[Bioc-devel] msPurity build fail on Mac OS X (morelia)

[Thomas Lawson]

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 at backend$getPeakList(x)
 3: FUN(X[[i]], ...)
 4: lapply(X = X, FUN = FUN, ...)
 5: sapply(scans, function(x) object at backend$getPeakList(x)$peaks,
simplify = FALSE)
 6: sapply(scans, function(x) object at backend$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 ...

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