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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MAIT
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* 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
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 4.5.1
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[713]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[713]: +[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[699]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[699]: +[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
objc[717]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[717]: +[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[718]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[718]: +[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.
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
--- failed re-building ‘MAIT_Vignette.Rnw’
SUMMARY: processing the following file failed:
‘MAIT_Vignette.Rnw’
Error: Vignette re-building failed.
Execution halted
