[MacPorts] #68162: R-tiledb @0.21.0 broken on macOS 12 and earlier when built with Clang

[MacPorts]

#68162: R-tiledb @0.21.0 broken on macOS 12 and earlier when built with Clang
--------------------------+----------------------
 Reporter:  barracuda156  |      Owner:  (none)
     Type:  defect        |     Status:  new
 Priority:  Normal        |  Milestone:
Component:  ports         |    Version:  2.8.1
 Keywords:                |       Port:  R-tiledb
--------------------------+----------------------
 Upstream issue: https://github.com/TileDB-Inc/TileDB-R/issues/589

 {{{
 /opt/local/bin/clang++-mp-15 -std=gnu++17 -dynamiclib
 -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
 -multiply_defined suppress
 -L/opt/local/Library/Frameworks/R.framework/Resources/lib -L/opt/local/lib
 -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc
 -Wl,-syslibroot,/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
 -arch x86_64 -o tiledb.so RcppExports.o arrowio.o batched.o
 column_buffer.o deprecation.o durations.o libtiledb.o nanoarrow.o
 nullable.o shmem.o utilities.o -L/opt/local/lib -ltiledb
 -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
 -Wl,CoreFoundation
 installing to /opt/local/var/macports/build
 /_opt_bblocal_var_buildworker_ports_build_ports_R_R-
 tiledb/R-tiledb/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library
 /00LOCK-tiledb/00new/tiledb/libs
 ** R
 ** inst
 ** byte-compile and prepare package for lazy loading
 ** help
 *** installing help indices
 ** building package indices
 ** installing vignettes
 ** testing if installed package can be loaded from temporary location
 sh: line 1:  4733 Illegal instruction: 4  R_TESTS=
 '/opt/local/Library/Frameworks/R.framework/Resources/bin/R' --no-save
 --no-restore --no-echo 2>&1 < '/opt/local/var/macports/build
 /_opt_bblocal_var_buildworker_ports_build_ports_R_R-
 tiledb/R-tiledb/work/.tmp/RtmpzRMoeB/fileefe9731c18'

  *** caught illegal operation ***
 address 0x10723c8de, cause 'illegal opcode'

 Traceback:
  1: dyn.load(file, DLLpath = DLLpath, ...)
  2: library.dynam(lib, package, package.lib)
  3: loadNamespace(package, lib.loc)
  4: doTryCatch(return(expr), name, parentenv, handler)
  5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <-
 loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos,
 deps, exclude, include.only)}, error = function(e) {    P <- if
 (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])
 else ""    msg <- gettextf("package or namespace load failed for %s%s:\n
 %s",         sQuote(package), P, conditionMessage(e))    if
 (logical.return && !quietly)         message(paste("Error:", msg), domain
 = NA)    else stop(msg, call. = FALSE, domain = NA)})
  8: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return
 = TRUE)
  9: withCallingHandlers(expr, packageStartupMessage = function(c)
 tryInvokeRestart("muffleMessage"))
 10: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
 character.only = TRUE, logical.return = TRUE))
 11: doTryCatch(return(expr), name, parentenv, handler)
 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13: tryCatchList(expr, classes, parentenv, handlers)
 14: 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, nlines = 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))})
 15: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
 character.only = TRUE, logical.return = TRUE)))
 16: tools:::.test_load_package("tiledb", "/opt/local/var/macports/build
 /_opt_bblocal_var_buildworker_ports_build_ports_R_R-
 tiledb/R-tiledb/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library
 /00LOCK-tiledb/00new")
 An irrecoverable exception occurred. R is aborting now ...
 ERROR: loading failed
 * removing ‘/opt/local/var/macports/build
 /_opt_bblocal_var_buildworker_ports_build_ports_R_R-
 tiledb/R-tiledb/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/tiledb’
 Command failed:  cd "/opt/local/var/macports/build
 /_opt_bblocal_var_buildworker_ports_build_ports_R_R-
 tiledb/R-tiledb/work/tiledb" && /opt/local/bin/R CMD INSTALL .
 --library=/opt/local/var/macports/build
 /_opt_bblocal_var_buildworker_ports_build_ports_R_R-
 tiledb/R-tiledb/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library
 Exit code: 1
 }}}

-- 
Ticket URL: <https://trac.macports.org/ticket/68162>
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