############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:rexposome.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings rexposome_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rexposome.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘rexposome/DESCRIPTION’ ... OK * this is package ‘rexposome’ version ‘1.27.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 loading without being on the library search path ... 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 : : no visible global function definition for ‘reformulate’ invExWAS,ExposomeSet : : no visible global function definition for ‘terms’ invExWAS,ExposomeSet : : 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 14.072 0.102 14.174 invExWAS-methods 9.454 0.074 9.529 plotCorrelation-methods 8.979 0.194 9.175 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 WARNINGs, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/rexposome.Rcheck/00check.log’ for details.