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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 JunctionSeq
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* checking for file ‘JunctionSeq/DESCRIPTION’ ... OK
* preparing ‘JunctionSeq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 25156 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpR6xqUS/xshell5b5223f8840a' 2>&1
ERROR
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for help.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, rowMaxs
The following object is masked from 'package:base':
apply
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:matrixStats':
rowRanges
> STARTING runJunctionSeqAnalyses (v1.5.0) (Fri Mar 3 20:36:08 2017)
> rJSA: sample.files: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/JctSeqData/extdata/tiny/SAMP1/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz, /Library/Frameworks/R.framework/Versions/3.4/Resources/library/JctSeqData/extdata/tiny/SAMP2/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz, /Library/Frameworks/R.framework/Versions/3.4/Resources/library/JctSeqData/extdata/tiny/SAMP3/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz, /Library/Frameworks/R.framework/Versions/3.4/Resources/library/JctSeqData/extdata/tiny/SAMP4/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz, /Library/Frameworks/R.framework/Versions/3.4/Resources/library/JctSeqData/extdata/tiny/SAMP5/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz, /Library/Frameworks/R.framework/Versions/3.4/Resources/library/JctSeqData/extdata/tiny/SAMP6/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz
> rJSA: sample.names: SAMP1, SAMP2, SAMP3, SAMP4, SAMP5, SAMP6
> rJSA: condition: CASE, CASE, CASE, CTRL, CTRL, CTRL
> rJSA: analysis.type: junctionsAndExons
> rJSA: use.junctions: TRUE
> rJSA: use.novel.junctions: TRUE
> rJSA: use.exons: TRUE
> rJSA: nCores: 1
> rJSA: use.covars:
> rJSA: test.formula0: ˜ sample + countbin
> rJSA: test.formula1: ˜ sample + countbin + condition:countbin
> rJSA: use.multigene.aggregates: FALSE
> rJSA: Reading Count files... Fri Mar 3 20:36:08 2017.
-> STARTING readJunctionSeqCounts (Fri Mar 3 20:36:08 2017)
---> RJSC; (v1.5.0)
---> RJSC: samplenames: SAMP1,SAMP2,SAMP3,SAMP4,SAMP5,SAMP6
---> RJSC: flat.gff.file: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/JctSeqData/extdata/tiny/withNovel.forJunctionSeq.gff.gz
---> RJSC: use.exons:TRUE
---> RJSC: use.junctions:TRUE
---> RJSC: use.novel.junctions:TRUE
---> File read complete.
---> Extracted counts. Found 1785 features so far.
---> Extracted gene-level counts. Found: 120 genes and aggregate-genes.
---> Removed gene features. Found: 1665 features to be included so far.
---> Note: 149 counting bins from overlapping genes
---> There are 3 multigene aggregates.
---> There are 8 genes that are part of an aggregate.
---> Removed multigene-aggregate features. Found: 1516 features to be included so far.
---> Final feature count: 1516 features to be included in the analysis.
---> Extracted feature counts.
---> counts complete.
-----> reading annotation...
-----> formatting annotation...
-----> initial generation...
-----> creating jscs...
-----> generating count vectors... (Fri Mar 3 20:36:09 2017)
> Using single-core execution.
getAllJunctionSeqCountVectors: dim(counts) = 1516,6 (Fri Mar 3 20:36:09 2017)
getAllJunctionSeqCountVectors: dim(gct) = 120,6
getAllJunctionSeqCountVectors: out generated. dim = 1516,12 (Fri Mar 3 20:36:09 2017)
-----> count vectors generated (Fri Mar 3 20:36:09 2017)
-----> generating DESeqDataSet... (Fri Mar 3 20:36:09 2017)
-----> DESeqDataSet generated (Fri Mar 3 20:36:10 2017)
> rJSA: Count files read. Fri Mar 3 20:36:10 2017.
> rJSA: Estimating Size Factors... Fri Mar 3 20:36:10 2017.
> rJSA: Size Factors Done. Size Factors are:.
> rJSA: SAMP1,SAMP2,SAMP3,SAMP4,SAMP5,SAMP6
> rJSA: 1.03314276312174,0.976723179655397,0.975727885927982,0.949619905979833,1.1414745469557,0.985415615635112
> rJSA: Estimating Dispersions... Fri Mar 3 20:36:10 2017.
---> STARTING estimateJunctionSeqDispersions: (v1.5.0) (Fri Mar 3 20:36:10 2017)
-----> ejsd: 1153 counting bins are marked 'testable'. across 60 genes.
(626 exonic regions, 514 known junctions, 13 novel junctions)
---------> Executing DESeq2 call: estimateUnsharedDispersions
using supplied model matrix
---------> Finished with DESeq2 call.
-----> ejsd: Dispersion estimation failed for 0 out of 1153 'testable' counting bins. Setting these features to be 'untestable'
---> FINISHED estimateJunctionSeqDispersions (Fri Mar 3 20:36:27 2017)
> rJSA: Dispersions estimated. Fri Mar 3 20:36:27 2017.
> rJSA: Fitting Dispersion Fcn... Fri Mar 3 20:36:27 2017.
> fitDispersionFunction() Starting (Fri Mar 3 20:36:27 2017)
> (fitType = parametric)
> (finalDispersionMethod = shrink)
> (fitDispersionsForExonsAndJunctionsSeparately = TRUE)
min(means[useForFit], na.rm=T)=0.146009972023612
> fdf: Fitting dispersions:
> (Iteration 1) Parametric Dispersion Coefs: [0.00441189552160493,0.237603951553493]
> (Iteration 2) Parametric Dispersion Coefs: [0.00241977307061871,0.248572808620474]
> (FINAL) Parametric Dispersion Coefs: [0.00241963664724755,0.248577200192]
> fdf: Fitting dispersions of exons and junctions to separate fitted trends.
> fdf: Fitting exon dispersions:
> (Iteration 1) Parametric Dispersion Coefs: [0.00443931330339071,0.301567751069055]
> (Iteration 2) Parametric Dispersion Coefs: [0.00187057883263236,0.312567414793755]
> (Iteration 3) Parametric Dispersion Coefs: [0.0018049098469947,0.301293360721244]
> (FINAL) Parametric Dispersion Coefs: [0.0018052495176776,0.301276852835131]
> fdf: Fitting splice-junction dispersions:
> (Iteration 1) Parametric Dispersion Coefs: [0.0036019286493397,0.197201296535263]
> (Iteration 2) Parametric Dispersion Coefs: [0.00347934994709991,0.198435795775607]
> (FINAL) Parametric Dispersion Coefs: [0.00347895676015746,0.198443617544811]
> fdf(): 'Shrinking' fitted and feature-specific dispersion estimates.
*** caught segfault ***
address 0x100000001, cause 'memory not mapped'
Traceback:
1: .Call("DESeq2_fitDisp", PACKAGE = "DESeq2", ySEXP, xSEXP, mu_hatSEXP, log_alphaSEXP, log_alpha_prior_meanSEXP, log_alpha_prior_sigmasqSEXP, min_log_alphaSEXP, kappa_0SEXP, tolSEXP, maxitSEXP, use_priorSEXP)
2: fitDisp(ySEXP = ySEXP, xSEXP = xSEXP, mu_hatSEXP = mu_hatSEXP, log_alphaSEXP = log_alphaSEXP, log_alpha_prior_meanSEXP = log_alpha_prior_meanSEXP, log_alpha_prior_sigmasqSEXP = log_alpha_prior_sigmasqSEXP, min_log_alphaSEXP = min_log_alphaSEXP, kappa_0SEXP = kappa_0SEXP, tolSEXP = tolSEXP, maxitSEXP = maxitSEXP, use_priorSEXP = use_priorSEXP)
3: fitDispWrapper(ySEXP = countVectors, xSEXP = modelMatrix, mu_hatSEXP = mu, log_alphaSEXP = log(dispInit), log_alpha_prior_meanSEXP = log(dispFitted), log_alpha_prior_sigmasqSEXP = log_alpha_prior_sigmasq, min_log_alphaSEXP = log(minDisp/10), kappa_0SEXP = kappa_0, tolSEXP = dispTol, maxitSEXP = maxit, use_priorSEXP = TRUE)
4: adapted.estimateDispersionsMAP(jscs = jscs, useRows = (isExon) & fData(jscs)$testable, verbose = verbose)
5: fitDispersionFunction_advancedMode(jscs, fitType = method.dispFit, verbose = verbose, finalDispersionMethod = method.dispFinal, fitDispersionsForExonsAndJunctionsSeparately = fitDispersionsForExonsAndJunctionsSeparately)
6: fitJunctionSeqDispersionFunction(jscs, method.GLM = method.GLM, method.dispFit = method.dispFit, method.dispFinal = method.dispFinal, verbose = verbose, fitDispersionsForExonsAndJunctionsSeparately = fitDispersionsForExonsAndJunctionsSeparately)
7: runJunctionSeqAnalyses(sample.files = countFiles, sample.names = decoder$sample.ID, condition = factor(decoder$group.ID), flat.gff.file = gff.file, nCores = 1, analysis.type = "junctionsAndExons")
8: eval(expr, envir, enclos)
9: eval(expr, envir, enclos)
10: withVisible(eval(expr, envir, enclos))
11: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
12: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
13: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
14: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
15: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
16: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
17: block_exec(params)
18: call_block(x)
19: process_group.block(group)
20: process_group(group)
21: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
22: process_file(text, output)
23: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pdf else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv())
24: engine$weave(file, quiet = quiet, encoding = enc)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA, call. = FALSE)})
29: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...