Nightly feedstock build failed

[github-actions]

Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary

[johnkerl]

#231

[jdblischak]

Documenting the errors:

# linux-64
* installing *source* package ‘tiledbsoma’ ...
** using staged installation
** updated src/Makevars for system library via pkg-config
** libs
Error: C++20 standard requested but CXX20 is not defined

# osx-64
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/tiledbsoma_types.h:23:
In file included from /Users/runner/miniforge3/conda-bld/tiledbsoma_1732068244867/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/tiledbsoma/tiledbsoma:51:
/Users/runner/miniforge3/conda-bld/tiledbsoma_1732068244867/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/tiledbsoma/soma/soma_collection.h:107:32: error: 'path' is unavailable: introduced in macOS 10.15 - see https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
  107 |               std::filesystem::path(uri).filename().string(),  // group name
      |                                ^
/Users/runner/miniforge3/conda-bld/tiledbsoma_1732068244867/_build_env/bin/../include/c++/v1/__filesystem/path.h:383:33: note: 'path' has been explicitly marked unavailable here
  383 | class _LIBCPP_EXPORTED_FROM_ABI path {
      |                                 ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [/Users/runner/miniforge3/conda-bld/tiledbsoma_1732068244867/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/etc/Makeconf:200: RcppExports.o] Error 1
ERROR: compilation failed for package ‘tiledbsoma’

# osx-arm64
/Users/runner/miniforge3/conda-bld/tiledbsoma_1732068269621/_build_env/bin/../include/c++/v1/__format/format_functions.h:427:15: note: in instantiation of function template specialization 'std::__vformat_to<std::back_insert_iterator<std::string>, char, std::back_insert_iterator<std::__format::__output_buffer<char>>>' requested here
  427 |   return std::__vformat_to(std::move(__out_it), __fmt, __args);
      |               ^
/Users/runner/miniforge3/conda-bld/tiledbsoma_1732068269621/_build_env/bin/../include/c++/v1/__format/format_functions.h:458:8: note: in instantiation of function template specialization 'std::vformat_to<std::back_insert_iterator<std::string>>' requested here
  458 |   std::vformat_to(std::back_inserter(__res), __fmt, __args);
      |        ^
/Users/runner/miniforge3/conda-bld/tiledbsoma_1732068269621/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/library/RcppSpdlog/include/spdl.h:39:86: note: in instantiation of function template specialization 'std::vformat<void>' requested here
   39 |     inline void trace(const char* fmt, Args&&... args ) { RcppSpdlog::log_trace(std::vformat(std::string_view(fmt), std::make_format_args(args...)).c_str()); }
      |                                                                                      ^
./rutilities.h:43:19: note: in instantiation of function template specialization 'spdl::trace<std::string, std::string>' requested here
   43 |             spdl::trace("[config_vector_to_map] adding '{}' = '{}'", std::string(namesvec[i]), std::string(confvec[i]));
      |                   ^
/Users/runner/miniforge3/conda-bld/tiledbsoma_1732068269621/_build_env/bin/../include/c++/v1/__charconv/to_chars_floating_point.h:42:1: note: 'to_chars' has been explicitly marked unavailable here
   42 | to_chars(char* __first, char* __last, long double __value, chars_format __fmt);
      | ^
9 errors generated.
make: *** [/Users/runner/miniforge3/conda-bld/tiledbsoma_1732068269621/_build_env/lib/R/etc/Makeconf:201: RcppExports.o] Error 1
ERROR: compilation failed for package ‘tiledbsoma’

[jdblischak]

Unfortunately I ran out of time today. I applied the update ab4c6f5 from #231 to the nightly build on my fork, but unfortunately it failed with the same errors.

[github-actions]

Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary

[jdblischak]

As expected, the R build continues to fail due to C++20 compilation issues.

Today I did another experiment. I purposefully skipped the R client build in order to query the status of the Python build with C++20. Note that this build used the commit single-cell-data/TileDB-SOMA@ea3cd1a that was merged earlier this morning.

First the good news:

• C++20 is being used to compile the Python client. Current builds on main (example) use the flag -std=c++17, whereas the nightly build uses -std=c++20
• The Python client could be built with C++20 for all architectures (linux-64, osx-64, osx-arm64) and Python versions (3.9, 3.10, 3.11, 3.12)

But then the bad news:

• The simple import test fails on both linux-64 and osx-64 (tests aren't run when cross-compiling osx-arm64 on osx-64 architecture).

The backtrace is super long (600+ lines) and only ends because Python core dumps. Below is the beginning and end of the backtrace. Note that I've also replaced the long conda installation path with $PREFIX for readability.

# linux-64 py39

import: 'tiledbsoma'
*** Error in `$PREFIX/bin/python': double free or corruption (out): 0x000055b5a86d6b90 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x7f8ced766329]
$PREFIX/lib/python3.9/site-packages/tiledbsoma/../../../libtiledbsoma.so(+0x647dd)[0x7f8cecc647dd]
$PREFIX/lib/python3.9/site-packages/tiledbsoma/../../../libtiledbsoma.so(+0x64b0e)[0x7f8cecc64b0e]
$PREFIX/lib/python3.9/site-packages/tiledbsoma/../../../libtiledbsoma.so(+0x1b9275)[0x7f8cecdb9275]
$PREFIX/lib/python3.9/site-packages/tiledbsoma/../../../././libspdlog.so.1.14(_ZN6spdlog6logger13set_formatterESt10unique_ptrINS_9formatterESt14default_deleteIS2_EE+0xc5)[0x7f8ceb2ecd95]
$PREFIX/lib/python3.9/site-packages/tiledbsoma/../../../././libspdlog.so.1.14(_ZN6spdlog6logger11set_patternENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_17pattern_time_typeE+0x4d)[0x7f8ceb2f765d]
$PREFIX/lib/python3.9/site-packages/tiledbsoma/../../.././libtiledb.so.2.26(+0xc3672a)[0x7f8cec63672a]
$PREFIX/lib/python3.9/site-packages/tiledbsoma/../../.././libtiledb.so.2.26(+0xc36ae9)[0x7f8cec636ae9]
$PREFIX/lib/python3.9/site-packages/tiledbsoma/../../.././libtiledb.so.2.26(+0xb27547)[0x7f8cec527547]
$PREFIX/lib/python3.9/site-packages/tiledbsoma/../../.././libtiledb.so.2.26(+0x1c5240)[0x7f8cebbc5240]
/lib64/ld-linux-x86-64.so.2(+0xf9c3)[0x7f8cee3e79c3]
/lib64/ld-linux-x86-64.so.2(+0x1459e)[0x7f8cee3ec59e]
/lib64/ld-linux-x86-64.so.2(+0xf7d4)[0x7f8cee3e77d4]
/lib64/ld-linux-x86-64.so.2(+0x13b8b)[0x7f8cee3ebb8b]
/lib64/libdl.so.2(+0xfab)[0x7f8cedfb8fab]
/lib64/ld-linux-x86-64.so.2(+0xf7d4)[0x7f8cee3e77d4]
/lib64/libdl.so.2(+0x15ad)[0x7f8cedfb95ad]
/lib64/libdl.so.2(dlopen+0x31)[0x7f8cedfb9041]
$PREFIX/bin/python(+0x1f220c)[0x55b5a719120c]

# omitted hundreds of lines of similar output

7f8cee5fa000-7f8cee5fb000 rw-p 00022000 08:01 5236909                    /usr/lib64/ld-2.17.so
7f8cee5fb000-7f8cee5fc000 rw-p 00000000 00:00 0 
7ffda295a000-7ffda297c000 rw-p 00000000 00:00 0                          [stack]
7ffda29b4000-7ffda29b8000 r--p 00000000 00:00 0                          [vvar]
7ffda29b8000-7ffda29ba000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 --xp 00000000 00:00 0                  [vsyscall]
/home/conda/feedstock_root/build_artifacts/tiledbsoma_1732208694265/test_tmp/conda_test_runner.sh: line 3:  4617 Aborted                 (core dumped) "$PREFIX/bin/python" -s "/home/conda/feedstock_root/build_artifacts/tiledbsoma_1732208694265/test_tmp/run_test.py"
WARNING: Tests failed for tiledbsoma-py-1.15.0rc3.dev20241119-py39h91c51d3_1.conda - moving package to /home/conda/feedstock_root/build_artifacts/broken

[jdblischak]

I searched for the error message from the failed R package build on linux-64: Error: C++20 standard requested but CXX20 is not defined

From what I could find, I think we may need to define CXX (and possibly a few other env vars, similar to what we are already doing for the osx-64 build) in ~/.R/Makevars (Shians/NanoMethViz#32 (comment), microsoft/microsoft-r-open#26 (comment))

[johnkerl]

@jdblischak I agree this is probably Makevars / Makevars.in ... I'll look soon

[jdblischak]

And for tinkering with the feedstock recipe and/or scripts, you can start from the branch nightly-build. It gets overwritten every night, so if you want your experiments to persist beyond a day, I recommend creating a new branch.