############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc-gpu/R/bin/R CMD INSTALL RbowtieCuda ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/R/site-library’ * installing *source* package ‘RbowtieCuda’ ... ** this is package ‘RbowtieCuda’ version ‘1.0.8’ ** using staged installation ** libs cd "../src/nvbio/build" && rm -f CMakeCache.txt && cmake .. CMake Warning at CMakeLists.txt:3 (message): CUDACXX= CMake Warning at CMakeLists.txt:4 (message): PATH=/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/opt/TurboVNC/bin/ CMake Warning at CMakeLists.txt:14 (message): CUDACXX not set. Searching for 'nvcc' or 'nvc++'... CMake Warning at CMakeLists.txt:29 (message): Found CUDA compiler: /usr/bin/nvcc -- The CXX compiler identification is GNU 13.3.0 -- The CUDA compiler identification is NVIDIA 12.0.140 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CUDA compiler ABI info -- Detecting CUDA compiler ABI info - done -- Check for working CUDA compiler: /usr/bin/nvcc - skipped -- Detecting CUDA compile features -- Detecting CUDA compile features - done CMake Warning at CMakeLists.txt:46 (message): --- CUDA Environment Diagnostic --- libthrust-dev is installed libcub-dev is installed cmake is installed Detected CUDA compiler version: '12.0' Driver supports up to CUDA: '12.2' Compiler '12.0' is compatible with driver Detected GCC version: '13.3' Max recommended GCC for CUDA '12.0' is '12.1' *** Incompatibility: CUDA '12.0' needs GCC ≤ '12.1', found '13.3' *** Install GCC 11 or lower On Debian/Ubuntu: sudo apt install gcc-11 g++-11 Use update-alternatives to switch versions nvcc path: /usr/bin/nvcc nvidia-smi path: /usr/bin/nvidia-smi Thu Sep 11 04:45:15 2025 +---------------------------------------------------------------------------------------+ | NVIDIA-SMI 535.247.01 Driver Version: 535.247.01 CUDA Version: 12.2 | |-----------------------------------------+----------------------+----------------------+ | GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |=========================================+======================+======================| | 0 GRID A100X-10C On | 00000000:04:00.0 Off | 0 | | N/A N/A P0 N/A / N/A | 0MiB / 10240MiB | 0% Default | | | | Disabled | +-----------------------------------------+----------------------+----------------------+ +---------------------------------------------------------------------------------------+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=======================================================================================| | No running processes found | +---------------------------------------------------------------------------------------+ CMake Warning at CMakeLists.txt:68 (message): Detected GPU architecture: 80 -- Found CUDAToolkit: /usr/include (found version "12.0.140") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found libcudacxx: /usr/share/cmake/libcudacxx/libcudacxx-config.cmake (found suitable version "1.9.0.0", minimum required is "1.8.0") -- Found Thrust: /usr/share/cmake/thrust/thrust-config.cmake (found version "2.0.1.0") -- Found CUB: /usr/share/cmake/cub/cub-config.cmake (found version "2.0.1.0") -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- The C compiler identification is GNU 13.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of off64_t -- Check size of off64_t - done -- Looking for fseeko -- Looking for fseeko - found -- Looking for unistd.h -- Looking for unistd.h - found -- Found OpenMP_CXX: -fopenmp (found version "4.5") CMake Warning at CMakeLists.txt:330 (message): ================================================ CUDA Configuration Summary Compiler: /usr/bin/nvcc Build type: Release GPU Architectures: 8.0 Detected NVCC Compiler. NVCC Flags: -gencode;arch=compute_80,code=compute_80;-gencode;arch=compute_80,code=sm_80 ================================================ -- Configuring done (4.0s) -- Generating done (0.0s) -- Build files have been written to: /media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build (cd "../src/nvbio/build" && make) make[1]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[2]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' 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nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/traceback.cu.o [ 96%] Linking CUDA device code CMakeFiles/nvbio-test.dir/cmake_device_link.o nvlink warning : Skipping incompatible '/usr/lib/x86_64-linux-gnu/librt.a' when searching for -lrt nvlink warning : Skipping incompatible '/usr/lib/x86_64-linux-gnu/libpthread.a' when searching for -lpthread nvlink warning : Skipping incompatible '/usr/lib/x86_64-linux-gnu/libdl.a' when searching for -ldl [ 97%] Linking CXX executable nvbio-test make[3]: Leaving directory '/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' [ 97%] Built target nvbio-test [ 97%] Linking CUDA device code CMakeFiles/nvBWT.dir/cmake_device_link.o nvlink warning : Skipping incompatible '/usr/lib/x86_64-linux-gnu/librt.a' when searching for -lrt nvlink warning : Skipping incompatible '/usr/lib/x86_64-linux-gnu/libpthread.a' when searching for -lpthread nvlink warning : Skipping incompatible '/usr/lib/x86_64-linux-gnu/libdl.a' when 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"../src/nvbio/build" && cp nvBWT/nvBWT ../../../inst cd "../src/nvbio/build" && cp nvBowtie/nvBowtie ../../../inst cd "../src/nvbio/build" && cp nvbio-test/nvbio-test ../../../inst ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RbowtieCuda)