############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL beachmat.tiledb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘beachmat.tiledb’ ... ** this is package ‘beachmat.tiledb’ version ‘0.99.1’ ** 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-3.21-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -c initialize.cpp -o initialize.o In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:38, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array.h:38, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb:49, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_tiledb/DenseMatrix.hpp:5, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_tiledb/tatami_tiledb.hpp:5, from initialize.cpp:3: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h: In member function ‘void tiledb::Attribute::dump(FILE*) const’: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:488:30: warning: ‘int32_t tiledb_attribute_dump(tiledb_ctx_t*, const tiledb_attribute_t*, FILE*)’ is deprecated [-Wdeprecated-declarations] 488 | tiledb_attribute_dump(ctx_.get().ptr().get(), attr_.get(), out)); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:58, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/core_interface.h:37, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/exception.h:37, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/capi_string.h:39, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:38: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/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-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:41, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:40: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h: In member function ‘void tiledb::Dimension::dump(FILE*) const’: /home/biocbuild/bbs-3.21-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-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:65: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/dimension/dimension_api_external.h:292:34: note: declared here 292 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_dimension_dump( | ^~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h: In member function ‘void tiledb::Domain::dump(FILE*) const’: /home/biocbuild/bbs-3.21-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)); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:66: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/domain/domain_api_external.h:227:34: note: declared here 227 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_domain_dump( | ^~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h: In member function ‘virtual void tiledb::ArraySchema::dump(FILE*) const’: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:170:33: warning: ‘int32_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-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:4409: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb_deprecated.h:61:34: note: declared here 61 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_array_schema_dump( | ^~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -c load_dense.cpp -o load_dense.o In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:38, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array.h:38, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb:49, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_tiledb/DenseMatrix.hpp:5, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_tiledb/tatami_tiledb.hpp:5, from load_dense.cpp:2: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h: In member function ‘void tiledb::Attribute::dump(FILE*) const’: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:488:30: warning: ‘int32_t tiledb_attribute_dump(tiledb_ctx_t*, const tiledb_attribute_t*, FILE*)’ is deprecated [-Wdeprecated-declarations] 488 | tiledb_attribute_dump(ctx_.get().ptr().get(), attr_.get(), out)); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:58, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/core_interface.h:37, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/exception.h:37, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/capi_string.h:39, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:38: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/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-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:41, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:40: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h: In member function ‘void tiledb::Dimension::dump(FILE*) const’: /home/biocbuild/bbs-3.21-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-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:65: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/dimension/dimension_api_external.h:292:34: note: declared here 292 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_dimension_dump( | ^~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h: In member function ‘void tiledb::Domain::dump(FILE*) const’: /home/biocbuild/bbs-3.21-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)); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:66: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/domain/domain_api_external.h:227:34: note: declared here 227 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_domain_dump( | ^~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h: In member function ‘virtual void tiledb::ArraySchema::dump(FILE*) const’: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:170:33: warning: ‘int32_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-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:4409: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb_deprecated.h:61:34: note: declared here 61 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_array_schema_dump( | ^~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I/usr/local/include -fpic -g -O2 -c load_sparse.cpp -o load_sparse.o In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:38, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array.h:38, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb:49, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_tiledb/DenseMatrix.hpp:5, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_tiledb/tatami_tiledb.hpp:5, from load_sparse.cpp:2: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h: In member function ‘void tiledb::Attribute::dump(FILE*) const’: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:488:30: warning: ‘int32_t tiledb_attribute_dump(tiledb_ctx_t*, const tiledb_attribute_t*, FILE*)’ is deprecated [-Wdeprecated-declarations] 488 | tiledb_attribute_dump(ctx_.get().ptr().get(), attr_.get(), out)); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:58, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/core_interface.h:37, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/exception.h:37, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/capi_string.h:39, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:38: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/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-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:41, from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:40: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h: In member function ‘void tiledb::Dimension::dump(FILE*) const’: /home/biocbuild/bbs-3.21-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-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:65: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/dimension/dimension_api_external.h:292:34: note: declared here 292 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_dimension_dump( | ^~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h: In member function ‘void tiledb::Domain::dump(FILE*) const’: /home/biocbuild/bbs-3.21-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)); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:66: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/api/c_api/domain/domain_api_external.h:227:34: note: declared here 227 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_domain_dump( | ^~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h: In member function ‘virtual void tiledb::ArraySchema::dump(FILE*) const’: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:170:33: warning: ‘int32_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-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb.h:4409: /home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/tiledb_deprecated.h:61:34: note: declared here 61 | TILEDB_DEPRECATED_EXPORT int32_t tiledb_array_schema_dump( | ^~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/site-library/tiledb/lib -L/home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/lib -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-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)