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[Bug] Can't install tiledbsoma for R on Fedora 40 #3390

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rcannood opened this issue Nov 26, 2024 · 3 comments
Open

[Bug] Can't install tiledbsoma for R on Fedora 40 #3390

rcannood opened this issue Nov 26, 2024 · 3 comments
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@johnkerl

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@rcannood
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rcannood commented Nov 26, 2024 •
edited
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Describe the bug

I can't install tiledbsoma in R. When I try to do so I get:

install.packages('tiledbsoma', repos = c('https://tiledb-inc.r-universe.dev',
                                         'https://cloud.r-project.org'))
In file included from RcppExports.cpp:4:
../inst/include/tiledbsoma_types.h:20:10: fatal error: nanoarrow/nanoarrow.h: No such file or directory
   20 | #include <nanoarrow/nanoarrow.h>            // for C interface to Arrow
      |          ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib64/R/etc/Makeconf:204: RcppExports.o] Error 1
ERROR: compilation failed for package ‘tiledbsoma’

I am able to install the nanoarrow R package via install.packages("nanoarrow"), but I don't think this is related.

Full log 
> install.packages('tiledbsoma', repos = c('https://tiledb-inc.r-universe.dev',
                                         'https://cloud.r-project.org'))
Installing package into ‘/home/rcannood/R/x86_64-redhat-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://tiledb-inc.r-universe.dev/src/contrib/tiledbsoma_1.14.5.tar.gz'
Content type 'application/gzip' length 1005216 bytes (981 KB)
==================================================
downloaded 981 KB

* installing *source* package ‘tiledbsoma’ ...
** using staged installation
-- Install prefix is /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/inst/tiledbsoma.
-- The C compiler identification is GNU 14.2.1
-- The CXX compiler identification is GNU 14.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - 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/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Starting TileDB-SOMA superbuild.
-- Could NOT find TileDB (missing: TileDB_DIR)
-- Adding TileDB as an external project
-- Could NOT find spdlog (missing: spdlog_DIR)
-- Adding spdlog as an external project
-- Not found clang-tidy
-- Not found clang-format
-- Configuring done (0.5s)
-- Generating done (0.0s)
-- Build files have been written to: /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib
[  4%] Creating directories for 'ep_tiledb'
[  8%] Performing download step (download, verify and extract) for 'ep_tiledb'
-- ep_tiledb download command succeeded.  See also /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/src/ep_tiledb-stamp/ep_tiledb-download-*.log
[ 12%] No update step for 'ep_tiledb'
[ 16%] No patch step for 'ep_tiledb'
[ 20%] No configure step for 'ep_tiledb'
[ 24%] No build step for 'ep_tiledb'
[ 28%] Performing install step for 'ep_tiledb'
[ 32%] No test step for 'ep_tiledb'
[ 36%] Completed 'ep_tiledb'
[ 36%] Built target ep_tiledb
[ 40%] Creating directories for 'ep_spdlog'
[ 44%] Performing download step (download, verify and extract) for 'ep_spdlog'
-- ep_spdlog download command succeeded.  See also /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/src/ep_spdlog-stamp/ep_spdlog-download-*.log
[ 48%] No update step for 'ep_spdlog'
[ 52%] Performing patch step for 'ep_spdlog'
patching file include/spdlog/logger-inl.h
[ 56%] Performing configure step for 'ep_spdlog'
-- ep_spdlog configure command succeeded.  See also /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/src/ep_spdlog-stamp/ep_spdlog-configure-*.log
[ 60%] Performing build step for 'ep_spdlog'
-- ep_spdlog build command succeeded.  See also /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/src/ep_spdlog-stamp/ep_spdlog-build-*.log
[ 64%] Performing install step for 'ep_spdlog'
-- ep_spdlog install command succeeded.  See also /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/src/ep_spdlog-stamp/ep_spdlog-install-*.log
[ 68%] Completed 'ep_spdlog'
[ 68%] Built target ep_spdlog
[ 72%] Creating directories for 'libtiledbsoma'
[ 76%] No download step for 'libtiledbsoma'
[ 80%] No update step for 'libtiledbsoma'
[ 84%] No patch step for 'libtiledbsoma'
[ 88%] Performing configure step for 'libtiledbsoma'
-- Install prefix is /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/inst/tiledbsoma.
-- The C compiler identification is GNU 14.2.1
-- The CXX compiler identification is GNU 14.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - 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/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Starting TileDB-SOMA regular build.
-- Performing Test HAVE_AVX2
-- Performing Test HAVE_AVX2 - Success
-- Found TileDB: /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/lib/libtiledb.so.2.26
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Starting TileDB-SOMA build.
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Configuring done (1.4s)
-- Generating done (0.0s)
-- Build files have been written to: /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/libtiledbsoma
[ 92%] Performing build step for 'libtiledbsoma'
[  4%] Building CXX object src/CMakeFiles/TILEDBSOMA_NANOARROW_OBJECT.dir/external/src/nanoarrow/nanoarrow.c.o
[  4%] Built target TILEDBSOMA_NANOARROW_OBJECT
[  8%] Building CXX object src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/reindexer/reindexer.cc.o
In file included from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/fmt.h:24,
                 from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/common.h:45,
                 from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/spdlog.h:12,
                 from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/src/utils/logger.h:54,
                 from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/src/reindexer/reindexer.cc:41:
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h: In instantiation of ‘constexpr fmt::v8::detail::value<Context> fmt::v8::detail::make_arg(T&&) [with bool IS_PACKED = true; Context = fmt::v8::basic_format_context<fmt::v8::appender, char>; type <anonymous> = fmt::v8::detail::type::string_type; T = fmt::v8::basic_string_view<char>&; typename std::enable_if<IS_PACKED, int>::type <anonymous> = 0]’:
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:1855:77:   required from ‘constexpr fmt::v8::format_arg_store<Context, Args>::format_arg_store(T&& ...) [with T = {fmt::v8::basic_string_view<char>&, const char (&)[3]}; Context = fmt::v8::basic_format_context<fmt::v8::appender, char>; Args = {fmt::v8::basic_string_view<char>, char [3]}]’
 1853 |         data_{detail::make_arg<
      |               ~~~~~~~~~~~~~~~~~                                              
 1854 |             is_packed, Context,
      |             ~~~~~~~~~~~~~~~~~~~                                              
 1855 |             detail::mapped_type_constant<remove_cvref_t<T>, Context>::value>(
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
 1856 |             std::forward<T>(args))...} {
      |             ~~~~~~~~~~~~~~~~~~~~~~                                           
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:1872:38:   required from ‘OutputIt fmt::v8::format_to(OutputIt, format_string<T ...>, T&& ...) [with OutputIt = appender; T = {basic_string_view<char>&, const char (&)[3]}; typename std::enable_if<detail::is_output_iterator<OutputIt, char>::value, int>::type <anonymous> = 0; format_string<T ...> = basic_format_string<char, basic_string_view<char>&, const char (&)[3]>]’
 1872 |   return {std::forward<Args>(args)...};
      |                                      ^
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/format-inl.h:78:14:   required from here
   78 |     format_to(it, FMT_STRING("{}{}"), message, SEP);
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:3148:52:   in ‘constexpr’ expansion of ‘fmt::v8::make_format_args<>(args#0, args#1)’
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:1706:15: error: possibly dangling reference to a temporary [-Werror=dangling-reference]
 1706 |   const auto& arg = arg_mapper<Context>().map(std::forward<T>(val));
      |               ^~~
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:1706:46: note: the temporary was destroyed at the end of the full expression ‘fmt::v8::detail::arg_mapper<fmt::v8::basic_format_context<fmt::v8::appender, char> >().fmt::v8::detail::arg_mapper<fmt::v8::basic_format_context<fmt::v8::appender, char> >::map<fmt::v8::basic_string_view<char> >((*(const fmt::v8::basic_string_view<char>*)(& std::forward<fmt::v8::basic_string_view<char>&>((* & val)))))’
 1706 |   const auto& arg = arg_mapper<Context>().map(std::forward<T>(val));
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
make[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:76: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/reindexer/reindexer.cc.o] Error 1
make[4]: *** [CMakeFiles/Makefile2:155: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/all] Error 2
make[3]: *** [Makefile:136: all] Error 2
make[2]: *** [CMakeFiles/libtiledbsoma.dir/build.make:86: libtiledbsoma-prefix/src/libtiledbsoma-stamp/libtiledbsoma-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:142: CMakeFiles/libtiledbsoma.dir/all] Error 2
make: *** [Makefile:91: all] Error 2
[  4%] Built target TILEDBSOMA_NANOARROW_OBJECT
[  8%] Building CXX object src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/reindexer/reindexer.cc.o
In file included from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/fmt.h:24,
                 from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/common.h:45,
                 from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/spdlog.h:12,
                 from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/src/utils/logger.h:54,
                 from /tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/src/reindexer/reindexer.cc:41:
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h: In instantiation of ‘constexpr fmt::v8::detail::value<Context> fmt::v8::detail::make_arg(T&&) [with bool IS_PACKED = true; Context = fmt::v8::basic_format_context<fmt::v8::appender, char>; type <anonymous> = fmt::v8::detail::type::string_type; T = fmt::v8::basic_string_view<char>&; typename std::enable_if<IS_PACKED, int>::type <anonymous> = 0]’:
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:1855:77:   required from ‘constexpr fmt::v8::format_arg_store<Context, Args>::format_arg_store(T&& ...) [with T = {fmt::v8::basic_string_view<char>&, const char (&)[3]}; Context = fmt::v8::basic_format_context<fmt::v8::appender, char>; Args = {fmt::v8::basic_string_view<char>, char [3]}]’
 1853 |         data_{detail::make_arg<
      |               ~~~~~~~~~~~~~~~~~                                              
 1854 |             is_packed, Context,
      |             ~~~~~~~~~~~~~~~~~~~                                              
 1855 |             detail::mapped_type_constant<remove_cvref_t<T>, Context>::value>(
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
 1856 |             std::forward<T>(args))...} {
      |             ~~~~~~~~~~~~~~~~~~~~~~                                           
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:1872:38:   required from ‘OutputIt fmt::v8::format_to(OutputIt, format_string<T ...>, T&& ...) [with OutputIt = appender; T = {basic_string_view<char>&, const char (&)[3]}; typename std::enable_if<detail::is_output_iterator<OutputIt, char>::value, int>::type <anonymous> = 0; format_string<T ...> = basic_format_string<char, basic_string_view<char>&, const char (&)[3]>]’
 1872 |   return {std::forward<Args>(args)...};
      |                                      ^
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/format-inl.h:78:14:   required from here
   78 |     format_to(it, FMT_STRING("{}{}"), message, SEP);
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:3148:52:   in ‘constexpr’ expansion of ‘fmt::v8::make_format_args<>(args#0, args#1)’
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:1706:15: error: possibly dangling reference to a temporary [-Werror=dangling-reference]
 1706 |   const auto& arg = arg_mapper<Context>().map(std::forward<T>(val));
      |               ^~~
/tmp/RtmpTBuTvc/R.INSTALL23d44563f108a/tiledbsoma/src/libtiledbsoma/build-lib/externals/install/include/spdlog/fmt/bundled/core.h:1706:46: note: the temporary was destroyed at the end of the full expression ‘fmt::v8::detail::arg_mapper<fmt::v8::basic_format_context<fmt::v8::appender, char> >().fmt::v8::detail::arg_mapper<fmt::v8::basic_format_context<fmt::v8::appender, char> >::map<fmt::v8::basic_string_view<char> >((*(const fmt::v8::basic_string_view<char>*)(& std::forward<fmt::v8::basic_string_view<char>&>((* & val)))))’
 1706 |   const auto& arg = arg_mapper<Context>().map(std::forward<T>(val));
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
make[6]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:76: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/reindexer/reindexer.cc.o] Error 1
make[5]: *** [CMakeFiles/Makefile2:155: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/all] Error 2
gmake[4]: *** [Makefile:136: all] Error 2
make[3]: *** [CMakeFiles/install-libtiledbsoma.dir/build.make:70: CMakeFiles/install-libtiledbsoma] Error 2
make[2]: *** [CMakeFiles/Makefile2:168: CMakeFiles/install-libtiledbsoma.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:175: CMakeFiles/install-libtiledbsoma.dir/rule] Error 2
make: *** [Makefile:163: install-libtiledbsoma] Error 2
** libs
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
using C++17
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -I../inst/tiledbsoma/include -I../inst/tiledbsoma/include/tiledbsoma   -I'/home/rcannood/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/rcannood/R/x86_64-redhat-linux-gnu-library/4.4/RcppSpdlog/include' -I'/home/rcannood/R/x86_64-redhat-linux-gnu-library/4.4/RcppInt64/include' -I'/home/rcannood/R/x86_64-redhat-linux-gnu-library/4.4/nanoarrow/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
../inst/include/tiledbsoma_types.h:20:10: fatal error: nanoarrow/nanoarrow.h: No such file or directory
   20 | #include <nanoarrow/nanoarrow.h>            // for C interface to Arrow
      |          ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib64/R/etc/Makeconf:204: RcppExports.o] Error 1
ERROR: compilation failed for package ‘tiledbsoma’
* removing ‘/home/rcannood/R/x86_64-redhat-linux-gnu-library/4.4/tiledbsoma’

The downloaded source packages are in
        ‘/tmp/RtmpRDeKDS/downloaded_packages’
Warning message:
In install.packages("tiledbsoma", repos = c("https://tiledb-inc.r-universe.dev",  :
  installation of package ‘tiledbsoma’ had non-zero exit status

To Reproduce

I can install tiledbsoma on rocker/r2u just fine:

docker run --rm -it --entrypoint=bash rocker/r2u:24.04
apt-get update
apt-get install -y cmake git
R
install.packages('tiledbsoma', repos = c('https://tiledb-inc.r-universe.dev', 'https://cloud.r-project.org'))
# works

But installing tiledbsoma in a fedora:40 image does not work:

docker run --rm -it --entrypoint=bash fedora:40
dnf install -y cmake git R-devel
R
install.packages('tiledbsoma', repos = c('https://tiledb-inc.r-universe.dev', 'https://cloud.r-project.org'))
# takes a very long time to run and eventually fails

...
using C++ compiler: ‘g++ (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0)’
using C++17
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I. -I../inst/include/ -I../inst/tiledb/include -I../inst/tiledbsoma/include -I../inst/tiledbsoma/include/tiledbsoma   -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/RcppSpdlog/include' -I'/usr/lib64/R/library/RcppInt64/include' -I'/usr/lib64/R/library/nanoarrow/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
../inst/include/tiledbsoma_types.h:20:10: fatal error: nanoarrow/nanoarrow.h: No such file or directory
   20 | #include <nanoarrow/nanoarrow.h>            // for C interface to Arrow
      |          ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib64/R/etc/Makeconf:204: RcppExports.o] Error 1
ERROR: compilation failed for package ‘tiledbsoma’
* removing ‘/usr/lib64/R/library/tiledbsoma’

Versions (please complete the following information):

  • TileDB-SOMA version: Latest
  • Language and language version: R 4.4.2
  • OS: Fedora 40
  • Note: you can use tiledbsoma.show_package_versions() (Python) or tiledbsoma::show_package_versions() (R): N/A since I can't get the package installed
@rcannood
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rcannood commented Dec 6, 2024

Kind reminder 🙏

@johnkerl johnkerl self-assigned this Dec 6, 2024
@johnkerl
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johnkerl commented Dec 6, 2024

@rcannood we are hoping for an improved user experience in our soon-to-be-released TileDB-SOMA 1.15.0.

@johnkerl
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johnkerl commented Dec 6, 2024 •
edited
Loading

For reference: #3087 was the Python analog for Fedora 40.

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