| Back to --- experimental! --- GPU-enabled build/check report for BioC 3.21 Report updated every hour |
This page was generated on 2025-04-09 14:35 -0400 (Wed, 09 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| biocgpu | Linux (Ubuntu 24.04.2 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 96 |
| kakapo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | R Under development (unstable) (2025-02-26 r87830) -- "Unsuffered Consequences" | 59 |
| 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 0.99.0 (landing page) Franck RICHARD
| biocgpu | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ||||||||
| kakapo1 | Linux (Ubuntu 24.04.2 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: 0.99.0 |
| Command: /home/biocbuild/bbs-3.21-bioc-gpu/R/bin/R CMD INSTALL RbowtieCuda |
| StartedAt: 2025-04-09 14:05:03 -0400 (Wed, 09 Apr 2025) |
| EndedAt: 2025-04-09 14:09:36 -0400 (Wed, 09 Apr 2025) |
| EllapsedTime: 272.5 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 ‘0.99.0’ ** using staged installation ** libs cd "../src/nvbio/build" && rm -f CMakeCache.txt && cmake .. -- The C compiler identification is GNU 13.3.0 -- The CXX 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/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found CUDAToolkit: /software/u24/nvhpc/24.7/Linux_x86_64/24.7/cuda/12.5/targets/x86_64-linux/include (found version "12.5.82") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Building Release -- 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) -- The CUDA compiler identification is NVIDIA 12.5.82 -- Detecting CUDA compiler ABI info -- Detecting CUDA compiler ABI info - done -- Check for working CUDA compiler: /software/u24/nvhpc/24.7/Linux_x86_64/24.7/compilers/bin/nvcc - skipped -- Detecting CUDA compile features -- Detecting CUDA compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- 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_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Configuring done (4.9s) -- 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' make[2]: 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' 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]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving 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]: Leaving 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]: Leaving 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]: Leaving 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' [ 1%] Building C object contrib/lz4/CMakeFiles/lz4.dir/lz4.c.o [ 2%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/adler32.c.o [ 3%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/trees.c.o [ 4%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/gzread.c.o [ 5%] Building C object contrib/lz4/CMakeFiles/lz4.dir/lz4hc.c.o [ 1%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/deflate.c.o [ 1%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/compress.c.o [ 1%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/adler32.c.o [ 1%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/gzclose.c.o [ 6%] Building C object contrib/lz4/CMakeFiles/lz4.dir/lz4frame.c.o [ 7%] Building CXX object contrib/crc/CMakeFiles/crcstatic.dir/crc.cpp.o [ 8%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/compress.c.o [ 9%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inftrees.c.o [ 10%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inffast.c.o [ 11%] Building CXX object contrib/moderngpu/CMakeFiles/moderngpu.dir/src/mmio.cpp.o [ 3%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/deflate.c.o [ 12%] Building CUDA object contrib/moderngpu/CMakeFiles/moderngpu.dir/src/mgpucontext.cu.o [ 12%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzread.c.o [ 13%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/crc32.c.o [ 14%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzwrite.c.o [ 14%] Building CXX object contrib/moderngpu/CMakeFiles/moderngpu.dir/src/mgpuutil.cpp.o [ 17%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/io/vcf.cu.o [ 19%] Building C object 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CUDA object nvbio/CMakeFiles/nvbio.dir/io/output/output_debug.cu.o [ 40%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/io/output/output_file.cu.o [ 41%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/io/output/output_batch.cu.o [ 42%] Linking CXX static library libcrcstatic.a [ 43%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/io/output/output_priv.cu.o [ 44%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/io/output/output_stats.cu.o [ 45%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/io/output/output_bam.cu.o [ 46%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/io/output/output_databuffer.cu.o [ 46%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/io/output/output_sam.cu.o [ 46%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/io/output/output_gzip.cu.o [ 47%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/atomics.cu.o [ 48%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/bnt.cu.o [ 48%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/console.cu.o [ 48%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/timer.cu.o [ 49%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/exceptions.cu.o make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' [ 49%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/mmap.cu.o [ 51%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/cuda/sort.cu.o [ 51%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/system.cu.o [ 52%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/html.cu.o [ 53%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/threads.cu.o [ 54%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/cuda/scan_test.cu.o [ 54%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/fmindex/paged_text.cu.o [ 55%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/sufsort/sufsort_priv.cu.o [ 56%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/sufsort/file_bwt.cu.o [ 56%] Built target crcstatic [ 56%] Building CUDA object 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CMakeFiles/nvbio-test.dir/cmake_device_link.o [ 98%] Linking CXX executable nvbio-test make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' [ 98%] Built target nvbio-test [ 99%] Linking CUDA device code CMakeFiles/nvBowtie.dir/cmake_device_link.o [100%] Linking CXX executable nvBowtie make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' [100%] Built target nvBowtie make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' cd "../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)