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This page was generated on 2024-02-18 02:28:16 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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 272/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
casper 2.37.0  (landing page)
David Rossell
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/casper
git_branch: devel
git_last_commit: fdb9dd6
git_last_commit_date: 2023-10-24 09:52:32 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD results for casper on merida1


To the developers/maintainers of the casper package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/casper.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.

raw results


Summary

Package: casper
Version: 2.37.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data casper
StartedAt: 2024-02-16 17:39:10 -0500 (Fri, 16 Feb 2024)
EndedAt: 2024-02-16 17:42:29 -0500 (Fri, 16 Feb 2024)
EllapsedTime: 199.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data casper
###
##############################################################################
##############################################################################


* checking for file ‘casper/DESCRIPTION’ ... OK
* preparing ‘casper’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 34569 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmptzVZ4y/xshell16a763e5516f5' 2>&1
 ERROR
--- re-building ‘casper.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, aperm, 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, table, tapply,
    union, unique, unsplit, 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")'.

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb

 *** caught segfault ***
address 0xe6, cause 'memory not mapped'

Traceback:
 1: calcKnownMultiple(exons = exons, exonwidth = exonwidth, transcripts = transcripts,     islandid = as.list(islandid), pc = pc, startcdf = startcdf,     lendis = lendis, lenvals = lenvals, readLength = readLength,     priorq = priorq, strand = strand, citype = citype, niter = niter,     burnin = burnin, verbose = verbose)
 2: f(islandid)
 3: .local(distrs, genomeDB, pc, readLength, islandid, rpkm, priorq,     priorqGeneExpr, citype, niter, burnin, mc.cores, verbose,     totReads)
 4: procExp(distrs, genomeDB, pc = pc@counts[[1]], readLength = readLength,     islandid = islandid, rpkm = rpkm, priorq = priorq, priorqGeneExpr = priorqGeneExpr,     niter = niter, burnin = burnin, mc.cores = mc.cores, citype = citype,     totReads = totReads)
 5: procExp(distrs, genomeDB, pc = pc@counts[[1]], readLength = readLength,     islandid = islandid, rpkm = rpkm, priorq = priorq, priorqGeneExpr = priorqGeneExpr,     niter = niter, burnin = burnin, mc.cores = mc.cores, citype = citype,     totReads = totReads)
 6: calcExp(distrs = distrs, genomeDB = hg19DB, pc = pc, readLength = 75,     rpkm = FALSE)
 7: eval(expr, .GlobalEnv)
 8: eval(expr, .GlobalEnv)
 9: withVisible(eval(expr, .GlobalEnv))
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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))})
14: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
15: evalFunc(ce, options)
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(evalFunc(ce, options), finally = {    cat("\n")    sink()})
18: driver$runcode(drobj, chunk, chunkopts)
19: utils::Sweave(...)
20: engine$weave(file, quiet = quiet, encoding = enc)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: 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)))})
25: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...