Hi BioConductor community, My package (msPurity) is passing the build on the Linux (*zin1*) and Windows servers (*moscato1*) but failing on the Mac OS X server (*morelia*). Also I cannot seem to replicate the failure either on a local installation of Mac OS X (el captain) or with Travis CI.
I should probably note that for Travis CI I did have to install the msPurityData dependency directly (without Bioconductor). See line 10 https://raw.githubusercontent.com/Viant-Metabolomics/msPurity/master/.travis.yml The error I think is coming from a function I have that uses the mzR::peaks() function but I am struggling to see why I am getting the error. Any help or suggestions would be really appreciated. Kind regards, Tom https://github.com/Bioconductor-mirror/msPurity http://bioconductor.org/checkResults/devel/bioc-LATEST/msPurity/morelia-buildsrc.html https://bioconductor.org/packages/devel/bioc/html/msPurity.html Travis Mac build report: https://travis-ci.org/Viant-Metabolomics/msPurity/jobs/159938167 ############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data msPurity ### ############################################################################## ############################################################################## * checking for file ‘msPurity/DESCRIPTION’ ... OK * preparing ‘msPurity’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ...sh: line 1: 62889 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpCXdH7K/xshellf59d5efb2aea' 2>&1 ERROR *** caught segfault *** address 0x0, cause 'memory not mapped' Traceback: 1: .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x7fb83b714be0>, dll = list(name = "Rcpp", path = "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/libs/Rcpp.so", dynamicLookup = TRUE, handle = <pointer: 0x7fb83b70ed10>, info = <pointer: 0x1052f30c0>), numParameters = -1L), <pointer: 0x7fb83b590710>, <pointer: 0x7fb83b5af740>, .pointer, ...) 2: object@backend$getPeakList(x) 3: FUN(X[[i]], ...) 4: lapply(X = X, FUN = FUN, ...) 5: sapply(scans, function(x) object@backend$getPeakList(x)$peaks, simplify = FALSE) 6: sapply(scans, function(x) object@backend$getPeakList(x)$peaks, simplify = FALSE) 7: .local(object, ...) 8: mzR::peaks(mr) 9: mzR::peaks(mr) 10: .fun(piece, ...) 11: (function (i) { piece <- pieces[[i]] if (.inform) { res <- try(.fun(piece, ...)) if (inherits(res, "try-error")) { piece <- paste(utils::capture.output(print(piece)), collapse = "\n") stop("with piece ", i, ": \n", piece, call. = FALSE) } } else { res <- .fun(piece, ...) } progress$step() res})(2L) 12: .Call(loop_apply_, as.integer(n), f, env) 13: loop_apply(n, do.ply) 14: llply(.data = pieces, .fun = .fun, ..., .progress = .progress, .inform = .inform, .parallel = .parallel, .paropts = .paropts) 15: plyr::alply(files, 1, function(x) { mr <- mzR::openMSfile(x) scan_peaks <- mzR::peaks(mr) return(scan_peaks)}) 16: getscans(filepths) 17: purityX(xset, offsets = c(0.5, 0.5), xgroups = c(1, 2)) 18: eval(expr, envir, enclos) 19: eval(expr, envir, enclos) 20: withVisible(eval(expr, envir, enclos)) 21: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) 22: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) 23: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler) 24: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)) 25: in_dir(opts_knit$get("root.dir") %n% input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))) 26: block_exec(params) 27: call_block(x) 28: process_group.block(group) 29: process_group(group) 30: 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$get("infile"), ") ") }) 31: process_file(text, output) 32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding) 33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv()) 34: vweave_rmarkdown(...) 35: engine$weave(file, quiet = quiet, encoding = enc) 36: doTryCatch(return(expr), name, parentenv, handler) 37: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 38: tryCatchList(expr, classes, parentenv, handlers) 39: 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)}) 40: tools::buildVignettes(dir = ".", tangle = TRUE) An irrecoverable exception occurred. R is aborting now ... [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel