Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:09 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2184/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Gavin Ha
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the TitanCNA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TitanCNA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: TitanCNA |
Version: 1.47.1 |
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TitanCNA |
StartedAt: 2025-08-29 03:34:23 -0000 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 03:36:03 -0000 (Fri, 29 Aug 2025) |
EllapsedTime: 100.0 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TitanCNA ### ############################################################################## ############################################################################## * checking for file ‘TitanCNA/DESCRIPTION’ ... OK * preparing ‘TitanCNA’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘TitanCNA.Rnw’ using Sweave Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’ Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’ Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’ Warning: replacing previous import ‘BiocGenerics::setequal’ by ‘dplyr::setequal’ when loading ‘TitanCNA’ Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’ Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’ Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’ Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’ Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’ Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’ Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’ Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’ Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’ Warning in fun(libname, pkgname) : Package 'TitanCNA' is deprecated and will be removed from Bioconductor version 3.23 titan: Loading data /home/biocbuild/tmp/RtmpfJQOEi/Rinst248cc25d38f2b9/TitanCNA/extdata/test_alleleCounts_chr2.txt Reading GC and mappability files Slurping: /home/biocbuild/tmp/RtmpfJQOEi/Rinst248cc25d38f2b9/TitanCNA/extdata/gc_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Slurping: /home/biocbuild/tmp/RtmpfJQOEi/Rinst248cc25d38f2b9/TitanCNA/extdata/map_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Loading tumour file:/home/biocbuild/tmp/RtmpfJQOEi/Rinst248cc25d38f2b9/TitanCNA/extdata/test_tum_chr2.wig Slurping: /home/biocbuild/tmp/RtmpfJQOEi/Rinst248cc25d38f2b9/TitanCNA/extdata/test_tum_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Loading normal file:/home/biocbuild/tmp/RtmpfJQOEi/Rinst248cc25d38f2b9/TitanCNA/extdata/test_norm_chr2.wig Slurping: /home/biocbuild/tmp/RtmpfJQOEi/Rinst248cc25d38f2b9/TitanCNA/extdata/test_norm_chr2.wig Parsing: fixedStep chrom=2 start=1 step=1000 span=1000 Sorting by decreasing chromosome size Warning in .replace_seqlevels_style(x_seqlevels, value) : found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one Warning in .replace_seqlevels_style(x_seqlevels, value) : found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one Warning in .replace_seqlevels_style(x_seqlevels, value) : found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one Warning in .replace_seqlevels_style(x_seqlevels, value) : found more than one best sequence renaming map compatible with seqname style "NCBI" for this object, using the first one Correcting Tumour Applying filter on data... Correcting for GC bias... Correcting for mappability bias... Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) : collapsing to unique 'x' values Correcting Normal Applying filter on data... Correcting for GC bias... Correcting for mappability bias... Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) : collapsing to unique 'x' values Normalizing Tumour by Normal Removed Chrs: titan: Running HMM... fwdBack: Iteration 1 chr: Warning: executing %dopar% sequentially: no parallel backend registered 1 Using Coordinate Descent iteration 11 with Fval=-30495 and n=0.3983 (map), s=[0.0083,0.3774], phi=1.501 fwdBack: loglik=-34153.2204 fwdBack: priorN=0.3632 fwdBack: priorS=-2.6655 fwdBack: priorVar=-437.5360 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.0958 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 1 complete loglik=-34532.8109 fwdBack: Elapsed time for iteration 1: 0.0486m fwdBack: Iteration 2 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26836 and n=0.2535 (map), s=[0.0092,0.4332], phi=1.467 fwdBack: loglik=-28991.8804 fwdBack: priorN=0.1270 fwdBack: priorS=-2.5220 fwdBack: priorVar=-748.9796 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.2627 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 2 complete loglik=-29683.1740 fwdBack: Elapsed time for iteration 2: 0.0481m fwdBack: Iteration 3 chr: 1 Using Coordinate Descent iteration 11 with Fval=-26078 and n=0.2115 (map), s=[0.0069,0.4528], phi=1.482 fwdBack: loglik=-26353.2551 fwdBack: priorN=0.0007 fwdBack: priorS=-2.7972 fwdBack: priorVar=-818.6579 fwdBack: priorVarR=0.0000 fwdBack: priorPhi=-1.1886 fwdBack: priorPiG=60.3628 fwdBack: priorPiZ=0.9808 fwdBack: EM iteration 3 complete loglik=-27114.5546 fwdBack: Elapsed time for iteration 3: 0.0490m fwdBack: Total elapsed time: 0.2242m outputTitanResults: Correcting results... outputTitanResults: Recomputing log-likelihood. titan: Running HMM... fwdBack: Iteration 1 chr: 1 *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback: 1: eval(xpr, envir = envir) 2: eval(xpr, envir = envir) 3: doTryCatch(return(expr), name, parentenv, handler) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5: tryCatchList(expr, classes, parentenv, handlers) 6: tryCatch(eval(xpr, envir = envir), error = function(e) e) 7: doTryCatch(return(expr), name, parentenv, handler) 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9: tryCatchList(expr, classes, parentenv, handlers) 10: tryCatch({ repeat { args <- nextElem(it) if (obj$verbose) { cat(sprintf("evaluation # %d:\n", i)) print(args) } for (a in names(args)) assign(a, args[[a]], pos = envir, inherits = FALSE) r <- tryCatch(eval(xpr, envir = envir), error = function(e) e) if (obj$verbose) { cat("result of evaluating expression:\n") print(r) } tryCatch(accumulator(list(r), i), error = function(e) { cat("error calling combine function:\n") print(e) NULL }) i <- i + 1 }}, error = function(e) { if (!identical(conditionMessage(e), "StopIteration")) stop(simpleError(conditionMessage(e), expr))}) 11: e$fun(obj, substitute(ex), parent.frame(), e$data) 12: foreach(c = 1:numChrs, .combine = rbind, .noexport = c("data")) %dopar% { if (verbose == TRUE) { message(c, " ", appendLF = FALSE) } .Call("fwd_backC_clonalCN", log(piGiZi[c, ]), py[, chrsI[[c]]], gNoOUTStateParams$ct, gNoOUTStateParams$ZS, Z, posn[chrsI[[c]]], txnZstrength * txnExpLen, txnExpLen, O) } 13: runEMclonalCN(data, newParams, maxiter = 1, txnExpLen = convergeParams$txn_exp_len, txnZstrength = convergeParams$txn_z_strength, useOutlierState = FALSE, normalEstimateMethod = "fixed", estimateS = FALSE, estimatePloidy = F, verbose = verbose) 14: removeEmptyClusters(data, convergeParams, outmat, proportionThreshold = proportionThreshold, proportionThresholdClonal = proportionThresholdClonal, recomputeLogLik = recomputeLogLik, verbose = verbose) 15: outputTitanResults(data, convergeParams, optimalPath, filename = NULL, posteriorProbs = FALSE, subcloneProfiles = TRUE, correctResults = TRUE, proportionThreshold = 0.05, proportionThresholdClonal = 0.05, is.haplotypeData = FALSE) 16: eval(expr, .GlobalEnv) 17: eval(expr, .GlobalEnv) 18: withVisible(eval(expr, .GlobalEnv)) 19: doTryCatch(return(expr), name, parentenv, handler) 20: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21: tryCatchList(expr, classes, parentenv, handlers) 22: 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, nlines = 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))}) 23: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE) 24: evalFunc(ce, options) 25: tryCatchList(expr, classes, parentenv, handlers) 26: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()}) 27: driver$runcode(drobj, chunk, chunkopts) 28: utils::Sweave(...) 29: engine$weave(file, quiet = quiet, encoding = enc) 30: doTryCatch(return(expr), name, parentenv, handler) 31: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 32: tryCatchList(expr, classes, parentenv, handlers) 33: 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)))}) 34: tools::buildVignettes(dir = ".", tangle = TRUE) An irrecoverable exception occurred. R is aborting now ...