############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MAIT ### ############################################################################## ############################################################################## * checking for file ‘MAIT/DESCRIPTION’ ... OK * preparing ‘MAIT’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘MAIT_Vignette.Rnw’ using Sweave Loading required package: CAMERA Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: xcms Loading required package: BiocParallel This is xcms version 4.4.0 Attaching package: ‘xcms’ The following object is masked from ‘package:stats’: sigma Loading required package: Rcpp Loading required package: pls Attaching package: ‘pls’ The following object is masked from ‘package:stats’: loadings Attaching package: ‘MAIT’ The following objects are masked from ‘package:pls’: loadings, scores The following object is masked from ‘package:BiocGenerics’: plotPCA The following object is masked from ‘package:stats’: loadings objc[34666]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. objc[34666]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug. Warning in parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result Error: processing vignette 'MAIT_Vignette.Rnw' failed with diagnostics: chunk 2 (label = sampleProcessing) Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment objc[34672]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. objc[34672]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug. objc[34671]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. objc[34671]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug. objc[34673]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. objc[34673]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug. --- failed re-building ‘MAIT_Vignette.Rnw’ SUMMARY: processing the following file failed: ‘MAIT_Vignette.Rnw’ Error: Vignette re-building failed. Execution halted