每当我尝试使用ggplot2的函数geom_smooth（）时，我都会遇到段错误。我发现问题是由于mcgv软件包，这是一个R推荐的软件包，只要包含它就会出现段错误。以下是其安装的输出：
> install.packages('mgcv')
Installing package into ‘/home/<username>/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/mgcv_1.8-17.tar.gz'
Content type 'unknown' length 849787 bytes (829 KB)
==================================================
downloaded 829 KB
* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c coxph.c -o coxph.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c discrete.c -o discrete.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c gdi.c -o gdi.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c init.c -o init.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c magic.c -o magic.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c mat.c -o mat.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c matrix.c -o matrix.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c mgcv.c -o mgcv.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c misc.c -o misc.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c mvn.c -o mvn.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c qp.c -o qp.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c soap.c -o soap.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c sparse-smooth.c -o sparse-smooth.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c tprs.c -o tprs.o
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib64/R/lib -lR
installing to /home/<username>/R/x86_64-pc-linux-gnu-library/3.4/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in fun(libname, pkgname) :
bytecode version mismatch; using eval
Warning: package ‘nlme’ was built under R version 3.4.0
*** caught segfault ***
address 0x6, cause 'memory not mapped'
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(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))})
8: try({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)})
9: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
10: .getRequiredPackages2(pkgInfo, quietly, lib.loc, useImports)
11: .getRequiredPackages(quietly = TRUE)
12: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
13: suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: 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))})
18: try({ suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE)) makeLazyLoading(pkg_name, lib, keep.source = keep.source)})
19: do_install_source(pkg_name, instdir, pkg, desc)
20: do_install(pkg)
21: tools:::.install_packages()
An irrecoverable exception occurred. R is aborting now ...
/usr/lib64/R/bin/INSTALL: line 34: 36723 Done echo 'tools:::.install_packages()'
36724 Segmentation fault | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
Warning in install.packages :
installation of package ‘mgcv’ had non-zero exit status
这是我的R版本：
> R.version
_
platform x86_64-redhat-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 3.3
year 2017
month 03
day 06
svn rev 72310
language R
version.string R version 3.3.3 (2017-03-06)
nickname Another Canoe
有关正在发生的事情的任何想法？
答案 0 :(得分：1)
将您的R版本升级到3.4.0。特别是，mgcv的编译成功（因为您已达到字节编译阶段）。问题在于其依赖包nlme，它需要R版本3.4.0
sudo apt-get update
sudo apt-get upgrade
我认为一旦升级R，您就不需要做任何其他事情了。 mgcv和nlme也会自动升级，因为它们是＆＃34;推荐＆＃34;。
我会试一试 - 但不幸的是我在这台机器上没有sudo，因此需要一段时间才能尝试升级它。我想知道在过渡时期是否有任何我可以尝试的解决方案。
您是否需要安装mgcv的其他版本？为什么不做library(mgcv)并使用与当前R版本兼容的版本？
请允许我重新制定The_Anomaly的最终本地解决方案：
在我正确地重新启动R studio的R会话（即手动重启，而不仅仅是从崩溃中恢复）之后，我再也无法加载我安装的任何软件包了。所以我开始看
.libPaths()，但惊奇地发现文件夹＆＃34; R / x86_64-redhat-linux-gnu-library / 3.3＆＃34;没有我的任何包裹，但是另一个文件夹＆＃34; ... / 3.4＆＃34;没有。出于某种原因，在重新启动之前，R版本3.3使用为R 3.4构建的软件包。您的解决方案可能会有效，因为它可以解决这种不匹配问题，因此我将其标记为正确 - 但对我来说，重启确实有效。