Franck RICHARD
| Snapshot Date: 2025-06-19 09:00 -0400 (Thu, 19 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/RbowtieCuda |
| git_branch: devel |
| git_last_commit: 41bf796 |
| git_last_commit_date: 2025-04-17 16:05:49 -0400 (Thu, 17 Apr 2025) |
| Back to --- experimental! --- GPU-enabled build/check report for BioC 3.22 Report updated every 6 hours |
This page was generated on 2025-06-19 10:45 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| biocgpu | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 Patched (2025-05-01 r88189) -- "How About a Twenty-Six" | 280 |
| amarone | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 282 |
| 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 2/3 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| RbowtieCuda 1.1.1 (landing page) Franck RICHARD
| biocgpu | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | |||||||
| amarone | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
|
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: 1.1.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RbowtieCuda.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RbowtieCuda_1.1.1.tar.gz |
| StartedAt: 2025-06-19 14:00:26 -0000 (Thu, 19 Jun 2025) |
| EndedAt: 2025-06-19 14:00:45 -0000 (Thu, 19 Jun 2025) |
| EllapsedTime: 19.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RbowtieCuda.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RbowtieCuda.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RbowtieCuda_1.1.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘RbowtieCuda/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RbowtieCuda’ version ‘1.1.1’
* 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 ... WARNING
Found the following significant warnings:
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:77:56: warning: ‘input_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:78:56: warning: ‘output_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:79:56: warning: ‘forward_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:80:56: warning: ‘bidirectional_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:81:56: warning: ‘random_access_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 44.3Mb
* 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
* 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: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda.Rcheck/00check.log’
for details.
RbowtieCuda.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RbowtieCuda
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘RbowtieCuda’ ...
** this is package ‘RbowtieCuda’ version ‘1.1.1’
** 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/cc - 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/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- 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
-- 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 12.9.41
-- 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
-- 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 (4.2s)
-- Generating done (0.1s)
-- Build files have been written to: /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build
(cd "../src/nvbio/build" && make)
make[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
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In file included from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/strided_iterator.h:31,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/reads.h:30,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/reads_txt.h:30,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/reads_txt.cpp:28:
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:77:56: warning: ‘input_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
77 | typedef thrust::input_universal_iterator_tag input_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/iterator_categories.h:217,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:37:
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:37:24: note: declared here
37 | struct CCCL_DEPRECATED input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:78:56: warning: ‘output_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
78 | typedef thrust::output_universal_iterator_tag output_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:51:24: note: declared here
51 | struct CCCL_DEPRECATED output_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:79:56: warning: ‘forward_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
79 | typedef thrust::forward_universal_iterator_tag forward_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:65:24: note: declared here
65 | struct CCCL_DEPRECATED forward_universal_iterator_tag : input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:80:56: warning: ‘bidirectional_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
80 | typedef thrust::bidirectional_universal_iterator_tag bidirectional_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:79:24: note: declared here
79 | struct CCCL_DEPRECATED bidirectional_universal_iterator_tag : forward_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:81:56: warning: ‘random_access_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
81 | typedef thrust::random_access_universal_iterator_tag random_access_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:103:24: note: declared here
103 | struct CCCL_DEPRECATED random_access_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/numbers.h:34,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/packedstream.h:31,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/bam.cpp:33:
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:77:56: warning: ‘input_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
77 | typedef thrust::input_universal_iterator_tag input_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/iterator_categories.h:217,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:37:
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:37:24: note: declared here
37 | struct CCCL_DEPRECATED input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:78:56: warning: ‘output_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
78 | typedef thrust::output_universal_iterator_tag output_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:51:24: note: declared here
51 | struct CCCL_DEPRECATED output_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:79:56: warning: ‘forward_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
79 | typedef thrust::forward_universal_iterator_tag forward_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:65:24: note: declared here
65 | struct CCCL_DEPRECATED forward_universal_iterator_tag : input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:80:56: warning: ‘bidirectional_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
80 | typedef thrust::bidirectional_universal_iterator_tag bidirectional_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:79:24: note: declared here
79 | struct CCCL_DEPRECATED bidirectional_universal_iterator_tag : forward_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:81:56: warning: ‘random_access_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
81 | typedef thrust::random_access_universal_iterator_tag random_access_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:103:24: note: declared here
103 | struct CCCL_DEPRECATED random_access_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/strided_iterator.h:31,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/reads.h:30,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/reads.cpp:28:
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:77:56: warning: ‘input_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
77 | typedef thrust::input_universal_iterator_tag input_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/iterator_categories.h:217,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:37:
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:37:24: note: declared here
37 | struct CCCL_DEPRECATED input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:78:56: warning: ‘output_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
78 | typedef thrust::output_universal_iterator_tag output_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:51:24: note: declared here
51 | struct CCCL_DEPRECATED output_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:79:56: warning: ‘forward_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
79 | typedef thrust::forward_universal_iterator_tag forward_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:65:24: note: declared here
65 | struct CCCL_DEPRECATED forward_universal_iterator_tag : input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:80:56: warning: ‘bidirectional_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
80 | typedef thrust::bidirectional_universal_iterator_tag bidirectional_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:79:24: note: declared here
79 | struct CCCL_DEPRECATED bidirectional_universal_iterator_tag : forward_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:81:56: warning: ‘random_access_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
81 | typedef thrust::random_access_universal_iterator_tag random_access_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/numbers.h:34,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/threads.h:31,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/contrib/bamtools/BGZF.cpp:15:
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:77:56: warning: ‘input_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
77 | typedef thrust::input_universal_iterator_tag input_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/iterator_categories.h:217,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:37:
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:37:24: note: declared here
37 | struct CCCL_DEPRECATED input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:78:56: warning: ‘output_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
78 | typedef thrust::output_universal_iterator_tag output_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:51:24: note: declared here
51 | struct CCCL_DEPRECATED output_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:79:56: warning: ‘forward_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
79 | typedef thrust::forward_universal_iterator_tag forward_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:65:24: note: declared here
65 | struct CCCL_DEPRECATED forward_universal_iterator_tag : input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:80:56: warning: ‘bidirectional_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
80 | typedef thrust::bidirectional_universal_iterator_tag bidirectional_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:79:24: note: declared here
79 | struct CCCL_DEPRECATED bidirectional_universal_iterator_tag : forward_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:103:24: note: declared here
103 | struct CCCL_DEPRECATED random_access_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:81:56: warning: ‘random_access_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
81 | typedef thrust::random_access_universal_iterator_tag random_access_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:103:24: note: declared here
103 | struct CCCL_DEPRECATED random_access_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/strided_iterator.h:31,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/reads.h:30,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/sam.h:32,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/sam.cpp:33:
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:77:56: warning: ‘input_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
77 | typedef thrust::input_universal_iterator_tag input_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/iterator_categories.h:217,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:37:
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:37:24: note: declared here
37 | struct CCCL_DEPRECATED input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:78:56: warning: ‘output_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
78 | typedef thrust::output_universal_iterator_tag output_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:51:24: note: declared here
51 | struct CCCL_DEPRECATED output_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:79:56: warning: ‘forward_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
79 | typedef thrust::forward_universal_iterator_tag forward_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:65:24: note: declared here
65 | struct CCCL_DEPRECATED forward_universal_iterator_tag : input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:80:56: warning: ‘bidirectional_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
80 | typedef thrust::bidirectional_universal_iterator_tag bidirectional_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:79:24: note: declared here
79 | struct CCCL_DEPRECATED bidirectional_universal_iterator_tag : forward_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:81:56: warning: ‘random_access_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
81 | typedef thrust::random_access_universal_iterator_tag random_access_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:103:24: note: declared here
103 | struct CCCL_DEPRECATED random_access_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/strided_iterator.h:31,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/reads.h:30,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/reads_fastq.h:30,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/io/reads/reads_fastq.cpp:28:
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:77:56: warning: ‘input_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
77 | typedef thrust::input_universal_iterator_tag input_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/iterator_categories.h:217,
from /home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:37:
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:37:24: note: declared here
37 | struct CCCL_DEPRECATED input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:78:56: warning: ‘output_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
78 | typedef thrust::output_universal_iterator_tag output_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:51:24: note: declared here
51 | struct CCCL_DEPRECATED output_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:79:56: warning: ‘forward_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
79 | typedef thrust::forward_universal_iterator_tag forward_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:65:24: note: declared here
65 | struct CCCL_DEPRECATED forward_universal_iterator_tag : input_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:80:56: warning: ‘bidirectional_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
80 | typedef thrust::bidirectional_universal_iterator_tag bidirectional_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:79:24: note: declared here
79 | struct CCCL_DEPRECATED bidirectional_universal_iterator_tag : forward_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/nvbio/basic/iterator.h:81:56: warning: ‘random_access_universal_iterator_tag’ is deprecated [-Wdeprecated-declarations]
81 | typedef thrust::random_access_universal_iterator_tag random_access_universal_iterator_tag;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/targets/x86_64-linux/include/thrust/iterator/detail/universal_categories.h:103:24: note: declared here
103 | struct CCCL_DEPRECATED random_access_universal_iterator_tag
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 59%] Linking CXX static library libbamtools.a
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[ 89%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/seed_hit_deque_array_test.cu.o
[ 90%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/sequence_test.cu.o
[ 90%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/score_best.cu.o
[ 91%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/reduce.cu.o
[ 93%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/scoring_queues_test.cu.o
[ 93%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/wavelet_test.cu.o
[ 93%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/traceback.cu.o
[ 94%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/score_ungapped.cu.o
[ 95%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/select.cu.o
[ 95%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/seed_hit_deque_array.cu.o
[ 96%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/stats.cu.o
[ 96%] Linking CUDA device code CMakeFiles/nvBWT.dir/cmake_device_link.o
[ 97%] Linking CXX executable nvBWT
make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
[ 97%] Built target nvBWT
[ 97%] Linking CUDA device code CMakeFiles/nvbio-test.dir/cmake_device_link.o
[ 98%] Linking CXX executable nvbio-test
make[3]: Leaving directory '/home/biocbuild/bbs-3.22-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-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
[100%] Built target nvBowtie
make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc-gpu/meat/RbowtieCuda/src/nvbio/build'
make[1]: Leaving directory '/home/biocbuild/bbs-3.22-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)
RbowtieCuda.Rcheck/tests/runTests.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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.
[22;32mverbose : cuda devices : 1
[22;32mverbose : device 0 has compute capability 8.9
[22;32mverbose : SM count : 142
[22;32mverbose : SM clock rate : 2520 Mhz
[22;32mverbose : memory clock rate : 9.0 Ghz
[22;32mverbose : chosen device 0
[22;32mverbose : device name : NVIDIA L40S
[22;32mverbose : compute capability : 8.9
[22;37minfo : alloc test... started
[22;37minfo : 1 MB:
[22;37minfo : cuda malloc : 0.07 ms, 14.888 GB/s
[22;37minfo : cuda free : 0.06 ms, 16.729 GB/s
[22;37minfo : malloc : 0.00 ms, 264.830 GB/s
[22;37minfo : free : 0.00 ms, 325.521 GB/s
[22;37minfo : 4 MB:
[22;37minfo : cuda malloc : 0.07 ms, 52.743 GB/s
[22;37minfo : cuda free : 0.06 ms, 66.278 GB/s
[22;37minfo : malloc : 0.00 ms, 961.538 GB/s
[22;37minfo : free : 0.00 ms, 1000.000 GB/s
[22;37minfo : 16 MB:
[22;37minfo : cuda malloc : 0.30 ms, 52.598 GB/s
[22;37minfo : cuda free : 0.07 ms, 226.449 GB/s
[22;37minfo : malloc : 0.00 ms, 3333.333 GB/s
[22;37minfo : free : 0.00 ms, 4901.959 GB/s
[22;37minfo : 64 MB:
[22;37minfo : cuda malloc : 0.99 ms, 62.962 GB/s
[22;37minfo : cuda free : 0.27 ms, 228.154 GB/s
[22;37minfo : malloc : 0.01 ms, 4926.107 GB/s
[22;37minfo : free : 0.01 ms, 6153.846 GB/s
[22;37minfo : 256 MB:
[22;37minfo : cuda malloc : 0.84 ms, 296.000 GB/s
[22;37minfo : cuda free : 1.20 ms, 208.046 GB/s
[22;37minfo : malloc : 0.01 ms, 18912.525 GB/s
[22;37minfo : free : 0.01 ms, 21505.379 GB/s
[22;37minfo : 1024 MB:
[22;37minfo : cuda malloc : 1.52 ms, 656.289 GB/s
[22;37minfo : cuda free : 2.66 ms, 375.843 GB/s
[22;37minfo : malloc : 0.01 ms, 70021.898 GB/s
[22;37minfo : free : 0.01 ms, 70329.664 GB/s
[22;37minfo : alloc test... done
[01;31merror : caught a std::runtime_error exception:
[01;31merror : parallel_for failed: cudaErrorUnsupportedPtxVersion: the provided PTX was compiled with an unsupported toolchain.
RUNIT TEST PROTOCOL -- Thu Jun 19 14:00:40 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
0.215 0.597 0.809
RbowtieCuda.Rcheck/RbowtieCuda-Ex.timings
| name | user | system | elapsed | |
| dot-callbinary2 | 0.004 | 0.004 | 0.011 | |
| nvBWT | 0.038 | 0.243 | 0.288 | |
| nvBowtie | 0.039 | 0.343 | 0.392 | |
| nvBowtie_usage | 0.006 | 0.001 | 0.020 | |
| nvBowtie_version | 0.004 | 0.003 | 0.007 | |
| nvbio_tests | 0.063 | 0.604 | 0.676 | |