Aaron Lun
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/beachmat.tiledb |
| git_branch: devel |
| git_last_commit: c0c20e1 |
| git_last_commit_date: 2025-07-14 01:24:42 -0400 (Mon, 14 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:03 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 158/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beachmat.tiledb 1.1.1 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | NA | NA | ||||||||||
|
To the developers/maintainers of the beachmat.tiledb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/beachmat.tiledb.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: beachmat.tiledb |
| Version: 1.1.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:beachmat.tiledb.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings beachmat.tiledb_1.1.1.tar.gz |
| StartedAt: 2025-10-24 21:29:50 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 21:32:29 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 158.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: beachmat.tiledb.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:beachmat.tiledb.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings beachmat.tiledb_1.1.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/beachmat.tiledb.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘beachmat.tiledb/DESCRIPTION’ ... OK
* this is package ‘beachmat.tiledb’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘beachmat.tiledb’ can be installed ... WARNING
Found the following significant warnings:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:489:30: warning: ‘int32_t tiledb_attribute_dump(tiledb_ctx_t*, const tiledb_attribute_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h:409:30: warning: ‘int32_t tiledb_dimension_dump(tiledb_ctx_t*, const tiledb_dimension_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:167:40: warning: ‘int32_t tiledb_domain_dump(tiledb_ctx_t*, const tiledb_domain_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:170:33: warning: ‘capi_return_t tiledb_array_schema_dump(tiledb_ctx_t*, const tiledb_array_schema_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.22-bioc/meat/beachmat.tiledb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 37.3Mb
sub-directories of 1Mb or more:
libs 37.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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, 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/beachmat.tiledb.Rcheck/00check.log’
for details.
beachmat.tiledb.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL beachmat.tiledb
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘beachmat.tiledb’ ...
** this is package ‘beachmat.tiledb’ version ‘1.1.1’
** using staged installation
checking if tiledb-R downloaded its own TileDB... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c initialize.cpp -o initialize.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:38,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array.h:38,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb:49,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/tatami_tiledb/utils.hpp:10,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/tatami_tiledb/DenseMatrix.hpp:5,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/tatami_tiledb/tatami_tiledb.hpp:5,
from initialize.cpp:3:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h: In member function ‘void tiledb::Attribute::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:489:30: warning: ‘int32_t tiledb_attribute_dump(tiledb_ctx_t*, const tiledb_attribute_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
489 | tiledb_attribute_dump(ctx_.get().ptr().get(), attr_.get(), out));
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/array_schema_api_external.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/array_api_external.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:58,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/core_interface.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/exception.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/capi_string.h:39,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:38:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../attribute/attribute_api_external.h:309:34: note: declared here
309 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_attribute_dump(
| ^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:41,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:40:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h: In member function ‘void tiledb::Dimension::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h:409:30: warning: ‘int32_t tiledb_dimension_dump(tiledb_ctx_t*, const tiledb_dimension_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
409 | tiledb_dimension_dump(ctx_.get().ptr().get(), dim_.get(), out));
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../domain/domain_api_external.h:34,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/array_schema_api_external.h:39:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../domain/../dimension/dimension_api_external.h:292:34: note: declared here
292 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_dimension_dump(
| ^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h: In member function ‘void tiledb::Domain::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:167:40: warning: ‘int32_t tiledb_domain_dump(tiledb_ctx_t*, const tiledb_domain_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
167 | ctx.handle_error(tiledb_domain_dump(ctx.ptr().get(), domain_.get(), out));
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../domain/domain_api_external.h:227:34: note: declared here
227 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_domain_dump(
| ^~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h: In member function ‘virtual void tiledb::ArraySchema::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:170:33: warning: ‘capi_return_t tiledb_array_schema_dump(tiledb_ctx_t*, const tiledb_array_schema_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
170 | tiledb_array_schema_dump(ctx.ptr().get(), schema_.get(), out));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb_deprecated.h:39,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:1529:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array_schema/array_schema_api_deprecated.h:59:40: note: declared here
59 | TILEDB_DEPRECATED_EXPORT capi_return_t tiledb_array_schema_dump(
| ^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c load_dense.cpp -o load_dense.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:38,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array.h:38,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb:49,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/tatami_tiledb/utils.hpp:10,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/tatami_tiledb/DenseMatrix.hpp:5,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/tatami_tiledb/tatami_tiledb.hpp:5,
from load_dense.cpp:2:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h: In member function ‘void tiledb::Attribute::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:489:30: warning: ‘int32_t tiledb_attribute_dump(tiledb_ctx_t*, const tiledb_attribute_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
489 | tiledb_attribute_dump(ctx_.get().ptr().get(), attr_.get(), out));
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/array_schema_api_external.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/array_api_external.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:58,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/core_interface.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/exception.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/capi_string.h:39,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:38:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../attribute/attribute_api_external.h:309:34: note: declared here
309 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_attribute_dump(
| ^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:41,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:40:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h: In member function ‘void tiledb::Dimension::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h:409:30: warning: ‘int32_t tiledb_dimension_dump(tiledb_ctx_t*, const tiledb_dimension_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
409 | tiledb_dimension_dump(ctx_.get().ptr().get(), dim_.get(), out));
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../domain/domain_api_external.h:34,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/array_schema_api_external.h:39:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../domain/../dimension/dimension_api_external.h:292:34: note: declared here
292 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_dimension_dump(
| ^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h: In member function ‘void tiledb::Domain::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:167:40: warning: ‘int32_t tiledb_domain_dump(tiledb_ctx_t*, const tiledb_domain_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
167 | ctx.handle_error(tiledb_domain_dump(ctx.ptr().get(), domain_.get(), out));
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../domain/domain_api_external.h:227:34: note: declared here
227 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_domain_dump(
| ^~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h: In member function ‘virtual void tiledb::ArraySchema::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:170:33: warning: ‘capi_return_t tiledb_array_schema_dump(tiledb_ctx_t*, const tiledb_array_schema_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
170 | tiledb_array_schema_dump(ctx.ptr().get(), schema_.get(), out));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb_deprecated.h:39,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:1529:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array_schema/array_schema_api_deprecated.h:59:40: note: declared here
59 | TILEDB_DEPRECATED_EXPORT capi_return_t tiledb_array_schema_dump(
| ^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c load_sparse.cpp -o load_sparse.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:38,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array.h:38,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb:49,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/tatami_tiledb/utils.hpp:10,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/tatami_tiledb/DenseMatrix.hpp:5,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/tatami_tiledb/tatami_tiledb.hpp:5,
from load_sparse.cpp:2:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h: In member function ‘void tiledb::Attribute::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:489:30: warning: ‘int32_t tiledb_attribute_dump(tiledb_ctx_t*, const tiledb_attribute_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
489 | tiledb_attribute_dump(ctx_.get().ptr().get(), attr_.get(), out));
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/array_schema_api_external.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/array_api_external.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:58,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/core_interface.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/exception.h:37,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/capi_string.h:39,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:38:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../attribute/attribute_api_external.h:309:34: note: declared here
309 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_attribute_dump(
| ^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:41,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:40:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h: In member function ‘void tiledb::Dimension::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h:409:30: warning: ‘int32_t tiledb_dimension_dump(tiledb_ctx_t*, const tiledb_dimension_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
409 | tiledb_dimension_dump(ctx_.get().ptr().get(), dim_.get(), out));
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../domain/domain_api_external.h:34,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/array_schema_api_external.h:39:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../domain/../dimension/dimension_api_external.h:292:34: note: declared here
292 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_dimension_dump(
| ^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h: In member function ‘void tiledb::Domain::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:167:40: warning: ‘int32_t tiledb_domain_dump(tiledb_ctx_t*, const tiledb_domain_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
167 | ctx.handle_error(tiledb_domain_dump(ctx.ptr().get(), domain_.get(), out));
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array/../array_schema/../domain/domain_api_external.h:227:34: note: declared here
227 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_domain_dump(
| ^~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h: In member function ‘virtual void tiledb::ArraySchema::dump(FILE*) const’:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:170:33: warning: ‘capi_return_t tiledb_array_schema_dump(tiledb_ctx_t*, const tiledb_array_schema_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
170 | tiledb_array_schema_dump(ctx.ptr().get(), schema_.get(), out));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb_deprecated.h:39,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:1529:
/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/array_schema/array_schema_api_deprecated.h:59:40: note: declared here
59 | TILEDB_DEPRECATED_EXPORT capi_return_t tiledb_array_schema_dump(
| ^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o beachmat.tiledb.so RcppExports.o initialize.o load_dense.o load_sparse.o -ltiledb -L/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/lib -L/home/biocbuild/bbs-3.22-bioc/R/site-library/tiledb/tiledb/lib -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-beachmat.tiledb/00new/beachmat.tiledb/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (beachmat.tiledb)
beachmat.tiledb.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "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.
> library(beachmat.tiledb)
> library(testthat)
> test_check("beachmat.tiledb")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 154 ]
>
> proc.time()
user system elapsed
9.713 6.072 12.660
beachmat.tiledb.Rcheck/beachmat.tiledb-Ex.timings
| name | user | system | elapsed | |
| initializeCpp | 0.231 | 0.036 | 0.259 | |
| initializeOptions | 0.000 | 0.000 | 0.001 | |
| loadIntoMemory | 0.262 | 0.045 | 0.282 | |