Error installing: libclidar/libLasProcess.c:1:10 on MacOS
Closed this issue · 4 comments
I am trying to install the package on MacOS 10.15.6 (19G73) but I am getting the following error message:
libclidar/libLasProcess.c:1:10: fatal error: 'stdio.h' file not found
#include "stdio.h"
^~~~~~~~~
1 error generated.
make: *** [libclidar/libLasProcess.o] Error 1
ERROR: compilation failed for package ‘rGEDI’
Thank you for your help!
Try to install llvm in your terminal:
brew install llvm
Hi, many thanks for your response.
I reinstalled llvm (it was already installed and update) and tried to install the packages again using "devtools::install_git("https://github.com/carlos-alberto-silva/rGEDI", dependencies = TRUE)", but I have the same error. The complete message is the following:
** libs
"/Library/Frameworks/R.framework/Resources/bin/Rscript" ../tools/deps.R
/usr/local/clang4/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/opt/szip/include -I/usr/local/Cellar/hdf5/1.12.0_1/include -I/usr/local/Cellar/gsl/2.6/include -DDLLEXPORT -D__STDC_FORMAT_MACROS -DUSEPHOTON -DWITHOUT_GDAL -Igedisimulator -Itools -Icmpfit-1.2 -Ilibclidar -I. -fPIC -Wall -g -O2 -c libclidar/libLasProcess.c -o libclidar/libLasProcess.o
libclidar/libLasProcess.c:1:10: fatal error: 'stdio.h' file not found
#include "stdio.h"
^~~~~~~~~
1 error generated.
make: *** [libclidar/libLasProcess.o] Error 1
ERROR: compilation failed for package ‘rGEDI’
- removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rGEDI’
Error: Failed to install 'unknown package' from Git:
(converted from warning) installation of package ‘/var/folders/8v/dn_5ptr10zg9tt5hq8bqcbkh0000gn/T//RtmpSS9hWv/file3a66d23c7ce/rGEDI_0.1.8.tar.gz’ had non-zero exit status
Thank you for your help!
Maybe you need to install xcode SDK for MacOS. I don't know exactly how to do that on MacOS, but take a look at this answer from StackOverflow: https://stackoverflow.com/a/52530212/2548351
Great! It's working now. Xcode was installed but with the upgrade to OSX Catalina, the folder /usr/include was removed. So I did the following:
-
xcode-select --install
-
sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/
-
export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
Many thanks!