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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data birte
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* checking for file ‘birte/DESCRIPTION’ ... OK
* preparing ‘birte’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 26579 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmpfsa4h4/xshell5cf94cac3c3c' 2>&1
ERROR
--- re-building ‘birte.Rnw’ using Sweave
Loading required package: RcppArmadillo
Loading required package: Rcpp
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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, setdiff, sort, table,
tapply, union, unique, unsplit, which, 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")'.
*** caught segfault ***
address 0x1da9c, cause 'memory not mapped'
Traceback:
1: birteStart(mRNAexpr = dat.mRNA, miRNAexpr = data.regulators2$miRNA, Qexpr = data.regulators2$other, nrep.mRNA = nrep.mRNA, nrep.miRNA = nrep.regulators$miRNA, nrep.TF = nrep.regulators$TF, nrep.Q = nrep.regulators$other, mRNA.data.type = "array", miRNA.data.type = regulators.data.type$miRNA, Qexpr.data.type = regulators.data.type$other, genesetsTF = genesets$TF, genesetsmiRNA = genesets$miRNA, genesetsothers = genesets$other, alpha_i = alpha$miRNA, alpha_i0 = alpha0$miRNA, alpha_i0Q = alpha0$other, alpha_iQ = alpha$other, alphamiR = alpha.para$miRNA, betamiR = beta.para$miRNA, alphaQ = alpha.para$other, betaQ = beta.para$other, niter = niter, burnin = nburnin, thin = thin, model = model, only_switches = only_switches, nomiRNA = is.null(genesets$miRNA), noTF = is.null(genesets$TF), affinitiesTF = affinities$TF, affinitiesmiRNA = affinities$miRNA, affinitiesothers = affinities$other, potential_swaps = potential_swaps2, theta_TF = theta.regulators2$TF, theta_miRNA = theta.regulators2$miRNA, theta_other = theta.regulators2$other, K = K, interactions = interactions, A_sigma = sigma.regulators2$miRNA, O_sigma = mRNA.Sigma, Q_sigma = sigma.regulators2$other, init_S = init.regulators2$miRNA, init_T = init.regulators2$TF, init_other = init.regulators2$other, TFexpr = data.regulators2$TF, TFexpr.data.type = regulators.data.type$TF, alpha_i0TF = alpha0$TF, alpha_iTF = alpha$TF, TF_sigma = sigma.regulators2$TF, alphaTF = alpha.para$TF, betaTF = beta.para$TF, alpha = alpha.mRNA, beta = beta.mRNA)
2: birteRun(dat.mRNA = dat.mRNA, mRNA.Sigma = O_Sigma, nrep.mRNA = nrep.mRNA, df.mRNA = df.mRNA, data.regulators = dat, sigma.regulators = sigma, nrep.regulators = nrep, diff.regulators = diff.exp, init.regulators = init.regulators, theta.regulators = theta.regulators, reg.interactions = reg.interactions, affinities = affinities, use.affinities = use.affinities, niter = niter, nburnin = nburnin, thin = thin, potential_swaps = potential_swaps, only_switches = only_switches, only.diff.TFs = only.diff.TFs, explain.LFC = explain.LFC, single.sample = single.sample, single.sample.estimator = single.sample.estimator, model = model)
3: birteLimma(dat.mRNA = mydat, limmamRNA = limmamRNA, affinities = affinities, niter = 500, nburnin = 5000, thin = 1)
4: eval(expr, .GlobalEnv)
5: eval(expr, .GlobalEnv)
6: withVisible(eval(expr, .GlobalEnv))
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
11: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
12: evalFunc(ce, options)
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
15: driver$runcode(drobj, chunk, chunkopts)
16: utils::Sweave(...)
17: engine$weave(file, quiet = quiet, encoding = enc)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
22: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
