Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 |
Package 1728/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rexposome 1.28.0 (landing page) Xavier Escribà Montagut
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the rexposome package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: rexposome |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rexposome_1.28.0.tar.gz |
StartedAt: 2024-12-21 06:35:45 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 06:38:41 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 175.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rexposome.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rexposome_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rexposome.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rexposome/DESCRIPTION’ ... OK * this is package ‘rexposome’ version ‘1.28.0’ * 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 for sufficient/correct file permissions ... OK * 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 ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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: ‘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 ... NOTE checkRd: (-1) exwas-methods.Rd:50: Lost braces 50 | An code{ExWAS} object with the result of the association study | ^ checkRd: (-1) invExWAS-methods.Rd:31: Lost braces 31 | An code{ExWAS} object with the result of the association study | ^ checkRd: (-1) standardize-methods.Rd:13: Lost braces 13 | #' @param object code{ExposomeSet} with 'set' will be summarized. | ^ * 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 Rd file 'ExWAS-class.Rd': 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 Rd file 'ExposomeSet-class.Rd' ‘robust’ Undocumented arguments in Rd file 'exwas-methods.Rd' ‘robust’ Undocumented arguments in Rd file 'imExposomeSet-class.Rd' ‘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 19.287 0.130 19.451 invExWAS-methods 10.476 0.259 10.745 plotCorrelation-methods 9.297 0.182 9.492 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/rexposome.Rcheck/00check.log’ for details.
rexposome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rexposome ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)
rexposome.Rcheck/rexposome-Ex.timings
name | user | system | elapsed | |
classification-methods | 0.023 | 0.006 | 0.028 | |
clustering-methods | 19.287 | 0.130 | 19.451 | |
correlation-methods | 3.751 | 0.141 | 3.896 | |
ex_imp | 0.017 | 0.003 | 0.019 | |
expo | 0.033 | 0.018 | 0.051 | |
expo_c | 0.017 | 0.003 | 0.020 | |
expos-methods | 0.267 | 0.006 | 0.273 | |
exposureNames-methods | 0.056 | 0.006 | 0.061 | |
exwas-methods | 0.390 | 0.008 | 0.398 | |
familyNames-methods | 0.030 | 0.005 | 0.035 | |
highAndLow-methods | 0.741 | 0.014 | 0.759 | |
ilod-methods | 0.000 | 0.001 | 0.000 | |
imputation-methods | 0 | 0 | 0 | |
imputeLOD | 0 | 0 | 0 | |
invExWAS-methods | 10.476 | 0.259 | 10.745 | |
loadExposome | 0.035 | 0.002 | 0.038 | |
loadExposome_plain | 0.035 | 0.002 | 0.038 | |
loadImputed | 0.014 | 0.002 | 0.017 | |
me | 0.002 | 0.001 | 0.003 | |
mexwas-methods | 0.644 | 0.009 | 0.654 | |
ndim-methods | 0.067 | 0.003 | 0.070 | |
normalityTest-methods | 0.848 | 0.017 | 0.865 | |
pca-methods | 0.090 | 0.005 | 0.093 | |
phenotypeNames-methods | 0.028 | 0.003 | 0.032 | |
plotClassification-methods | 0 | 0 | 0 | |
plotCorrelation-methods | 9.297 | 0.182 | 9.492 | |
plotEXP-methods | 0.265 | 0.010 | 0.275 | |
plotEffect-methods | 0.550 | 0.015 | 0.569 | |
plotExwas-methods | 0.382 | 0.008 | 0.391 | |
plotFamily-methods | 2.911 | 0.057 | 2.974 | |
plotHistogram-methods | 0.255 | 0.009 | 0.266 | |
plotLOD-methods | 0.283 | 0.009 | 0.296 | |
plotMissings-methods | 0.328 | 0.006 | 0.336 | |
plotPCA-methods | 1.036 | 0.011 | 1.049 | |
plotPHE-methods | 0.242 | 0.006 | 0.247 | |
readExposome | 0.038 | 0.002 | 0.039 | |
standardize-methods | 0.752 | 0.020 | 0.772 | |
tableLOD-methods | 0.131 | 0.005 | 0.136 | |
tableMissings-methods | 0.030 | 0.004 | 0.034 | |
tef-methods | 0.284 | 0.015 | 0.300 | |
toES | 0.076 | 0.002 | 0.078 | |
trans-methods | 0.165 | 0.006 | 0.173 | |
volcano_plot | 0.653 | 0.031 | 0.685 | |