##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc-gpu/R/bin/R CMD INSTALL RbowtieCuda
###
##############################################################################
##############################################################################


* installing to library ‘/home/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=/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/biocbuild/bbs-3.21-bioc/R/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/local/cuda/bin/nvcc


-- The CXX compiler identification is GNU 13.3.0
-- The CUDA compiler identification is NVIDIA 12.9.41
-- 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/local/cuda/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: '12.9'

  Driver supports up to CUDA: '12.9'

  Compiler '12.9' is compatible with driver



  Detected GCC version: '13.3'

  Max recommended GCC for CUDA '12.9' is '14.9'

  GCC '13.3' is compatible



  nvcc path: /usr/local/cuda/bin/nvcc

  nvidia-smi path: /usr/bin/nvidia-smi



  Mon Sep 1 14:46:23 2025


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


  | NVIDIA-SMI 575.51.03 Driver Version: 575.51.03 CUDA Version: 12.9 |


  |-----------------------------------------+------------------------+----------------------+


  | 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 NVIDIA L40S Off | 00000000:B5:00.0 Off | 0 |

  | N/A 30C P0 33W / 350W | 0MiB / 46068MiB | 0% Default |

  | | | N/A |


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


                                                                                           

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


  | 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: 89


-- Found CUDAToolkit: /usr/local/cuda/targets/x86_64-linux/include (found version "12.9.41") 
-- 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/local/cuda/bin/nvcc

  Build type: Release

  GPU Architectures: 8.9

  Detected NVCC Compiler.  NVCC Flags:
  -gencode;arch=compute_89,code=compute_89;-gencode;arch=compute_89,code=sm_89


  ================================================


-- Configuring done (3.6s)
-- Generating done (0.0s)
-- Build files have been written to: /home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build
(cd "../src/nvbio/build" && make)
make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
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make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
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cd "../src/nvbio/build" && cp nvBWT/nvBWT ../../../inst
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** 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)