"fatal error: bits/libc-header-start.h: No such file or directory"

[NathanSkene]

Got the following error message during installation. Found this issue reported for another package which seemed similar: sirfz/tesserocr#130

The solution stated in that package was to run: sudo apt-get install gcc-multilib g++-multilib

That worked for me (for this issue at least). Probably worth adding that line to the installation instructions.

setting BOOST home directory to /home/nskene/R/x86_64-pc-linux-gnu-library/3.6/BH/
checking for BOOST headers... checking for /home/nskene/R/x86_64-pc-linux-gnu-library/3.6/BH//include/boost/version.hpp... yes
setting R home directory to /usr/lib/R
checking for R... yes
setting R header files to /usr/share/R/include
configure: creating ./config.status
config.status: creating src/Makefile
** libs
** arch -
g++ -O2 -funroll-loops -fomit-frame-pointer -ffast-math -I/usr/local/cuda-10.1/include -I/home/nskene/R/x86_64-pc-linux-gnu-library/3.6/BH//include -I/usr/share/R/include -Wall -fPIC -D_GNU_SOURCE -m32 headers.hpp
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include-fixed/limits.h:194:0,
from /usr/lib/gcc/x86_64-linux-gnu/7/include-fixed/syslimits.h:7,
from /usr/lib/gcc/x86_64-linux-gnu/7/include-fixed/limits.h:34,
from /usr/local/cuda-10.1/include/driver_types.h:77,
from /usr/local/cuda-10.1/include/builtin_types.h:59,
from /usr/local/cuda-10.1/include/cuda_runtime.h:91,
from headers.hpp:42:
/usr/include/limits.h:26:10: fatal error: bits/libc-header-start.h: No such file or directory
#include <bits/libc-header-start.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
Makefile:90: recipe for target 'headers.hpp.gch' failed
make: *** [headers.hpp.gch] Error 1
ERROR: compilation failed for package ‘Rgtsvm’

• removing ‘/home/nskene/R/x86_64-pc-linux-gnu-library/3.6/Rgtsvm’

[wzhy2000]

Thank you for your feedback.

[bjw34032]

I had a similar error on my Ubuntu 20.04 system. Turns out the configure process couldn't find ${CUDA_HOME}/lib64/libcublas.so and therefore assumed a 32-bit build. I replaced the string ${CUDA_HOME}/lib64/libcublas.so with ${CUDA_HOME}/lib/x86_64-linux-gnu/libcublas.so in the configure file so it correctly assumed a 64-bit build when executing

R CMD INSTALL --configure-args="--with-cuda-home=/usr --with-boost-home=/usr" Rgtsvm

and received the following output

...
checking for CUDA headers... checking for /usr/include/cublas.h... yes
checking whether this is a 64-bit version of CUDA... checking for /usr/lib/x86_64-linux-gnu/libcublas.so... yes
...
* DONE (Rgtsvm)