致命错误:auc_.cpp:2:10:致命错误:omp.h:没有这样的文件或目录 [英] Fatal error: auc_.cpp:2:10: fatal error: omp.h: No such file or directory

问题描述

我正在AWS的Linux机器上运行RServer Studio.

I'm running RServer Studio on a Linux box on AWS.

我尝试安装ModelMetrics(caret的依赖项)，并收到此错误:

I tried to install ModelMetrics, a dependency for caret, and received this error:

auc_.cpp:2:10: fatal error: omp.h: No such file or directory
 #include <omp.h>
          ^~~~~~~
compilation terminated.
make: *** [auc_.o] Error 1
ERROR: compilation failed for package ‘ModelMetrics’

这是完整的输出消息

Installing package into ‘/home/User/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/ModelMetrics_1.2.2.tar.gz'
Content type 'application/x-gzip' length 16974 bytes (16 KB)
==================================================
downloaded 16 KB

* installing *source* package ‘ModelMetrics’ ...
** package ‘ModelMetrics’ successfully unpacked and MD5 sums checked
** libs
g++  -I"/opt/R/3.5.3/lib64/R/include" -DNDEBUG  -I"/home/User/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++  -I"/opt/R/3.5.3/lib64/R/include" -DNDEBUG  -I"/home/User/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c auc_.cpp -o auc_.o
auc_.cpp:2:10: fatal error: omp.h: No such file or directory
 #include <omp.h>
          ^~~~~~~
compilation terminated.
make: *** [auc_.o] Error 1
ERROR: compilation failed for package ‘ModelMetrics’
* removing ‘/home/User/R/x86_64-pc-linux-gnu-library/3.5/ModelMetrics’
Warning in install.packages :
  installation of package ‘ModelMetrics’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmpr06k8i/downloaded_packages’

我环顾四周，看起来编译器有错误.我尝试在此处列出的解决方案，特别是我运行了这些命令

I looked around SO and it looks like there is an error with the compiler. I tried the solutions listed here, specifically I ran these commands

yum groupinstall 'Development Tools'
mkdir ~/.R
echo "CC=gcc64" >> ~/.R/Makevars
sudo sed -i 's/CC = gcc -m64/CC = gcc64 -m64/g' /usr/lib64/R/etc/Makeconf

即使重新启动RStudio服务器之后，我也会得到相同的输出和错误消息.

Even after restarting RStudio Server, I get the same output and error message.

此错误看起来与这里的问题.遵循这些说明后，我仍然没有解决方案，但是我确实找到了omp.h文件的位置.

It looks like this error is very similar to the problem here. I still don't have a solution after following those instructions, but I did find the location of my omp.h file.

/usr/lib/gcc/x86_64-amazon-linux/4.4.6/include/omp.h
/usr/lib/gcc/x86_64-amazon-linux/4.8.5/include/omp.h
/usr/lib/gcc/x86_64-amazon-linux/6.4.1/include/omp.h

我安装了Developer Tools并使用这些命令更新了Makeconf文件.

I installed Developer Tools and updated the Makeconf file using these commands.

sudo sed -i 's/CC = gcc -m64/CC = gcc64 -m64/g' /usr/lib64/R/etc/Makeconf
sudo yum groupinstall 'Development Tools'

然后，我将这些行添加到Makevars配置文件中.

Then, I added these lines to the Makevars config file.

mkdir ~/.R
vi ~/.R/Makevars

CC=gcc
VER=64
CC=gcc$(VER)
CXX=g++$(VER)
CXX11=g++$(VER)
CXX14=g++$(VER)

我重新启动了RStudio服务器，并尝试安装ModelMetrics并收到此错误，与以前相同.

I restarted the RStudio Server and tried to install ModelMetrics and received this error, the same as before.

Installing package into ‘/home/User/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/ModelMetrics_1.2.2.tar.gz'
Content type 'application/x-gzip' length 16974 bytes (16 KB)
==================================================
downloaded 16 KB

* installing *source* package ‘ModelMetrics’ ...
** package ‘ModelMetrics’ successfully unpacked and MD5 sums checked
** libs
g++  -I"/opt/R/3.5.3/lib64/R/include" -DNDEBUG  -I"/home/User/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++  -I"/opt/R/3.5.3/lib64/R/include" -DNDEBUG  -I"/home/User/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -c auc_.cpp -o auc_.o
auc_.cpp:2:10: fatal error: omp.h: No such file or directory
 #include <omp.h>
          ^~~~~~~
compilation terminated.
make: *** [auc_.o] Error 1
ERROR: compilation failed for package ‘ModelMetrics’
* removing ‘/home/User/R/x86_64-pc-linux-gnu-library/3.5/ModelMetrics’
Warning in install.packages :
  installation of package ‘ModelMetrics’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpTSUlz4/downloaded_packages’

推荐答案

事实证明，Linux机器上的gcc版本存在问题.

It turns out that there was something wrong with the version of gcc on the linux box.

按照此处的说明，我可以通过这两行代码.

Per the instructions here, I was able to fix the problem with these two lines of code.

sudo yum remove gcc72-c++.x86_64 libgcc72.x86_64
sudo yum groupinstall 'Development Tools'

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