##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD build --keep-empty-dirs --no-resave-data RbowtieCuda
###
##############################################################################
##############################################################################


* checking for file ‘RbowtieCuda/DESCRIPTION’ ... OK
* preparing ‘RbowtieCuda’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
      -----------------------------------
* installing *source* package ‘RbowtieCuda’ ...
** this is package ‘RbowtieCuda’ version ‘1.4.2’
** 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:38 (message):
  CUDACXX not set.  Searching for 'nvcc' or 'nvc++'...


CMake Warning at CMakeLists.txt:53 (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
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-- Detecting CUDA compiler ABI info
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-- Check for working CUDA compiler: /usr/bin/nvcc - skipped
-- Detecting CUDA compile features
-- Detecting CUDA compile features - done
CMake Warning at CMakeLists.txt:70 (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



  Fri May 8 10:50:53 2026


  +---------------------------------------------------------------------------------------+


  | 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:92 (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
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-- Looking for sys/types.h
-- Looking for sys/types.h - found
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-- Check size of off64_t
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-- 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:332 (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 (4.1s)
-- Generating done (0.0s)
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(cd "../src/nvbio/build" && make)
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[ 77%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/work_queue_test.cu.o
[ 78%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/sequence_test.cu.o
[ 79%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/wavelet_test.cu.o
[ 79%] 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
[ 80%] Linking CXX executable nvbio-test
make[3]: Leaving directory '/tmp/Rtmpul9FpX/Rbuild63d839fb14b6/RbowtieCuda/src/nvbio/build'
[ 80%] Built target nvbio-test
[ 80%] 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 searching for -ldl
[ 81%] Linking CXX executable nvBWT
make[3]: Leaving directory '/tmp/Rtmpul9FpX/Rbuild63d839fb14b6/RbowtieCuda/src/nvbio/build'
[ 81%] Built target nvBWT
make[2]: Leaving directory '/tmp/Rtmpul9FpX/Rbuild63d839fb14b6/RbowtieCuda/src/nvbio/build'
make[1]: *** [Makefile:136: all] Error 2
make[1]: Leaving directory '/tmp/Rtmpul9FpX/Rbuild63d839fb14b6/RbowtieCuda/src/nvbio/build'
make: *** [Makefile:12: all] Error 2
ERROR: compilation failed for package ‘RbowtieCuda’
* removing ‘/tmp/Rtmpul9FpX/Rinst63d8552ffb1b/RbowtieCuda’
      -----------------------------------
ERROR: package installation failed