Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

BUILD report for rain on merida1

This page was generated on 2021-05-06 12:36:17 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the rain package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1447/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rain 1.24.0  (landing page)
Paul F. Thaben
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/rain
Branch: RELEASE_3_12
Last Commit: 55cddbc
Last Changed Date: 2020-10-27 10:58:43 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: rain
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rain
StartedAt: 2021-05-05 21:32:24 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 21:32:36 -0400 (Wed, 05 May 2021)
EllapsedTime: 12.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* checking for file ‘rain/DESCRIPTION’ ... OK
* preparing ‘rain’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 91812 Illegal instruction: 4  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmp7BLZE4/xshell165ee487edd56' 2>&1
 ERROR
--- re-building ‘rain.Rnw’ using Sweave
Loading required package: lattice
Loading required package: rain
Loading required package: gmp

Attaching package: ‘gmp’

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

    %*%, apply, crossprod, matrix, tcrossprod

Loading required package: multtest
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:gmp’:

    which.max, which.min

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

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")'.


 *** caught illegal operation ***
address 0x106b0ff7d, cause 'illegal opcode'

Traceback:
 1: as.bigz(matrix(c(1, rep(0, ceiling(maxval/2) - 1)), nrow = 1))
 2: harding(sequences[[i]], c(1 + relpeak[i]), cycl = TRUE)
 3: umbrellaCirc(x, nr.series = 1, per, peak.border, type = 3, adjp.method = adjp.method,     measure.sequence, verbose = verbose)
 4: rain(measure, period = 24, deltat = 2, peak.border = c(0.1, 0.9),     verbose = FALSE)
 5: eval(expr, .GlobalEnv)
 6: eval(expr, .GlobalEnv)
 7: withVisible(eval(expr, .GlobalEnv))
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: 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)[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))})
12: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
13: evalFunc(ce, options)
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(evalFunc(ce, options), finally = {    cat("\n")    sink()})
16: driver$runcode(drobj, chunk, chunkopts)
17: utils::Sweave(...)
18: engine$weave(file, quiet = quiet, encoding = enc)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: 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)))})
23: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...