############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GeomxTools ### ############################################################################## ############################################################################## * checking for file ‘GeomxTools/DESCRIPTION’ ... OK * preparing ‘GeomxTools’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ...sh: line 1: 5600 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpQ9SmQQ/xshell150f28a188e9' 2>&1 ERROR --- re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ using rmarkdown --- finished re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ --- re-building ‘GeomxSet_coercions.Rmd’ using rmarkdown 2024-04-16 18:57:50.183 R[5600:449481194] XType: Using static font registry. Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |=================================== | 50% | |======================================================================| 100% Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |=================================== | 50% | |======================================================================| 100% Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| --- finished re-building ‘GeomxSet_coercions.Rmd’ --- re-building ‘Protein_in_GeomxTools.Rmd’ using rmarkdown *** caught segfault *** address 0x100000001, cause 'invalid permissions' *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation *** recursive gc invocation Traceback: 1: duplicated.default(nm) 2: duplicated(nm) 3: xpdrows.data.frame(x, rows, new.rows) 4: `[<-.data.frame`(`*tmp*`, nrow(lookup_df) + 1, , value = list( "RTS0021560", "HRH1", "Hs_R_NGS_WTA_v1.0", "Endogenous", "36211", "3269", "HRH1")) 5: `[<-`(`*tmp*`, nrow(lookup_df) + 1, , value = list("RTS0021560", "HRH1", "Hs_R_NGS_WTA_v1.0", "Endogenous", "36211", "3269", "HRH1")) 6: generate_pkc_lookup(jsons_vec = pkc_json_list) 7: readPKCFile(pkcFiles, default_pkc_vers = defaultPKCVersions) 8: readNanoStringGeoMxSet(dccFiles = DCCFiles, pkcFiles = PKCFiles, phenoDataFile = SampleAnnotationFile, phenoDataSheet = "Annotations", phenoDataDccColName = "Sample_ID", protocolDataColNames = c("Tissue", "Segment_Type", "ROI.Size"), configFile = NULL, analyte = "RNA", phenoDataColPrefix = "", experimentDataColNames = NULL) 9: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 10: suppressWarnings(readNanoStringGeoMxSet(dccFiles = DCCFiles, pkcFiles = PKCFiles, phenoDataFile = SampleAnnotationFile, phenoDataSheet = "Annotations", phenoDataDccColName = "Sample_ID", protocolDataColNames = c("Tissue", "Segment_Type", "ROI.Size"), configFile = NULL, analyte = "RNA", phenoDataColPrefix = "", experimentDataColNames = NULL)) 11: eval(expr, envir, enclos) 12: eval(expr, envir, enclos) 13: eval_with_user_handlers(expr, envir, enclos, user_handlers) 14: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)) 15: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler) 16: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)) 17: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))) 18: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing) 19: evaluate::evaluate(...) 20: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 21: in_dir(input_dir(), expr) 22: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 23: eng_r(options) 24: block_exec(params) 25: call_block(x) 26: process_group.block(group) 27: process_group(group) 28: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 29: withCallingHandlers(expr, error = function(e) { loc = paste0(current_lines(), label, sprintf(" (%s)", knit_concord$get("infile"))) message(one_string(handler(e, loc)))}) 30: handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i])) 31: process_file(text, output) 32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 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) 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)))}) 40: tools::buildVignettes(dir = ".", tangle = TRUE) An irrecoverable exception occurred. R is aborting now ...