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

[Martin Morgan]

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}
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