[R-SIG-Mac] R crashes after installing certain packages
Rainer M Krug
Rainer at krugs.de
Mon Nov 14 09:26:12 CET 2016
"Charabuddi, Chaitanya Krishna Reddy" <cxc155530 at utdallas.edu> writes:
> Hello,
>
> I’m running R (3.3.1) with R-Studio (0.99.903) and Xquatrz (2.7.11) on my Macbook Pro with macOS Sierra (10.12.1).
>
> I’m facing a weird problem, after installing basic packages such as –
> car, plyr, etc. They get installed just fine when I use
> install.packages() command but the problem comes when I’m calling the
> package using library() command. As soon as I run this command (ex:
> library(car)), R crashes and I have to restart R again. I tried
> installing and re-installing all the applications (R, R-studio and
> X-Quartz) but can’t get around the problem.
>
> Can you please help me?
1) You are asking about R-studio which is different GUI - so if you want
to get this solved, w=you have to ask on their mailing list.
Now to your problem:
R-GUI: R for 3.2.4 GUI 1.67 Mavericks build (7152)
In R console: I can load the package car
In RStudio : I can load the package car
in R-GUI : R crashes with the following info:
,----
| > sessionInfo()
| R version 3.3.2 (2016-10-31)
| Platform: x86_64-apple-darwin16.1.0 (64-bit)
| Running under: macOS Sierra 10.12.1
|
| locale:
| [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
| > library(car)
|
| *** caught segfault ***
| address 0x18, cause 'memory not mapped'
|
| Traceback:
| 1: dyn.load(file, DLLpath = DLLpath, ...)
| 2: library.dynam(lib, package, package.lib)
| 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
| 4: asNamespace(ns)
| 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
| 6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
| 7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
| 8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
| 9: asNamespace(ns)
| 10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
| 11: loadNamespace(package, lib.loc)
| 12: doTryCatch(return(expr), name, parentenv, handler)
| 13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
| 14: tryCatchList(expr, classes, parentenv, handlers)
| 15: 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 msg <- conditionMessage(e) sm <- strsplit(msg, "\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 && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
| 16: try({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)})
| 17: library(car)
|
| Possible actions:
| 1: abort (with core dump, if enabled)
| 2: normal R exit
| 3: exit R without saving workspace
| 4: exit R saving workspace
| Selection:
`----
Trying to re-install car in R-GUI gives the following error:
,----
| > install.packages("car")
| Installing package into ‘/Users/rainerkrug/Library/R/3.3/library’
| (as ‘lib’ is unspecified)
| trying URL 'http://cran.univ-paris1.fr/src/contrib/car_2.1-3.tar.gz'
| Content type 'application/x-gzip' length 622922 bytes (608 KB)
| ==================================================
| downloaded 608 KB
|
| * installing *source* package ‘car’ ...
| ** package ‘car’ successfully unpacked and MD5 sums checked
| ** R
| ** data
| *** moving datasets to lazyload DB
| ** inst
| ** byte-compile and prepare package for lazy loading
|
| *** caught segfault ***
| address 0x18, cause 'memory not mapped'
|
| Traceback:
| 1: dyn.load(file, DLLpath = DLLpath, ...)
| 2: library.dynam(lib, package, package.lib)
| 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
| 4: asNamespace(ns)
| 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
| 6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
| 7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
| 8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
| 9: asNamespace(ns)
| 10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
| 11: loadNamespace(package, lib.loc, keep.source, partial = TRUE)
| 12: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
| 13: suppressPackageStartupMessages(loadNamespace(package, lib.loc, keep.source, partial = TRUE))
| 14: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source, compress = compress)
| 15: makeLazyLoading(pkg_name, lib, keep.source = keep.source)
| 16: doTryCatch(return(expr), name, parentenv, handler)
| 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
| 18: tryCatchList(expr, classes, parentenv, handlers)
| 19: 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 msg <- conditionMessage(e) sm <- strsplit(msg, "\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 && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
| 20: try({ suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE)) makeLazyLoading(pkg_name, lib, keep.source = keep.source)})
| 21: do_install_source(pkg_name, instdir, pkg, desc)
| 22: do_install(pkg)
| 23: tools:::.install_packages()
| The downloaded source packages are in
| ‘/private/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/RtmpK6Dn5L/downloaded_packages’
|
| An irrecoverable exception occurred. R is aborting now ...
| Warning message:
| In install.packages("car") :
| installation of package ‘car’ had non-zero exit status
| /usr/local/Cellar/r/3.3.2/R.framework/Resources/bin/INSTALL: line 34: 64396 Done echo 'tools:::.install_packages()'
| 64397 Segmentation fault: 11 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
| >
`----
So something is not proper here.
In general: trying to load a package which is not present results in a
segfault:
,----
| > library(fff)
| Error in library(fff) : there is no package called ‘fff’
|
| *** caught segfault ***
| address 0x18, cause 'memory not mapped'
|
| Possible actions:
| 1: abort (with core dump, if enabled)
| 2: normal R exit
| 3: exit R without saving workspace
| 4: exit R saving workspace
| Selection:
`----
R, R-GUI, and RStudio are all installed using homebrew.
I can do further tests if needed.
Cheers,
Rainer
>
> Note: I’m not very technically sound in these issues and a solution
> explained in a layman language will be much appreciated.
>
> Thanks,
> Chaitanya
> Graduate student
> MS in Business Analytics
> University of Texas at Dallas
>
> [[alternative HTML version deleted]]
>
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--
Rainer M. Krug
email: Rainer<at>krugs<dot>de
PGP: 0x0F52F982
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