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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 Risa
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* checking for file ‘Risa/DESCRIPTION’ ... OK
* preparing ‘Risa’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Risa.Rnw’ using Sweave
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’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, 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: Rcpp
Loading required package: biocViews
Loading required package: affy
Loading required package: faahKO
Loading required package: xcms
Loading required package: BiocParallel
This is xcms version 4.2.0
Attaching package: ‘xcms’
The following object is masked from ‘package:stats’:
sigma
objc[32862]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[32862]: +[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[32863]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[32863]: +[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[32864]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[32864]: +[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[32865]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[32865]: +[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 'Risa.Rnw' failed with diagnostics:
chunk 3 (label = Risa-processXcmsSet)
Error in reducer$value.cache[[as.character(idx)]] <- values :
wrong args for environment subassignment
Error: tangling vignette 'Risa.Rnw' failed with diagnostics:
no Sweave file with name ‘Risa.Rnw’ found
--- failed re-building ‘Risa.Rnw’
SUMMARY: processing the following files failed:
‘Risa.Rnw’ ‘Risa.Rnw’
Error: Vignette re-building failed.
Execution halted