* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘tiledb’ ...
** package ‘tiledb’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++-13 -std=gnu++17 accepts -g... yes
checking for g++-13 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++-13 -std=gnu++17 accepts -g... (cached) yes
checking for g++-13 -std=gnu++17 option to enable C++11 features... (cached) none needed
checking whether g++-13 -std=gnu++17 supports C++17 features by default... yes
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows TileDB... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for filesystem... yes
checking for tiledb/tiledb... no
downloading x86_64 TileDB library...
installing TileDB for Debian GNU/Linux:...
downloading https://github.com/TileDB-Inc/TileDB/releases/download/2.22.0/tiledb-linux-x86_64-noavx2-2.22.0-52e981e.tar.gz
using inst/tiledb/{lib,include}
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
using C++17
make[1]: Entering directory '/tmp/RtmpsdtmgY/R.INSTALL2b850018f1b5bc/tiledb/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c arrowio.cpp -o arrowio.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c batched.cpp -o batched.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c column_buffer.cpp -o column_buffer.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c deprecation.cpp -o deprecation.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c durations.cpp -o durations.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c libtiledb.cpp -o libtiledb.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nanoarrow.c -o nanoarrow.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nullable.cpp -o nullable.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppInt64/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/nanoarrow/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c shmem.cpp -o shmem.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o tiledb.so RcppExports.o arrowio.o batched.o column_buffer.o deprecation.o durations.o libtiledb.o nanoarrow.o nullable.o shmem.o -ltiledb -L../inst/tiledb/lib -Wl,-rpath,$ORIGIN/../tiledb/lib -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpsdtmgY/R.INSTALL2b850018f1b5bc/tiledb/src'
make[1]: Entering directory '/tmp/RtmpsdtmgY/R.INSTALL2b850018f1b5bc/tiledb/src'
make[1]: Leaving directory '/tmp/RtmpsdtmgY/R.INSTALL2b850018f1b5bc/tiledb/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-tiledb/00new/tiledb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘tiledb’
finding HTML links ... done
array_consolidate html
array_vacuum html
as.data.frame.tiledb_config html
as.vector.tiledb_config html
attrs-set-tiledb_array-method html
attrs-tiledb_array-ANY-method html
attrs-tiledb_array_schema-ANY-method html
attrs-tiledb_array_schema-character-method
html
attrs-tiledb_array_schema-numeric-method
html
cell_order-tiledb_array_schema-method html
completedBatched html
config-tiledb_ctx-method html
createBatched html
datatype-tiledb_attr-method html
datatype-tiledb_dim-method html
datatype-tiledb_domain-method html
datetimes_as_int64-set-tiledb_array-method
html
datetimes_as_int64-tiledb_array-method
html
describe html
dim.tiledb_array_schema html
dim.tiledb_dim html
dim.tiledb_domain html
dimensions-tiledb_array_schema-method html
dimensions-tiledb_domain-method html
domain-tiledb_array_schema-method html
domain-tiledb_dim-method html
extended-set-tiledb_array-method html
extended-tiledb_array-method html
fetchBatched html
filter_list-set-tiledb_attr-method html
filter_list-set-tiledb_dim-method html
filter_list-tiledb_array_schema-method
html
filter_list-tiledb_attr-method html
filter_list-tiledb_dim-method html
fromDataFrame html
fromMatrix html
fromSparseMatrix html
generics html
has_attribute html
is.anonymous html
is.anonymous.tiledb_dim html
is.integral-tiledb_domain-method html
is.sparse-tiledb_array_schema-method html
limitTileDBCores html
name-tiledb_attr-method html
name-tiledb_dim-method html
nfilters-tiledb_filter_list-method html
parse_query_condition html
print.tiledb_metadata html
query_condition-set-tiledb_array-method
html
query_condition-tiledb_array-method html
query_layout-set-tiledb_array-method html
query_layout-tiledb_array-method html
query_statistics-set-tiledb_array-method
html
query_statistics-tiledb_array-method html
r_to_tiledb_type html
raw_dump-tiledb_array_schema-method html
raw_dump-tiledb_attr-method html
raw_dump-tiledb_domain-method html
return.array-set-tiledb_array-method html
return.array-tiledb_array-method html
return.data.frame-set-tiledb_array-method
html
return.data.frame-tiledb_array-method html
return.matrix-set-tiledb_array-method html
return.matrix-tiledb_array-method html
return_as-set-tiledb_array-method html
return_as-tiledb_array-method html
save_allocation_size_preference html
save_return_as_preference html
schema-character-method html
schema-tiledb_array-method html
selected_points-set-tiledb_array-method
html
selected_points-tiledb_array-method html
selected_ranges-set-tiledb_array-method
html
selected_ranges-tiledb_array-method html
show-tiledb_array-method html
show-tiledb_array_schema-method html
show-tiledb_attr-method html
show-tiledb_config-method html
show-tiledb_dim-method html
show-tiledb_domain-method html
show-tiledb_filter-method html
show-tiledb_filter_list-method html
show-tiledb_group-method html
statusBatched html
strings_as_factors-set-tiledb_array-method
html
strings_as_factors-tiledb_array-method
html
sub-tiledb_array-ANY-method html
sub-tiledb_config-ANY-method html
sub-tiledb_filter_list-ANY-method html
subset-tiledb_array-ANY-ANY-ANY-method
html
subset-tiledb_config-ANY-ANY-ANY-method
html
tdb_collect-tiledb_array-method html
tdb_filter-tiledb_array-method html
tdb_select-tiledb_array-method html
tile-tiledb_dim-method html
tile_order-tiledb_array_schema-method html
tiledb-package html
tiledb_array-class html
tiledb_array html
tiledb_array_apply_aggregate html
tiledb_array_close html
tiledb_array_create html
tiledb_array_delete_fragments html
tiledb_array_get_non_empty_domain_from_index
html
tiledb_array_get_non_empty_domain_from_name
html
tiledb_array_has_enumeration html
tiledb_array_is_heterogeneous html
tiledb_array_is_homogeneous html
tiledb_array_is_open html
tiledb_array_open html
tiledb_array_open_at html
tiledb_array_schema-class html
tiledb_array_schema html
tiledb_array_schema_check html
tiledb_array_schema_evolution-class html
tiledb_array_schema_evolution html
tiledb_array_schema_evolution_add_attribute
html
tiledb_array_schema_evolution_add_enumeration
html
tiledb_array_schema_evolution_add_enumeration_empty
html
tiledb_array_schema_evolution_array_evolve
html
tiledb_array_schema_evolution_drop_attribute
html
tiledb_array_schema_evolution_drop_enumeration
html
tiledb_array_schema_evolution_extend_enumeration
html
tiledb_array_schema_get_allows_dups html
tiledb_array_schema_get_capacity html
tiledb_array_schema_set_allows_dups html
tiledb_array_schema_set_capacity html
tiledb_array_schema_set_coords_filter_list
html
tiledb_array_schema_set_enumeration_empty
html
tiledb_array_schema_set_offsets_filter_list
html
tiledb_array_schema_set_validity_filter_list
html
tiledb_array_schema_version html
tiledb_array_upgrade_version html
tiledb_arrow_array_ptr html
tiledb_attr-class html
tiledb_attr html
tiledb_attribute_get_cell_size html
tiledb_attribute_get_cell_val_num html
tiledb_attribute_get_enumeration html
tiledb_attribute_get_fill_value html
tiledb_attribute_get_nullable html
tiledb_attribute_has_enumeration html
tiledb_attribute_is_ordered_enumeration_ptr
html
tiledb_attribute_is_variable_sized html
tiledb_attribute_set_cell_val_num html
tiledb_attribute_set_enumeration_name html
tiledb_attribute_set_fill_value html
tiledb_attribute_set_nullable html
tiledb_config-class html
tiledb_config html
tiledb_config_as_built_json html
tiledb_config_as_built_show html
tiledb_config_load html
tiledb_config_save html
tiledb_config_unset html
tiledb_ctx-class html
tiledb_ctx html
tiledb_ctx_set_default_tags html
tiledb_ctx_set_tag html
tiledb_ctx_stats html
tiledb_datatype_R_type html
tiledb_delete_metadata html
tiledb_dim-class html
tiledb_dim html
tiledb_dim_get_cell_val_num html
tiledb_domain-class html
tiledb_domain html
tiledb_domain_get_dimension_from_index
html
tiledb_domain_get_dimension_from_name html
tiledb_domain_has_dimension html
tiledb_error_message html
tiledb_filestore_buffer_export html
tiledb_filestore_buffer_import html
tiledb_filestore_schema_create html
tiledb_filestore_size html
tiledb_filestore_uri_export html
tiledb_filestore_uri_import html
tiledb_filter-class html
tiledb_filter html
tiledb_filter_get_option html
tiledb_filter_list-class html
tiledb_filter_list html
tiledb_filter_list_get_max_chunk_size html
tiledb_filter_list_set_max_chunk_size html
tiledb_filter_set_option html
tiledb_filter_type html
tiledb_fragment_info-class html
tiledb_fragment_info html
tiledb_fragment_info_dense html
tiledb_fragment_info_dump html
tiledb_fragment_info_get_cell_num html
tiledb_fragment_info_get_non_empty_domain_index
html
tiledb_fragment_info_get_non_empty_domain_name
html
tiledb_fragment_info_get_non_empty_domain_var_index
html
tiledb_fragment_info_get_non_empty_domain_var_name
html
tiledb_fragment_info_get_num html
tiledb_fragment_info_get_size html
tiledb_fragment_info_get_timestamp_range
html
tiledb_fragment_info_get_to_vacuum_num
html
tiledb_fragment_info_get_to_vacuum_uri
html
tiledb_fragment_info_get_unconsolidated_metadata_num
html
tiledb_fragment_info_get_version html
tiledb_fragment_info_has_consolidated_metadata
html
tiledb_fragment_info_sparse html
tiledb_fragment_info_uri html
tiledb_get_all_metadata html
tiledb_get_context html
tiledb_get_metadata html
tiledb_get_query_status html
tiledb_get_vfs html
tiledb_group-class html
tiledb_group html
tiledb_group_add_member html
tiledb_group_close html
tiledb_group_create html
tiledb_group_delete_metadata html
tiledb_group_get_all_metadata html
tiledb_group_get_config html
tiledb_group_get_metadata html
tiledb_group_get_metadata_from_index html
tiledb_group_has_metadata html
tiledb_group_is_open html
tiledb_group_is_relative html
tiledb_group_member html
tiledb_group_member_count html
tiledb_group_member_dump html
tiledb_group_metadata_num html
tiledb_group_open html
tiledb_group_put_metadata html
tiledb_group_query_type html
tiledb_group_remove_member html
tiledb_group_set_config html
tiledb_group_uri html
tiledb_has_metadata html
tiledb_is_supported_fs html
tiledb_ndim-tiledb_array_schema-method
html
tiledb_ndim-tiledb_dim-method html
tiledb_ndim-tiledb_domain-method html
tiledb_num_metadata html
tiledb_object_ls html
tiledb_object_mv html
tiledb_object_rm html
tiledb_object_type html
tiledb_object_walk html
tiledb_put_metadata html
tiledb_query-class html
tiledb_query html
tiledb_query_add_range html
tiledb_query_add_range_with_type html
tiledb_query_alloc_buffer_ptr_char html
tiledb_query_apply_aggregate html
tiledb_query_buffer_alloc_ptr html
tiledb_query_condition-class html
tiledb_query_condition html
tiledb_query_condition_combine html
tiledb_query_condition_create html
tiledb_query_condition_init html
tiledb_query_condition_set_use_enumeration
html
tiledb_query_create_buffer_ptr html
tiledb_query_create_buffer_ptr_char html
tiledb_query_ctx html
tiledb_query_export_buffer html
tiledb_query_finalize html
tiledb_query_get_buffer_char html
tiledb_query_get_buffer_ptr html
tiledb_query_get_est_result_size html
tiledb_query_get_est_result_size_var html
tiledb_query_get_fragment_num html
tiledb_query_get_fragment_timestamp_range
html
tiledb_query_get_fragment_uri html
tiledb_query_get_layout html
tiledb_query_get_range html
tiledb_query_get_range_num html
tiledb_query_get_range_var html
tiledb_query_import_buffer html
tiledb_query_result_buffer_elements html
tiledb_query_result_buffer_elements_vec
html
tiledb_query_set_buffer html
tiledb_query_set_buffer_ptr html
tiledb_query_set_buffer_ptr_char html
tiledb_query_set_condition html
tiledb_query_set_layout html
tiledb_query_set_subarray html
tiledb_query_stats html
tiledb_query_status html
tiledb_query_submit html
tiledb_query_submit_async html
tiledb_query_type html
tiledb_schema_get_dim_attr_status html
tiledb_schema_get_enumeration_status html
tiledb_schema_get_names html
tiledb_schema_get_types html
tiledb_schema_object html
tiledb_set_context html
tiledb_set_vfs html
tiledb_stats_disable html
tiledb_stats_dump html
tiledb_stats_enable html
tiledb_stats_print html
tiledb_stats_raw_dump html
tiledb_stats_raw_get html
tiledb_stats_raw_print html
tiledb_stats_reset html
tiledb_subarray-class html
tiledb_subarray html
tiledb_subarray_to_query html
tiledb_version html
tiledb_vfs-class html
tiledb_vfs html
tiledb_vfs_close html
tiledb_vfs_copy_file html
tiledb_vfs_create_bucket html
tiledb_vfs_create_dir html
tiledb_vfs_dir_size html
tiledb_vfs_empty_bucket html
tiledb_vfs_file_size html
tiledb_vfs_is_bucket html
tiledb_vfs_is_dir html
tiledb_vfs_is_empty_bucket html
tiledb_vfs_is_file html
tiledb_vfs_ls html
tiledb_vfs_ls_recursive html
tiledb_vfs_move_dir html
tiledb_vfs_move_file html
tiledb_vfs_open html
tiledb_vfs_read html
tiledb_vfs_remove_bucket html
tiledb_vfs_remove_dir html
tiledb_vfs_remove_file html
tiledb_vfs_serialize html
tiledb_vfs_sync html
tiledb_vfs_touch html
tiledb_vfs_unserialize html
tiledb_vfs_write html
** 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 (tiledb)