[Bioc-devel] Help with merida1 R CMD install error

[Benjamin Jean-Marie Tremblay]

Fantastic! Thank you.

Ben

> Le 1 janv. 2020 à 20:38, Martin Morgan <mtmorgan.bioc using gmail.com> a écrit :
> 
> This is from the bibtex package
> 
>  https://github.com/romainfrancois/bibtex/issues/23
> 
> And the solution is to either not use that package (settling for base R functionality) or wait for the upstream fix.
> 
> Martin
> 
> 
> On 1/2/20, 7:06 AM, "Bioc-devel on behalf of Benjamin Jean-Marie Tremblay" <bioc-devel-bounces using r-project.org on behalf of benjamin.tremblay using uwaterloo.ca> wrote:
> 
>    Dear bioc-devel,
> 
>    My package has been getting a strange error on merida1 (also celaya2)
>    during the initial install phase. I've pasted it at the bottom of this message.
> 
>    My question is: what can I do to figure out what the problem is? I already work
>    on a Mac currently, and R CMD check runs fine. I've also recently patched the
>    package, but that was for a different error -- the one in question was also
>    occurring for the previous version, which used to pass without issues. I’ve
>    downloaded the bioconductor_full docker image to try and replicate the test
>    environment, but that went fine too. Perhaps it's OS/hardware specific? (I use
>    macOS Catalina).
> 
>    Any help would be greatly appreciated. My package is over at:
>    http://bioconductor.org/packages/release/bioc/html/universalmotif.html
> 
>    Thank you,
> 
>    Ben T
> 
>    The error in question. Something appears to go wrong when processing the Rd files.
> 
>    ** help
> 
>     *** caught segfault ***
>    address 0x0, cause 'memory not mapped'
> 
>    Traceback:
>     1: doTryCatch(return(expr), name, parentenv, handler)
>     2: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>     3: tryCatchList(expr, classes, parentenv, handlers)
>     4: tryCatch(.External("do_read_bib", file = file, encoding = encoding,     srcfile = srcfile), error = function(e) {    if (!any(grepl("unprotect_ptr", e)))         stop(geterrmessage(), call. = FALSE)    else stop("Invalid bib file", call. = FALSE)})
>     5: withCallingHandlers(tryCatch(.External("do_read_bib", file = file,     encoding = encoding, srcfile = srcfile), error = function(e) {    if (!any(grepl("unprotect_ptr", e)))         stop(geterrmessage(), call. = FALSE)    else stop("Invalid bib file", call. = FALSE)}), warning = function(w) {    if (any(grepl("syntax error, unexpected [$]end", w)))         invokeRestart("muffleWarning")})
>     6: read.bib(file = fn, encoding = encoding)
>     7: get_bibentries(package = package, ..., stop_on_error = FALSE)
>     8: Rdpack::insert_citeOnly(key = "euclidean", package = "universalmotif",     cached_env = .Rdpack.currefs)
>     9: eval(expr, env)
>    10: eval(expr, env)
>    11: withVisible(eval(expr, env))
>    12: doTryCatch(return(expr), name, parentenv, handler)
>    13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>    14: tryCatchList(expr, classes, parentenv, handlers)
>    15: tryCatch(withVisible(eval(expr, env)), error = function(e) e)
>    16: evalWithOpt(ce, options, env)
>    17: processRdChunk(block, stage, options, env, macros = macros)
>    18: recurse(block[[i]])
>    19: recurse(block[[i]])
>    20: recurse(block[[i]])
>    21: recurse(block)
>    22: getDynamicFlags(block)
>    23: recurse(block)
>    24: expandDynamicFlags(recurse(block), options)
>    25: processRdSexprs(Rd, "build", options, macros = attr(Rd, "macros"))
>    26: prepare_Rd(f, encoding = encoding, defines = os, stages = stages,     warningCalls = FALSE, stage2 = step > 1L, stage3 = step >         2L, macros = macros)
>    27: FUN(X[[i]], ...)
>    28: lapply(files, .fetch_Rd_object)
>    29: .build_Rd_db(dir, manfiles, db_file = db_file, encoding = encoding,     built_file = built_file)
>    30: .install_package_Rd_objects(".", instdir, encoding)
>    31: doTryCatch(return(expr), name, parentenv, handler)
>    32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>    33: tryCatchList(expr, classes, parentenv, handlers)
>    34: 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))})
>    35: try(.install_package_Rd_objects(".", instdir, encoding))
>    36: do_install_source(pkg_name, instdir, pkg, desc)
>    37: do_install(pkg)
>    38: tools:::.install_packages()
>    An irrecoverable exception occurred. R is aborting now ...
>    /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 14976 Done                    echo 'tools:::.install_packages()'
>         14977 Segmentation fault: 11  | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
>    _______________________________________________
>    Bioc-devel using r-project.org mailing list
>    https://stat.ethz.ch/mailman/listinfo/bioc-devel
>