Error: running command '"D:/program files/R-3.3.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD config CC' had status 2

Question

[Francis]

Hi,everyone. I want to install a package from githup on windows.

library(devtools) 
install_github("satijalab/seurat")

I chose no because Rtools has installed.

Then there is a error:

Error: running command '"D:/program files/R-3.3.3/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD config CC' had status 2

I check the Rtools:

> system('g++ -v')
Using built-in specs.
COLLECT_GCC=D:\program files\Rtools\mingw_32\bin\g++.exe
COLLECT_LTO_WRAPPER=D:/program\ files/Rtools/mingw_32/bin/../libexec/gcc/i686-w64-mingw32/4.9.3/lto-wrapper.exe
Target: i686-w64-mingw32
Configured with: ../../../src/gcc-4.9.3/configure --host=i686-w64-mingw32 --build=i686-w64-mingw32 --target=i686-w64-mingw32 --prefix=/mingw32 --with-sysroot=/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32 --with-gxx-include-dir=/mingw32/i686-w64-mingw32/include/c++ --enable-static --disable-shared --disable-multilib --enable-languages=c,c++,fortran,lto --enable-libstdcxx-time=yes --enable-threads=posix --enable-libgomp --enable-libatomic --enable-lto --enable-graphite --enable-checking=release --enable-fully-dynamic-string --enable-version-specific-runtime-libs --disable-sjlj-exceptions --with-dwarf2 --disable-isl-version-check --disable-cloog-version-check --disable-libstdcxx-pch --disable-libstdcxx-debug --enable-bootstrap --disable-rpath --disable-win32-registry --disable-nls --disable-werror --disable-symvers --with-gnu-as --with-gnu-ld --with-arch=i686 --with-tune=generic --with-libiconv --with-system-zlib --with-gmp=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i6... <truncated>
Thread model: posix
gcc version 4.9.3 (i686-posix-dwarf, Built by MinGW-W64 project) 
> system('where make')
D:\program files\Rtools\bin\make.exe

Rtools is installed successfully.

So i don`t know how to resolve this error? Any ideas will be helpful.

Thank you.

[h.mon]

Have you seen this?

[Francis]

Thank you. The problem is same as my error. But i still fail to install. It does not because the packages. And, the step 1 "install Rtools", where is the Rtools to install? My install locations：

R: D:\program files\R-3.3.3\bin\x64
Rstudio: D:\program files\RStudio\bin
Rtools: D:\program files\Rtools\bin

Do R and Rtools install the same folder? I do not get the step 1. Many thanks.

Answer 1

[Francis]

I install successfully! I uninstall the R, Rtools and reinstall. I changed the installed site from D to C (default). And the guild is correct and i installed many other packages. However, i installed the seurat successfully!!

Thanks!