* installing *source* package ‘tiledb’ ...
** this is package ‘tiledb’ version ‘0.32.0’
** 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 /usr/local/clang21/bin/clang++ -std=gnu++17 accepts -g... yes
checking for /usr/local/clang21/bin/clang++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... /usr/local/clang21/bin/clang++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether /usr/local/clang21/bin/clang++ -std=gnu++17 accepts -g... (cached) yes
checking for /usr/local/clang21/bin/clang++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking whether /usr/local/clang21/bin/clang++ -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 Fedora Linux:42...
downloading https://github.com/TileDB-Inc/TileDB/releases/download/2.28.0/tiledb-linux-x86_64-noavx2-2.28.0-4764907.tar.gz
using inst/tiledb/{lib,include}
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘clang version 21.1.0-rc3’
using C++ compiler: ‘clang version 21.1.0-rc3’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/tiledb/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c arrowio.cpp -o arrowio.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c batched.cpp -o batched.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c column_buffer.cpp -o column_buffer.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c deprecation.cpp -o deprecation.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c durations.cpp -o durations.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c libtiledb.cpp -o libtiledb.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c nanoarrow.c -o nanoarrow.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c nullable.cpp -o nullable.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c shmem.cpp -o shmem.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c virtualfile.cpp -o virtualfile.o
/usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -DTILEDB_SILENT_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppInt64/include' -I'/data/gannet/ripley/R/test-clang/nanoarrow/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c connection/connection.c -o connection/connection.o
virtualfile.cpp:104:7: warning: variable 'description' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
104 | if (TYPEOF(description_) == STRSXP) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
virtualfile.cpp:129:36: note: uninitialized use occurs here
129 | SEXP rc = PROTECT(new_connection(description, "rb", "vfile", &con));
| ^~~~~~~~~~~
virtualfile.cpp:104:3: note: remove the 'if' if its condition is always true
104 | if (TYPEOF(description_) == STRSXP) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
105 | vstate->is_file = TRUE;
106 | description = (char *)CHAR(STRING_ELT(description_, 0));
107 | spdl::debug(tfm::format("[vfile_c_impl_] file %s", description));
108 | vstate->uri = description;
109 | } else {
| ~~~~~~
110 | /* vstate->is_file = FALSE; */
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
111 | /* description = "vfile(connection)"; */
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
112 | /* vstate->inner = R_GetConnection(description_); */
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
113 | /* if (vstate->inner->isopen) { */
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
114 | /* error("vfile_(): inner connection must not already be open"); */
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
115 | /* } */
| ~~~~~~~
116 | /* // Ensure we start with EOF not set, as this is not zeroed in all cases
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
117 | */
| ~~
118 | /* // within R/connections.c */
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
119 | /* vstate->inner->EOF_signalled = FALSE; */
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
virtualfile.cpp:103:20: note: initialize the variable 'description' to silence this warning
103 | char *description;
| ^
| = nullptr
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o tiledb.so RcppExports.o arrowio.o batched.o column_buffer.o deprecation.o durations.o libtiledb.o nanoarrow.o nullable.o shmem.o virtualfile.o -ltiledb -L../inst/tiledb/lib -Wl,-rpath,$ORIGIN/../tiledb/lib
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/tiledb/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/tiledb/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/tiledb/src'
installing to /data/gannet/ripley/R/packages/tests-clang/tiledb.Rcheck/00LOCK-tiledb/00new/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 (tiledb)