##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD check --install=check:RbowtieCuda.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc-gpu/R/site-library --timings RbowtieCuda_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/RbowtieCuda.Rcheck’
* using R Under development (unstable) (2025年11月17日 r89032)
* 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 ‘1.3.0’
* 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 16.194 0.801 17.514
* 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-3.23-bioc-gpu/meat/RbowtieCuda.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD INSTALL RbowtieCuda
###
##############################################################################
##############################################################################
* installing to library ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/R/site-library’
* installing *source* package ‘RbowtieCuda’ ...
** this is package ‘RbowtieCuda’ version ‘1.3.0’
** 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
-- 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: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
 Thu Dec 4 04:45:19 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: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
-- 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: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 (4.6s)
-- Generating done (0.0s)
-- Build files have been written to: /media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/RbowtieCuda/src/nvbio/build
(cd "../src/nvbio/build" && make)
make[1]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[2]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/media/volume/biocgpu2/biocbuild/bbs-3.23-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)

R Under development (unstable) (2025年11月17日 r89032) -- "Unsuffered Consequences"
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.
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'help.start()' for an HTML browser interface to help.
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> 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 : 0.42 ms, 2.321 GB/s
info : cuda free : 0.41 ms, 2.368 GB/s
info : malloc : 0.00 ms, 801.282 GB/s
info : free : 0.00 ms, 10416.666 GB/s
info : 4 MB:
info : cuda malloc : 0.43 ms, 9.049 GB/s
info : cuda free : 0.45 ms, 8.775 GB/s
info : malloc : 0.00 ms, 2659.574 GB/s
info : free : 0.00 ms, 4464.286 GB/s
info : 16 MB:
info : cuda malloc : 0.52 ms, 29.899 GB/s
info : cuda free : 0.56 ms, 28.103 GB/s
info : malloc : 0.00 ms, 7812.499 GB/s
info : free : 0.00 ms, 71428.570 GB/s
info : 64 MB:
info : cuda malloc : 0.38 ms, 165.508 GB/s
info : cuda free : 0.39 ms, 159.872 GB/s
info : malloc : 0.01 ms, 5405.407 GB/s
info : free : 0.01 ms, 9803.920 GB/s
info : 256 MB:
info : cuda malloc : 0.40 ms, 617.951 GB/s
info : cuda free : 0.50 ms, 504.191 GB/s
info : malloc : 0.01 ms, 23121.393 GB/s
info : free : 0.01 ms, 27586.205 GB/s
info : 1024 MB:
info : cuda malloc : 29.03 ms, 34.443 GB/s
info : cuda free : 0.91 ms, 1096.191 GB/s
info : malloc : 0.01 ms, 81218.289 GB/s
info : free : 0.02 ms, 45390.066 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: 12.9 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 : 1134.786 ns
info : 0.657 ns/CTA
info : 1.5M CTAs retired/s
info : fast scan... started (1728 CTAs)
info : fast scan test... done:
info : 33.927 ns
info : 0.020 ns/CTA
info : 50.9M CTAs retired/s
info : fast chaining... started
info : fast chaining test... done:
info : 27.789 ns
info : 0.016 ns/CTA
info : 62.2M 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: 0.44 GSYMS
 test sparse -> concat copy... started
 test sparse -> concat copy... done: 134.22 GSYMS
 test sparse -> packed-concat copy... started
 test sparse -> packed-concat copy... done: 130.41 GSYMS
 test concat -> packed-concat copy... started
 test concat -> packed-concat copy... done: 251.63 GSYMS
 test sparse -> strided copy... started
 test sparse -> strided copy... done: 126.55 GSYMS
 test packed-concat -> strided copy... started
 test packed-concat -> strided copy... done: 175.13 GSYMS
 test packed-sparse -> strided copy... started
 test packed-sparse -> strided copy... done: 332.22 GSYMS
 test packed-sparse (tex) -> strided copy... started
 test packed-sparse (tex) -> strided copy... done: 328.64 GSYMS
 test strided-packed -> strided copy... started
 test strided-packed -> strided copy... done: 411.71 GSYMS
 test concat -> strided-packed copy... started
 test concat -> strided-packed copy... done: 145.67 GSYMS
 test packed-concat -> strided-packed copy... started
 test packed-concat -> strided-packed copy... done: 710.90 GSYMS
 test packed-sparse -> strided-packed copy... started
 test packed-sparse -> strided-packed copy... done: 578.03 GSYMS
nvbio/basic/string_set test... done
all test... started
 all<2> throughput: 265.778 G vectors/s, 531.555 G threads/s
 all<4> throughput: 229.040 G vectors/s, 916.162 G threads/s
 all<8> throughput: 113.744 G vectors/s, 909.951 G threads/s
 all<16> throughput: 57.456 G vectors/s, 919.299 G threads/s
 all<32> throughput: 30.727 G vectors/s, 983.280 G threads/s
 all<64> throughput: 9.404 G vectors/s, 601.873 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: 516.222 G vectors/s, 1032.444 G threads/s
 any<4> throughput: 262.144 G vectors/s, 1048.576 G threads/s
 any<8> throughput: 131.072 G vectors/s, 1048.576 G threads/s
 any<16> throughput: 65.536 G vectors/s, 1048.576 G threads/s
 any<32> throughput: 34.664 G vectors/s, 1109.237 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 : 7.2 37.5
 semi-global : 45.0 36.5
 local : 39.2 27.6
 testing Hamming Distance scoring speed...
 semi-global : 157.8 109.7
 local : 121.7 56.9
 testing Smith-Waterman scoring speed...
 global : 46.1 36.8
 semi-global : 45.1 35.3
 local : 41.7 27.3
 testing Gotoh scoring speed...
 global : 19.6 27.2
 semi-global : 27.4 27.1
 local : 24.4 22.0
 testing banded Edit Distance scoring speed...
 global : 39.85 19.28 GCUPS
 semi-global : 40.87 19.60 GCUPS
 local : 37.94 15.24 GCUPS
 testing banded Smith-Waterman scoring speed...
 global : 41.05 20.09 GCUPS
 semi-global : 39.52 20.31 GCUPS
 local : 38.56 15.74 GCUPS
 testing banded Gotoh scoring speed...
 global : 35.53 16.01 GCUPS
 semi-global : 34.26 16.22 GCUPS
 local : 15.95 13.05 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: 36.0 M/s
info : lookup: 89.9 M/s
info : gpu test
info : insertion: 13642.6 M/s
info : lookup: 25974.0 M/s
info : bloom filter test... done
RUNIT TEST PROTOCOL -- Thu Dec 4 05:10:13 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 
 16.326 0.853 17.679