Franck RICHARD
| Snapshot Date: 2025-09-29 04:00 -0400 (Mon, 29 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/RbowtieCuda |
| git_branch: RELEASE_3_21 |
| git_last_commit: 1ae5b73 |
| git_last_commit_date: 2025-09-12 06:31:23 -0400 (Fri, 12 Sep 2025) |
| Back to --- experimental! --- GPU-enabled build/check report for BioC 3.21 Report updated every 6 hours |
This page was generated on 2025-09-29 07:45 -0400 (Mon, 29 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| biocgpu | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 196 |
| kakapo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 192 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1/1 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| RbowtieCuda 1.0.9 (landing page) Franck RICHARD
| biocgpu | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | |||||||
| kakapo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
|
To the developers/maintainers of the RbowtieCuda package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: RbowtieCuda |
| Version: 1.0.9 |
| Command: /home/biocbuild/bbs-3.21-bioc-gpu/R/bin/R CMD INSTALL RbowtieCuda |
| StartedAt: 2025-09-29 08:46:21 -0000 (Mon, 29 Sep 2025) |
| EndedAt: 2025-09-29 08:48:06 -0000 (Mon, 29 Sep 2025) |
| EllapsedTime: 104.6 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### 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 ‘1.0.9’
** 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 29 08:46:23 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 32C P0 37W / 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 (3.7s)
-- 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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** 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)