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

[Benjamin Jean-Marie Tremblay]

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}