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BUILD report for birte on malbec2

This page was generated on 2019-10-16 12:06:09 -0400 (Wed, 16 Oct 2019).

Package 175/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birte 1.20.0
Holger Froehlich
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/birte
Branch: RELEASE_3_9
Last Commit: a84a8e5
Last Changed Date: 2019-05-02 11:53:53 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: birte
Version: 1.20.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data birte
StartedAt: 2019-10-15 21:16:59 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 21:17:38 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 38.9 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data birte
###
##############################################################################
##############################################################################


* checking for file ‘birte/DESCRIPTION’ ... OK
* preparing ‘birte’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... 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 0xf2, 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 ...
Segmentation fault (core dumped)