"Charabuddi, Chaitanya Krishna Reddy" <cxc155...@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]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug email: Rainer<at>krugs<dot>de PGP: 0x0F52F982
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