Hello all, I am running the R 4.4 on an M2 mac chip. Since updating R to 4.4 I
have not been able to install the R units package, which is needed to install
the sf package. I am hoping someone here can point out something silly I have
done to help here. Thanks in advance.
To resolve the issue I have tried:
* install.packages(�units�)
* install.packages("units", configure.args =
c("--with-udunits2-include=/opt/homebrew/Cellar/udunits/2.2.28/include",
"--with-udunits2-lib=/opt/homebrew/Cellar/udunits/2.2.28/lib"))
* reinstalling udunits
* reinstalling r
* running with my normal as well as with a blank MAKEVARS file.
The same error results each time and is copied below:
Installing package into �/opt/homebrew/lib/R/4.4/site-library�
(as �lib� is unspecified)
* installing *source* package �units� ...
** using staged installation
configure: units: 0.8-5
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether /opt/homebrew/bin/ccache /opt/homebrew/opt/llvm/bin/clang++
accepts -g... yes
checking for /opt/homebrew/bin/ccache /opt/homebrew/opt/llvm/bin/clang++ option
to enable C++11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for _Bool... no
checking for stdbool.h that conforms to C99... yes
checking for error_at_line... no
checking for gcc... /opt/homebrew/bin/ccache /opt/homebrew/opt/llvm/bin/clang
checking whether the compiler supports GNU C... yes
checking whether /opt/homebrew/bin/ccache /opt/homebrew/opt/llvm/bin/clang
accepts -g... yes
checking for /opt/homebrew/bin/ccache /opt/homebrew/opt/llvm/bin/clang option
to enable C11 features... none needed
checking for XML_ParserCreate in -lexpat... yes
checking for udunits2.h... yes
checking for ut_read_xml in -ludunits2... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: �Homebrew clang version 18.1.6�
using SDK: �MacOSX14.4.sdk�
/opt/homebrew/bin/ccache /opt/homebrew/opt/llvm/bin/clang++
-I"/opt/homebrew/Cellar/r/4.4.0_1/lib/R/include" -DNDEBUG -DUDUNITS2_DIR=0
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/opt/homebrew/include -I/opt/homebrew/opt/llvm/include
-I/opt/homebrew/opt/openssl/include -I/opt/homebrew/opt/gettext/include
-I/opt/homebrew/opt/tcl-tk/include
-I'/opt/homebrew/lib/R/4.4/site-library/Rcpp/include' -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/opt/homebrew/include
-I/opt/homebrew/opt/llvm/include -I/opt/homebrew/opt/openssl/include
-I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/tcl-tk/include -fPIC
-g -O3 -Wall -pedantic -mtune=native -pipe -c RcppExports.cpp -o RcppExports.o
/opt/homebrew/bin/ccache /opt/homebrew/opt/llvm/bin/clang++
-I"/opt/homebrew/Cellar/r/4.4.0_1/lib/R/include" -DNDEBUG -DUDUNITS2_DIR=0
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/opt/homebrew/include -I/opt/homebrew/opt/llvm/include
-I/opt/homebrew/opt/openssl/include -I/opt/homebrew/opt/gettext/include
-I/opt/homebrew/opt/tcl-tk/include
-I'/opt/homebrew/lib/R/4.4/site-library/Rcpp/include' -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/opt/homebrew/include
-I/opt/homebrew/opt/llvm/include -I/opt/homebrew/opt/openssl/include
-I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/tcl-tk/include -fPIC
-g -O3 -Wall -pedantic -mtune=native -pipe -c udunits.cpp -o udunits.o
/opt/homebrew/bin/ccache /opt/homebrew/opt/llvm/bin/clang++ -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup
-L/opt/homebrew/Cellar/r/4.4.0_1/lib/R/lib -L/opt/homebrew/opt/gettext/lib
-L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/xz/lib -L/opt/homebrew/lib
-L/opt/homebrew/opt/llvm/lib -Wl,-rpath,/opt/homebrew/opt/llvm/lib -o units.so
RcppExports.o udunits.o -lexpat -lexpat -ludunits2
-L/opt/homebrew/Cellar/r/4.4.0_1/lib/R/lib -lR -lintl -Wl,-framework
-Wl,CoreFoundation
ld: warning: ignoring duplicate libraries: '-lexpat'
ld: warning: reexported library with install name
'/opt/homebrew/opt/llvm/lib/libunwind.1.dylib' found at
'/opt/homebrew/Cellar/llvm/18.1.6/lib/libunwind.1.0.dylib' couldn't be matched
with any parent library and will be linked directly
installing to /opt/homebrew/lib/R/4.4/site-library/00LOCK-units/00new/units/libs
** R
** demo
** 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: 53460 Bus error: 10 R_TESTS=
'/opt/homebrew/Cellar/r/4.4.0_1/lib/R/bin/R' --no-save --no-restore --no-echo
2>&1 <
'/var/folders/q_/0m_xd5dd1qlcshyjbgnzrw9w0000gp/T//Rtmpu95vVt/filec9f5215fbb15'
*** caught bus error ***
address 0x0, cause 'invalid alignment'
Traceback:
1: R_ut_parse(u)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: 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))})
6: try(R_ut_parse(u), silent = TRUE)
7: ud_is_parseable("B")
8: fun(libname, pkgname)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(fun(libname, pkgname), error = identity)
13: runHook(".onLoad", env, package.lib, package)
14: loadNamespace(package, lib.loc)
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: 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)})
19: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return =
TRUE)
20: withCallingHandlers(expr, packageStartupMessage = function(c)
tryInvokeRestart("muffleMessage"))
21: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE))
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: 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))})
26: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE)))
27: tools:::.test_load_package("units",
"/opt/homebrew/lib/R/4.4/site-library/00LOCK-units/00new")
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing �/opt/homebrew/lib/R/4.4/site-library/units�
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
