R:无法更新包clang找不到头文件 [英] R: can't update packages clang can't find head files
问题描述
我有几个R软件包无法从源代码更新/完成.以下是错误消息的摘要;
I have several R packages failed to be updated/complied from the source. Followings are snippets of error messages;
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.2_2/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppArmadillo/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include/RcppCommon.h:29:
In file included from /Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include/Rcpp/r/headers.h:59:
In file included from /Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include/Rcpp/platform/compiler.h:100:
In file included from /usr/local/Cellar/llvm/7.0.1/include/c++/v1/cmath:305:
/usr/local/Cellar/llvm/7.0.1/include/c++/v1/math.h:301:15: **fatal error: 'math.h' file not found**
另一个;
> ** libs clang -I"/usr/local/Cellar/r/3.5.2_2/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Matrix/include"
> -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -fPIC -g -O2 -c irlb.c -o irlb.o irlb.c:19:10: fatal error: 'stdlib.h' file not found
> #include <stdlib.h>
错误消息指向几个缺少的标题,但它们都在我的
Error messages point to several missing headers but they are all there in my
/usr/local/Cellar/llvm/7.0.1/include/c ++/v1
/usr/local/Cellar/llvm/7.0.1/include/c++/v1
对于解决此问题的任何帮助,我们将不胜感激.
I'd appreciate any help solving this issue.
sw_vers
ProductName: Mac OS X
ProductVersion: 10.14.3
BuildVersion: 18D4
clang -v
clang version 7.0.1 (tags/RELEASE_701/final)
Target: x86_64-apple-darwin18.2.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin
gcc --version
gcc (Homebrew GCC 8.2.0) 8.2.0
setting value
version R version 3.5.2 (2018-12-20)
os macOS Mojave 10.14.3
system x86_64, darwin17.7.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2019-02-06
推荐答案
更新;
我只记得在其他Mac上安装OSX Mojave时遇到了完全相同的问题.事实证明,即使您安装命令工具,也没有/usr/include,特别是对于 Xcode-select install
的最新版本.
I just remembered that I had the exact same issue when I installed OSX Mojave in my other Mac. It turns out that /usr/include is absent even when you install command tools, particularly for the latest version by Xcode-select install
.
我安装的Xcode是
pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 10.1.0.0.1.1539992718
volume: /
location: /
install-time: 1549499389
groups: com.apple.FindSystemFiles.pkg-group
此CLT pkg将安装/include
This CLT pkg will install /include in
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
/Library/Developer/CommandLineTools/usr/include
因此,您所需要做的就是将其中一个包含文件夹复制或链接到/usr,但要执行此操作,必须通过在恢复模式下激发crstutil来禁用系统完整性保护.
So all you have to do is either copy or link one of these include folders to /usr but in order to do this, you have to take disable System Integrity Protection by provoking crstutil in the recovery mode.
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