Hi,
I'm quite new to bioinformatics and I'm on an M2 Max Apple Silicon Sonoma.
I tried to run the code, but it seems I keep getting en error for the htslib
git clone https://github.com/GWW/scsnv.git
cd scsnv
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
fatal: destination path 'scsnv' already exists and is not an empty directory.
mkdir: build: File exists
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.
HDF5 LIBRARY: hdf5-shared;hdf5_cpp-shared
HDF5 LIBRARY CXX: hdf5_cpp-shared
HDF5 INCLUDE: /opt/homebrew/include
BUILD TYPE: Release
INSTALL PREFIX: /usr/local
-- Configuring done (0.1s)
-- Generating done (0.0s)
-- Build files have been written to: /Users/sai/scsnv/build
[ 1%] Performing configure step for 'htslib'
checking for gcc... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
checking whether the C compiler works... no
configure: error: in '/Users/sai/scsnv/external/htslib':
configure: error: C compiler cannot create executables
See 'config.log' for more details
make[2]: [htslib-prefix/src/htslib-stamp/htslib-configure] Error 77
make[1]: [CMakeFiles/htslib.dir/all] Error 2
make: *** [all] Error 2
sai@Sais-MacBook-Pro build %
I seem to be able to run codes like cc test.c -o test, which indicates my compiler installation was ok.
Hi, I'm quite new to bioinformatics and I'm on an M2 Max Apple Silicon Sonoma. I tried to run the code, but it seems I keep getting en error for the htslib
git clone https://github.com/GWW/scsnv.git cd scsnv mkdir build cd build cmake -DCMAKE_BUILD_TYPE=Release .. make fatal: destination path 'scsnv' already exists and is not an empty directory. mkdir: build: File exists CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.
Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.
HDF5 LIBRARY: hdf5-shared;hdf5_cpp-shared HDF5 LIBRARY CXX: hdf5_cpp-shared HDF5 INCLUDE: /opt/homebrew/include BUILD TYPE: Release INSTALL PREFIX: /usr/local -- Configuring done (0.1s) -- Generating done (0.0s) -- Build files have been written to: /Users/sai/scsnv/build [ 1%] Performing configure step for 'htslib' checking for gcc... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc checking whether the C compiler works... no configure: error: in '/Users/sai/scsnv/external/htslib': configure: error: C compiler cannot create executables See 'config.log' for more details make[2]: [htslib-prefix/src/htslib-stamp/htslib-configure] Error 77 make[1]: [CMakeFiles/htslib.dir/all] Error 2 make: *** [all] Error 2 sai@Sais-MacBook-Pro build %
I seem to be able to run codes like cc test.c -o test, which indicates my compiler installation was ok.
Thanks,