在Mac OS X Mavericks（10.9.2）上加载R 3.1.0下的软件包时，我遇到了data.table软件包1.9.2的问题。一旦我想加载预编译的包，R就会崩溃。编译也崩溃了。
这是我做库（data.table）的输出：
*** 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, c(which.lib.loc, 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({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) env <- attachNamespace(ns, pos = pos, deps)})
17: library(data.table)
以下是我使用install.packages进行自我编译的输出（＆＃34; data.table＆＃34;，type =＆＃34; source＆＃34;）：
> install.packages("data.table", type = "source")
Installing package into ‘/Users/sascha/Library/R/3.1/library’
(as ‘lib’ is unspecified)
versuche URL 'http://cran.rstudio.com/src/contrib/data.table_1.9.2.tar.gz'
Content type 'application/x-gzip' length 1021871 bytes (997 Kb)
URL geöffnet
==================================================
downloaded 997 Kb
Loading packages…
Welcome to R at 12:45:18
* installing *source* package ‘data.table’ ...
** Paket ‘data.table’ erfolgreich entpackt und MD5 Summen überprüft
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c assign.c -o assign.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bmerge.c -o bmerge.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c chmatch.c -o chmatch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c dogroups.c -o dogroups.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fastmean.c -o fastmean.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fastradixdouble.c -o fastradixdouble.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fastradixint.c -o fastradixint.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fcast.c -o fcast.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fmelt.c -o fmelt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c forder.c -o forder.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fread.c -o fread.o
fread.c:602:95: warning: while loop has empty body [-Wempty-body]
if (ch<eof && *ch=='\"') {while(++ch<eof && *ch!=eol && !(*ch=='\"' && *(ch-1)!='\\')); if (ch<eof && *ch++!='\"') {sprintf(errormsg, "Format error on line %d: '%.*s'", nline, (int)(ch-pos+1), pos);EXIT();} }
^
fread.c:602:95: note: put the semicolon on a separate line to silence this warning
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c gsumm.c -o gsumm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c rbindlist.c -o rbindlist.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c reorder.c -o reorder.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c uniqlist.c -o uniqlist.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c vecseq.c -o vecseq.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c wrappers.c -o wrappers.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o data.table.so assign.o bmerge.o chmatch.o dogroups.o fastmean.o fastradixdouble.o fastradixint.o fcast.o fmelt.o forder.o fread.o gsumm.o init.o rbindlist.o reorder.o uniqlist.o vecseq.o wrappers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mv data.table.so datatable.so
installing to /Users/sascha/Library/R/3.1/library/data.table/libs
** R
** 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()
aborting ...
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 577 Done echo 'tools:::.install_packages()'
578 Segmentation fault: 11 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
Warning in install.packages :
installation of package ‘data.table’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/df/4k_zm03d1jl4dfmy51py_qxc0000gn/T/Rtmp3Kk7aK/downloaded_packages’
有什么想法吗？！？
答案 0 :(得分：1)
我刚刚经历了一次痛苦的类似经历，得知data.table依赖于OpenMP，但data.table设置的默认线程数似乎是其可用的最大数量。在运行之前将环境变量OMP_NUM_THREADS设置为1时，我的问题已解决。在运行R和我的R作业之前，请先在csh脚本中使用EG
setenv OMP_NUM_THREADS 1