############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MetaVolcanoR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MetaVolcanoR_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MetaVolcanoR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘MetaVolcanoR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetaVolcanoR’ version ‘1.14.0’ * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MetaVolcanoR’ can be installed ... OK * checking installed package size ... OK * 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 loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE combining_mv: no visible binding for global variable ‘study’ combining_mv: no visible binding for global variable ‘value’ combining_mv: no visible binding for global variable ‘metap’ combining_mv: no visible binding for global variable ‘idx’ draw_cum_freq: no visible binding for global variable ‘ndatasets’ draw_cum_freq: no visible binding for global variable ‘DEGs’ draw_degbar: no visible binding for global variable ‘dataset’ draw_degbar: no visible binding for global variable ‘Regulation’ draw_forest: no visible binding for global variable ‘group’ plot_mv: no visible binding for global variable ‘metap’ plot_mv: no visible binding for global variable ‘degcomb’ plot_mv: no visible binding for global variable ‘ddeg’ plot_mv: no visible binding for global variable ‘ndeg’ plot_mv: no visible binding for global variable ‘degvcount’ plot_rem: no visible binding for global variable ‘signcon’ plot_rem: no visible binding for global variable ‘randomCi.ub’ plot_rem: no visible binding for global variable ‘randomCi.lb’ plot_rem: no visible binding for global variable ‘randomSummary’ plot_rem: no visible binding for global variable ‘randomP’ plot_rem: no visible binding for global variable ‘signcon2’ plot_rem: no visible binding for global variable ‘Ci.ub’ plot_rem: no visible binding for global variable ‘Ci.lb’ rem_mv: no visible binding for global variable ‘error’ rem_mv: no visible binding for global variable ‘randomCi.ub’ rem_mv: no visible binding for global variable ‘randomCi.lb’ rem_mv: no visible binding for global variable ‘index’ rem_mv: no visible global function definition for ‘head’ votecount_mv: no visible binding for global variable ‘ddeg’ votecount_mv: no visible binding for global variable ‘ndeg’ votecount_mv: no visible binding for global variable ‘idx’ Undefined global functions or variables: Ci.lb Ci.ub DEGs Regulation dataset ddeg degcomb degvcount error group head idx index metap ndatasets ndeg randomCi.lb randomCi.ub randomP randomSummary signcon signcon2 study value Consider adding importFrom("utils", "head") 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘MetaVolcano.Rmd’ using ‘UTF-8’... OK ‘PrepareDatasets.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘MetaVolcano.Rmd’ using rmarkdown Quitting from lines 64-66 [unnamed-chunk-1] (MetaVolcano.Rmd) Error: processing vignette 'MetaVolcano.Rmd' failed with diagnostics: there is no package called 'BiocManager' --- failed re-building ‘MetaVolcano.Rmd’ --- re-building ‘PrepareDatasets.Rmd’ using rmarkdown [WARNING] This document format requires a nonempty element. Please specify either 'title' or 'pagetitle' in the metadata, e.g. by using --metadata pagetitle="..." on the command line. Falling back to 'PrepareDatasets.knit' --- finished re-building ‘PrepareDatasets.Rmd’ SUMMARY: processing the following file failed: ‘MetaVolcano.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/MetaVolcanoR.Rcheck/00check.log’ for details.