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GPU-enabled build/check report for BioC 3.21
Report updated every 6 hours

This page was generated on 2025-09-11 07:45 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
biocgpuLinux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 196
kakapo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (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 1/1HostnameOS / ArchINSTALLBUILDCHECK
RbowtieCuda 1.0.8  (landing page)
Franck RICHARD
Snapshot Date: 2025-09-11 04:00 -0400 (Thu, 11 Sep 2025)
git_url: https://git.bioconductor.org/packages/RbowtieCuda
git_branch: RELEASE_3_21
git_last_commit: 1368d77
git_last_commit_date: 2025-09-10 16:04:42 -0400 (Wed, 10 Sep 2025)
biocgpuLinux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  YES
kakapo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  

CHECK results for RbowtieCuda on biocgpu

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.

raw results


Summary

Package: RbowtieCuda
Version: 1.0.8
Command: /home/biocbuild/bbs-3.21-bioc-gpu/R/bin/R CMD check --install=check:RbowtieCuda.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc-gpu/R/site-library --timings RbowtieCuda_1.0.8.tar.gz
StartedAt: 2025-09-11 04:54:03 -0400 (Thu, 11 Sep 2025)
EndedAt: 2025-09-11 04:55:19 -0400 (Thu, 11 Sep 2025)
EllapsedTime: 76.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RbowtieCuda.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc-gpu/R/bin/R CMD check --install=check:RbowtieCuda.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc-gpu/R/site-library --timings RbowtieCuda_1.0.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RbowtieCuda/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RbowtieCuda’ version ‘1.0.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RbowtieCuda’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 49.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub records with missing/empty fields:
  Record: 1 Field(s): ORGANIZATION
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
nvbio_tests 16.149  0.801  17.568
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/biocgpu2/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda.Rcheck/00check.log’
for details.

Installation output

RbowtieCuda.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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'
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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)

Tests output

RbowtieCuda.Rcheck/tests/runTests.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("RbowtieCuda")
RbowtieCuda is distributed under the BSD 3-Clause License.
Please read the LICENSE file carefully before use.

Note:
- Redistribution and use (source/binary, with/without modification) are permitted
  under certain conditions.
- The name of NVIDIA CORPORATION and its contributors may not be used to endorse
  or promote derived products without written permission.
- This software is provided "AS IS", without warranty of any kind.

verbose :   cuda devices : 1
verbose :   device 0 has compute capability 8.0
verbose :     SM count          : 108
verbose :     SM clock rate     : 1410 Mhz
verbose :     memory clock rate : 1.2 Ghz
verbose :   chosen device 0
verbose :     device name        : GRID A100X-10C
verbose :     compute capability : 8.0
info    : alloc test... started
info    :   1 MB:
info    :     cuda malloc : 0.32 ms, 3.082 GB/s
info    :     cuda free   : 0.33 ms, 2.958 GB/s
info    :     malloc      : 0.00 ms, 822.368 GB/s
info    :     free        : 0.00 ms, 15625.000 GB/s
info    :   4 MB:
info    :     cuda malloc : 0.31 ms, 12.536 GB/s
info    :     cuda free   : 0.33 ms, 11.810 GB/s
info    :     malloc      : 0.00 ms, 3906.250 GB/s
info    :     free        : 0.00 ms, 3289.474 GB/s
info    :   16 MB:
info    :     cuda malloc : 0.35 ms, 44.920 GB/s
info    :     cuda free   : 0.35 ms, 44.033 GB/s
info    :     malloc      : 0.00 ms, 11111.110 GB/s
info    :     free        : 0.00 ms, 13888.889 GB/s
info    :   64 MB:
info    :     cuda malloc : 0.36 ms, 173.837 GB/s
info    :     cuda free   : 0.39 ms, 162.009 GB/s
info    :     malloc      : 0.01 ms, 6153.846 GB/s
info    :     free        : 0.01 ms, 7633.589 GB/s
info    :   256 MB:
info    :     cuda malloc : 0.76 ms, 330.551 GB/s
info    :     cuda free   : 0.49 ms, 506.073 GB/s
info    :     malloc      : 0.01 ms, 23952.100 GB/s
info    :     free        : 0.01 ms, 27681.660 GB/s
info    :   1024 MB:
info    :     cuda malloc : 28.78 ms, 34.746 GB/s
info    :     cuda free   : 0.98 ms, 1017.747 GB/s
info    :     malloc      : 0.01 ms, 84880.633 GB/s
info    :     free        : 0.03 ms, 35010.945 GB/s
info    : alloc test... done
info    : syncblocks test... started
info    :   1728 blocks
info    :   correctness test... started
info    :   correctness test... done
info    :   speed test... started
info    :   speed test... done: 12.0 ns
info    : syncblocks test... done
info    : condition test... started
info    :   1728 blocks
info    :   correctness test... started
info    :   correctness test... done
info    :   speed test... started
info    :   speed test... done:
info    :     1091.749 ns
info    :     0.632 ns/CTA
info    :     1.6M CTAs retired/s
info    :   fast scan... started (1728 CTAs)
info    :   fast scan test... done:
info    :     33.193 ns
info    :     0.019 ns/CTA
info    :     52.1M CTAs retired/s
info    :   fast chaining... started
info    :   fast chaining test... done:
info    :     27.497 ns
info    :     0.016 ns/CTA
info    :     62.8M CTAs retired/s
info    : condition test... done
nvbio/basic/string_set test... started
  test cpu packed-sparse  -> strided        copy... started
  test cpu packed-sparse  -> strided        copy... done:   0.23 GSYMS
  test cpu packed-sparse  -> strided-packed copy... started
  test cpu packed-sparse  -> strided-packed copy... done:   0.43 GSYMS
  test sparse         -> concat         copy... started
  test sparse         -> concat         copy... done:   130.18 GSYMS
  test sparse         -> packed-concat  copy... started
  test sparse         -> packed-concat  copy... done:   131.07 GSYMS
  test concat         -> packed-concat  copy... started
  test concat         -> packed-concat  copy... done:   260.62 GSYMS
  test sparse         -> strided        copy... started
  test sparse         -> strided        copy... done:   124.18 GSYMS
  test packed-concat  -> strided        copy... started
  test packed-concat  -> strided        copy... done:   166.48 GSYMS
  test packed-sparse  -> strided        copy... started
  test packed-sparse  -> strided        copy... done:   331.07 GSYMS
  test packed-sparse (tex) -> strided   copy... started
  test packed-sparse (tex) -> strided   copy... done:   288.64 GSYMS
  test strided-packed -> strided        copy... started
  test strided-packed -> strided        copy... done:   411.21 GSYMS
  test concat         -> strided-packed copy... started
  test concat         -> strided-packed copy... done:   139.58 GSYMS
  test packed-concat  -> strided-packed copy... started
  test packed-concat  -> strided-packed copy... done:   691.84 GSYMS
  test packed-sparse  -> strided-packed copy... started
  test packed-sparse  -> strided-packed copy... done:   593.36 GSYMS
nvbio/basic/string_set test... done
all test... started
  all<2> throughput: 208.737 G vectors/s, 417.473 G threads/s
  all<4> throughput: 229.040 G vectors/s, 916.162 G threads/s
  all<8> throughput: 115.705 G vectors/s, 925.639 G threads/s
  all<16> throughput: 57.260 G vectors/s, 916.162 G threads/s
  all<32> throughput: 30.615 G vectors/s, 979.691 G threads/s
  all<64> throughput: 9.576 G vectors/s, 612.866 G threads/s
  all<128> throughput: 3.725 G vectors/s, 476.795 G threads/s
all test... done
any test... started
  any<2> throughput: 530.505 G vectors/s, 1061.010 G threads/s
  any<4> throughput: 258.111 G vectors/s, 1032.444 G threads/s
  any<8> throughput: 131.072 G vectors/s, 1048.576 G threads/s
  any<16> throughput: 66.576 G vectors/s, 1065.220 G threads/s
  any<32> throughput: 34.953 G vectors/s, 1118.481 G threads/s
  any<64> throughput: 9.664 G vectors/s, 618.515 G threads/s
  any<128> throughput: 4.692 G vectors/s, 600.527 G threads/s
any test... done
testing alignment... started
  synthetic Edit Distance test 1... passed!
  synthetic Edit Distance test 2... passed!
  synthetic Edit Distance test 3... passed!
  synthetic Edit Distance test 4... passed!
  synthetic Edit Distance test 5... passed!
  synthetic Edit Distance test 6... passed!
  testing Gotoh scoring...
             global : -7 - 6M4D2M - [1:13] x [0:8]


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:AACATTGATGACACA
str:ACATGACA
result=-17


verbose : alignment ok !  score=-17
verbose : 
verbose : 
             global : -17 - 2D7M5D1M - [0:15] x [0:8]
verbose : cigar ok !  score=-17  2D7M5D1M
verbose : 
verbose : 
result=-17


verbose : alignment ok !  score=-17
verbose : 
verbose : 
             global : -17 - 2D7M5D1M - [8:15] x [0:8]
verbose : cigar ok !  score=-17  2D7M5D1M
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:AACATTGATGACACA
str:ACGGGACA
result=-17


verbose : alignment ok !  score=-17
verbose : 
verbose : 
             global : -17 - 7M7D1M - [0:15] x [0:8]
verbose : cigar ok !  score=-17  7M7D1M
verbose : 
verbose : 
result=-17


verbose : alignment ok !  score=-17
verbose : 
verbose : 
             global : -17 - 7M7D1M - [8:15] x [0:8]
verbose : cigar ok !  score=-17  7M7D1M
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:ATCGGATTCTTTCTTACTTGTAGGTGGTCTGGTTTTTGCCTTTTAAGCTTCTGCAAAAAACAACAACAAACTTGTGGTATTACACTGACTCTACAGATCAATTTGGGGACAACTTCCATGTGTTCCACCACCAATACTGAATCTTTCAATCGACTGACGTGGTATCTCTCTCTCCATCTAT
str:TTATGTAGGTGGTCTGGTTTTTGCCTTTTAAGCTTCTGCAAAAAACAACAACAAACTTGTGGTATTACACTGACTCTACAGATCAATTTGGGGACAACTTCCATGTGTTCCACCACCAATACTGAATCTTTCAATCGACTGACGTGGTAT
result=-43


verbose : alignment ok !  score=-43
verbose : 
verbose : 
             global : -43 - 16D148M15D2M - [0:181] x [0:150]
verbose : cigar ok !  score=-43  16D148M15D2M
verbose : 
verbose : 
result=-43


verbose : alignment ok !  score=-43
verbose : 
verbose : 
             global : -43 - 16D148M15D2M - [150:181] x [0:150]
verbose : cigar ok !  score=-43  16D148M15D2M
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:AACCATACTCGG
str:AGGATCGG
result=-14


verbose : alignment ok !  score=-14
verbose : 
verbose : 
             global : -14 - 7M4D1M - [0:12] x [0:8]
verbose : cigar ok !  score=-14  7M4D1M
verbose : 
verbose : 
result=-14


verbose : alignment ok !  score=-14
verbose : 
verbose : 
             global : -14 - 7M4D1M - [8:12] x [0:8]
verbose : cigar ok !  score=-14  7M4D1M
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:GAACACCCTAACACACTAAG
str:ACAACTA
result=-25


verbose : alignment ok !  score=-25
verbose : 
verbose : 
             global : -25 - 2D4M11D3M - [0:20] x [0:7]
verbose : cigar ok !  score=-25  2D4M11D3M
verbose : 
verbose : 
result=-25


verbose : alignment ok !  score=-25
verbose : 
verbose : 
             global : -25 - 2D4M11D3M - [7:20] x [0:7]
verbose : cigar ok !  score=-25  2D4M11D3M
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:GAACACCCTAACACACTAAG
str:ACCCGAA
result=-23


verbose : alignment ok !  score=-23
verbose : 
verbose : 
             global : -23 - 9D7M4D - [0:20] x [0:7]
verbose : cigar ok !  score=-23  9D7M4D
verbose : 
verbose : 
result=-23


verbose : alignment ok !  score=-23
verbose : 
verbose : 
             global : -23 - 9D7M4D - [7:20] x [0:7]
verbose : cigar ok !  score=-23  9D7M4D
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:AAACACCCTAACACACTAA
str:AAACATAACACACTAA
result=-7


verbose : alignment ok !  score=-7
verbose : 
verbose : 
             global : -7 - 11M3D5M - [0:19] x [0:16]
verbose : cigar ok !  score=-7  11M3D5M
verbose : 
verbose : 
result=-7


verbose : alignment ok !  score=-7
verbose : 
verbose : 
             global : -7 - 11M3D5M - [16:19] x [0:16]
verbose : cigar ok !  score=-7  11M3D5M
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:ATCGGATTCTTTCTTACTTGTAGGTGGTCTGGTTTTTGCCTTTTAAGCTTCTGCAAAAAACAACAACAAACTTGTGGTATTACACTGACTCTACAGATCAATTTGGGGACAACTTCCATGTGTTCCACCACCAATACTGAATCTTTCAATCGACTGACGTGGTATCTCTCTCTCCATCTAT
str:TATGTAGT
result=-185


verbose : alignment ok !  score=-185
verbose : 
verbose : 
             global : -185 - 153D8M20D - [0:181] x [0:8]
verbose : cigar ok !  score=-185  153D8M20D
verbose : 
verbose : 
result=-185


verbose : alignment ok !  score=-185
verbose : 
verbose : 
             global : -185 - 153D8M20D - [8:181] x [0:8]
verbose : cigar ok !  score=-185  153D8M20D
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:ATCGGATTCTTTCTTACTTGTAGGTGGTCTGGTTTTTGCCTTTTAAGCTTCTGCAAAAAACAACAACAAACTTGTGGTATTACACTGACTCTACAGATCAATTTGGGGACAACTTCCATGTGTTCCACCACCAATACTGAATCTTTCAATCGACTGACGTGGTATCTCTCTCTCCATCTAT
str:TTATGTAGGTGGTCTGGTTTTTGCCTTTTAAGCTTCTGCAAAAAACAACAACAAACTTGTGGTATTACACTGACTCTACAGATCAATTTGGGGACAACTTCCATGTGTTCCACCACCAATACTGAATCTTTCAATCGACTGACGTGGTAT
result=-43


verbose : alignment ok !  score=-43
verbose : 
verbose : 
             global : -43 - 16D148M15D2M - [0:181] x [0:150]
verbose : cigar ok !  score=-43  16D148M15D2M
verbose : 
verbose : 
result=-43


verbose : alignment ok !  score=-43
verbose : 
verbose : 
             global : -43 - 16D148M15D2M - [150:181] x [0:150]
verbose : cigar ok !  score=-43  16D148M15D2M
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:CATCAATAGAAAACCGGATTAAAAACATCGAAAATTATTGAAAAAATATTAAGTGTAGTGTGGAAATGAATGAGTAGAAAAAAAGATAAATTAGAAAACAGAACATCAACTTCGTAAATAGTAAAACGCTAAGCCAGACTAGGTAGAACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
str:GAGCTAAGAAGGCGCTCATCAATAGAAAACCGGATTAAAAACATCGAAAATTATTGAAAAAATATTAAGTGTAGTGTGGAAATGAATGAGTAGAAAAAAGATAAATTAGAAAACAGAACATCAACTTCGTAAATAGTAAAACGCTAAGCC
result=-75


verbose : alignment ok !  score=-75
verbose : 
verbose : 
             global : -75 - 46D51M1D83M16I - [0:181] x [0:150]
verbose : cigar ok !  score=-75  46D51M1D83M16I
verbose : 
verbose : 
result=-75


verbose : alignment ok !  score=-75
verbose : 
verbose : 
             global : -75 - 46D51M1D83M16I - [118:181] x [0:150]
verbose : cigar ok !  score=-75  46D51M1D83M16I
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:CTAAATACGAAACCCACACTCGTTTTAATTCAAATCTCATAACCATAAAAAAAAAGCACAATTCAACTTGAGCACGCACACTAAGTAGTAACAACGTTCATTTACAGTAAAGCGAACGGACGAAACAAATAAAAGAAAGGCATAGTGAGNAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
str:TTTACGGGATCTGTCTAAATACGAAACACACACTCGTTTTAGTTCAAATATCATAACCATAAAAAAAAAAGCACAATTCAACTTGAGCACGCACACTAAGTAGTAACAACGTTCATTTACAGTAAAGCGAACGGACGAAACAAATAAAAG
result=-79


verbose : alignment ok !  score=-79
verbose : 
verbose : 
             global : -79 - 46D80M1I55M14I - [0:181] x [0:150]
verbose : cigar ok !  score=-79  46D80M1I55M14I
verbose : 
verbose : 
result=-79


verbose : alignment ok !  score=-79
verbose : 
verbose : 
             global : -79 - 46D80M1I55M14I - [120:181] x [0:150]
verbose : cigar ok !  score=-79  46D80M1I55M14I
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:TGCTGTTGTTGCTGTTGCTGTTGTTGCTGTTGCTGTTGTTGCTGTTGTTGGAGATGATTCTGAGTGTAGTGAGCCTGAAATTCCATTTTATCAAAACGCTGAGGAATATTCATCGATCCCTGCATGCTAGTAGGGGTTGTCATAACGCTATTGATCGAGCTCAAAGGCATTTTTTGTTGTT
str:TGCTGTTGTTGCTGTTGCTGTTGTTGCTGTTGCTGTTGTTGCTGTTGTTGGAGATGATTCTGAGTGTAGTGAGCCTGAAATTCCATTTTATCAAAACGCTGAGGAATATTCATCGATCCCTGCATGCTAGTAGGGGTTGTCATAACGCTA
result=-35


verbose : alignment ok !  score=-35
verbose : 
verbose : 
             global : -35 - 31D150M - [0:181] x [0:150]
verbose : cigar ok !  score=-35  31D150M
verbose : 
verbose : 
result=-35


verbose : alignment ok !  score=-35
verbose : 
verbose : 
             global : -35 - 31D150M - [150:181] x [0:150]
verbose : cigar ok !  score=-35  31D150M
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:2 gap_open:4 gap_ext:1)
ref:TAGTGGGTGACCATACGCGAAACTCAGGTGCTGCAATCTTTTTTTTTTTTCCGCGCGCAAGCACGTTACCCGGACCCCGTCTTAGCACACGCACACGCACACGCAGCGCTCACAGACCAGCGAAACAGACCTGAGAGCCACGATGCAGCACACGCTTACCCGGACCGCCTCTCTGCCAGAA
str:NGCGAAACTCAGGTGCTGCAATCTTTATTTCTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTGTGTTTGTTTGGGTTGTTTTTTTTTTTAATTTT
result=-241


verbose : alignment ok !  score=-241
verbose : 
verbose : 
             global : -241 - 1M3I71M26D42M7I26M15D - [0:181] x [0:150]
verbose : cigar ok !  score=-241  1M3I71M26D42M7I26M15D
verbose : 
verbose : 
result=-241


verbose : alignment ok !  score=-241
verbose : 
verbose : 
             global : -241 - 1M3I71M26D42M7I26M15D - [130:181] x [0:150]
verbose : cigar ok !  score=-241  1M3I71M26D42M7I26M15D
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:1 gap_open:1 gap_ext:1)
ref:ATGATGAGACACCTGTTTTTGGTCAGGATCAAAATACCACGAAGTCCAAGGTTGTTCAATTGATTGGCGCCGTACAGACATTACTGAGGAGTATGTTATGTTGATGGAGAACGGTTAAAGTTACATTTCATCAGTTTTTTCCCGTTCTTTTTCACCTTTTGTGAGAAAATTTTACTAACGT
str:TTTTTGGTCAGGATCAAAATACCACGAAGTCCAAGGTTGTTCAATTGATTGGCGCCGTACAGACATTACTGAGGATACCATTAATTGGAATAAATATACTGGTGATTGTTTATGAATTGCTATTGGGATGAACTAAGCGTACAAAGCAAA
result=-76


verbose : alignment ok !  score=-76
verbose : 
verbose : 
        semi-global : -76 - 3D51M3D9M4D3M5D12M1D75M15D - [0:181] x [0:150]
verbose : cigar ok !  score=-76  3D51M3D9M4D3M5D12M1D75M15D
verbose : 
verbose : 
result=-76


verbose : alignment ok !  score=-76
verbose : 
verbose : 
        semi-global : -76 - 3D51M3D9M4D3M5D12M1D75M15D - [150:181] x [0:150]
verbose : cigar ok !  score=-76  3D51M3D9M4D3M5D12M1D75M15D
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:1 gap_open:1 gap_ext:1)
ref:TCGTCCTTGTCCAAAAAGTCTTGATAACATTAAAAGTCACTACCGTCAAATCCATCATCAAATCCGCCGTCGAACCCACCAGCATCATCAAATCCGCCGTCGGACCCACCAGCATCATCACCGTAGTAATTGTTCTCGACAACGACAGTGTCTGGTCCGTCATAGTTGTGGTCGTCAAATG
str:GCTTATATCATTTTATCGTCCTTGCCCAAAAAGTCTTGATAACATTAAAAGTCACCACCGTCAAATCCATCATCAAATCCGCCGTCGAACCCACCAGCATCATCACCGTAGTAATTGTTCTCGACAACGACAGTGTCTGGTTCGTCATAG
result=-67


verbose : alignment ok !  score=-67
verbose : 
verbose : 
             global : -67 - 16D45M30D90M15I - [0:181] x [0:150]
verbose : cigar ok !  score=-67  16D45M30D90M15I
verbose : 
verbose : 
result=-67


verbose : alignment ok !  score=-67
verbose : 
verbose : 
             global : -67 - 16D45M30D90M15I - [120:181] x [0:150]
verbose : cigar ok !  score=-67  16D45M30D90M15I
verbose : 
verbose : 


testing Wfa scoring... (match:0 mismatch:1 gap_open:1 gap_ext:1)
ref:GCCGACCTCTGTTTCGGCATCGGGCAAGAAGATCTTGACACCATTTCTGGCAGCTGGCCCCTTTTTCAAGTATTTGAATCCGACTCGTACCTTGCTATACGTTTTATTGTTTAGCTGGTCCATTATCTTGGCATAGCCATTGAACCAGTACTTTTGATCTACTAGGTCCCTTCTTGACTTTGAAATCACCCAGTTTAACGCAGCTTCTACTGGTGTGATACTTTCGTCCAATTCATGACCATACAAACACATACCAGCTTCCAACCTTAAACTGTCTCTAGCAGCCAGTCCGATAGGCTTCATTACTGGATTGGCCAAGAGTTGCTCCGCAAACTCAACCGCTTTCTCATTTGCAATGCTTATCTCAAATCCATCTTCACCAGTGTACCCGCCTCTAGCAATTTGAACCAAAGAACCGTCCTTTAACGCAAATTCATGTCTTTGTCCAAAAAATAACTCTTTTAGATCCTTTCCAGGAGCTGTTTTTGATAAAAGTGGTT
str:TGTTTAGCTGGTCCATTATCTTGGCATAGCCATTGAACCAGTACTTTTGATCTACTAGGTCCCTTCTTGACTTTGAAATCACCCAGTTTAACGCAGCTTCTACTGGTGTGATACTTTCGTCCAATTCATGACCATACAAACACATACCAG
result=-352


verbose : alignment ok !  score=-352
verbose : 
verbose : 
        semi-global : -352 - 243D150M107D - [0:500] x [0:150]
verbose : cigar ok !  score=-352  243D150M107D
verbose : 
verbose : 
result=-352


verbose : alignment ok !  score=-352
verbose : 
verbose : 
        semi-global : -352 - 243D150M107D - [150:500] x [0:150]
verbose : cigar ok !  score=-352  243D150M107D
verbose : 
verbose : 
  testing real banded Gotoh problem...
    banded-semi-global : -11 - 147M2D3M - [13:165] x [0:150]
  testing Edit Distance scoring speed...
             global :     6.6   35.9
        semi-global :    43.9   35.8
              local :    38.0   27.1
  testing Hamming Distance scoring speed...
        semi-global :   147.6  102.1
              local :   115.5   55.4
  testing Smith-Waterman scoring speed...
             global :    44.4   36.0
        semi-global :    44.1   34.4
              local :    40.9   27.1
  testing Gotoh scoring speed...
             global :    19.2   27.0
        semi-global :    26.9   26.8
              local :    24.1   21.7
  testing banded Edit Distance scoring speed...
             global :   36.63  17.73 GCUPS
        semi-global :   37.79  17.60 GCUPS
              local :   35.14  14.54 GCUPS
  testing banded Smith-Waterman scoring speed...
             global :   37.49  18.93 GCUPS
        semi-global :   37.20  18.67 GCUPS
              local :   34.01  14.61 GCUPS
  testing banded Gotoh scoring speed...
             global :   32.17  14.88 GCUPS
        semi-global :   32.50  14.74 GCUPS
              local :   13.53  12.40 GCUPS
testing alignment... done
bwt test... started
  arch    : 64 bit
  length  : 10.00 M bps
  memory  : 40.5 MB
sum tree... started
sum tree... done
cache test... started
  test overflow... started
  test overflow... done
cache test... done
  construction... started
  construction... done: 0m:0s
bwt test... done
rank test... started
  32-bit test
    memory  : 4.8 MB
  64-bit test
    memory  : 4.8 MB
rank test... done
info    : testing sequence-data... started
info    : testing sequence-data... done
info    : wavelet test... started
info    : wavelet test... done
info    : bloom filter test... started (0.5 MB)
verbose :   cpu: 8 threads
info    :   cpu test
info    :     insertion: 14.0 M/s
info    :     lookup: 89.0 M/s
info    :   gpu test
info    :     insertion: 13531.8 M/s
info    :     lookup: 26246.7 M/s
info    : bloom filter test... done


RUNIT TEST PROTOCOL -- Thu Sep 11 04:54:56 2025 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RbowtieCuda RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 17.159   1.156  18.405

Example timings

RbowtieCuda.Rcheck/RbowtieCuda-Ex.timings

nameusersystemelapsed
dot-callbinary20.0020.0050.036
nvBWT0.1480.9261.132
nvBowtie0.6102.4543.070
nvBowtie_usage0.0050.0000.005
nvBowtie_version0.0020.0030.006
nvbio_tests16.149 0.80117.568