-methods | 0.22 | 0.02 | 0.23 | |
| toES | 0.11 | 0.00 | 0.11 | |
| trans-methods | 0.20 | 0.00 | 0.21 | |
| volcano_plot | 0.60 | 0.00 | 0.59 | |