[Bug] Can't install tiledbsoma for Python on Fedora 40

[rcannood]

Describe the bug

Hi all!

Unfortunately, I don't manage to install the latest version of tiledbsoma on my Fedora 40 system. I managed to preproduce it with a Fedora 40 container. I didn't try on other platforms.

Thanks in advance!

To Reproduce

docker run --rm -it fedora:40

dnf install -y python3-devel python3-pip git g++ make

pip install tiledbsoma

Full log

  ...
      [ 89%] Linking CXX static library libCatch2.a
      [ 89%] Built target Catch2
      [ 89%] Building CXX object _deps/catch2-build/src/CMakeFiles/Catch2WithMain.dir/catch2/internal/catch_main.cpp.o
      [ 90%] Linking CXX static library libCatch2Main.a
      [ 90%] Built target Catch2WithMain
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:286: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/utils/logger.cc.o] Error 1
      gmake[5]: *** Waiting for unfinished jobs....
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:328: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/utils/version.cc.o] Error 1
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:188: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/soma/soma_context.cc.o] Error 1
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:244: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/soma/array_buffers.cc.o] Error 1
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:76: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/reindexer/reindexer.cc.o] Error 1
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:258: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/soma/column_buffer.cc.o] Error 1
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:90: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/soma/managed_query.cc.o] Error 1
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:314: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/utils/util.cc.o] Error 1
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:272: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/utils/arrow_adapter.cc.o] Error 1
      cc1plus: all warnings being treated as errors
      gmake[5]: *** [src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/build.make:104: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/soma/soma_array.cc.o] Error 1
      gmake[4]: *** [CMakeFiles/Makefile2:211: src/CMakeFiles/TILEDB_SOMA_OBJECTS.dir/all] Error 2
      gmake[3]: *** [Makefile:146: all] Error 2
      gmake[2]: *** [CMakeFiles/libtiledbsoma.dir/build.make:86: libtiledbsoma-prefix/src/libtiledbsoma-stamp/libtiledbsoma-build] Error 2
      gmake[1]: *** [CMakeFiles/Makefile2:142: CMakeFiles/libtiledbsoma.dir/all] Error 2
      gmake: *** [Makefile:91: all] Error 2
      Checking: /tmp/pip-install-6wj9pvw9/tiledbsoma_afd25373037d471e8556541bbc3a3ce2/dist_links/dist/lib/libtiledbsoma.so exists: False
      Checking: /tmp/pip-install-6wj9pvw9/tiledbsoma_afd25373037d471e8556541bbc3a3ce2/dist_links/dist/lib64/libtiledbsoma.so exists: False
      Checking: /tmp/pip-install-6wj9pvw9/tiledbsoma_afd25373037d471e8556541bbc3a3ce2/dist_links/dist/lib/x86_64-linux-gnu/libtiledbsoma.so exists: False
      libtiledbsoma.so: cannot open shared object file: No such file or directory
      Traceback (most recent call last):
        File "/usr/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/usr/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/usr/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
          return _build_backend().build_wheel(wheel_directory, config_settings,
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-mm81khxq/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 421, in build_wheel
          return self._build_with_temp_dir(
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-mm81khxq/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 403, in _build_with_temp_dir
          self.run_setup()
        File "/tmp/pip-build-env-mm81khxq/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 318, in run_setup
          exec(code, locals())
        File "<string>", line 269, in <module>
        File "/tmp/pip-build-env-mm81khxq/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-mm81khxq/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 183, in setup
          return run_commands(dist)
                 ^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-mm81khxq/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 199, in run_commands
          dist.run_commands()
        File "/tmp/pip-build-env-mm81khxq/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands
          self.run_command(cmd)
        File "/tmp/pip-build-env-mm81khxq/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 950, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-mm81khxq/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
          cmd_obj.run()
        File "<string>", line 224, in run
        File "<string>", line 186, in find_or_build_package_data
        File "/usr/lib64/python3.12/subprocess.py", line 571, in run
          raise CalledProcessError(retcode, process.args,
      subprocess.CalledProcessError: Command '['./bld', '--tiledb=/tmp/pip-install-6wj9pvw9/tiledbsoma_afd25373037d471e8556541bbc3a3ce2/dist_links/dist']' returned non-zero exit status 2.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for tiledbsoma
Failed to build tiledbsoma
ERROR: Could not build wheels for tiledbsoma, which is required to install pyproject.toml-based projects

Versions (please complete the following information):

• TileDB-SOMA version: 1.14.2
• Language and language version (e.g. Python 3.9, R 4.3.2): Python 3.12
• OS (e.g. MacOS, Ubuntu Linux): Fedora 40
• Note: you can use tiledbsoma.show_package_versions() (Python) or tiledbsoma::show_package_versions() (R)

Additional context
Add any other context about the problem here.

[johnkerl]

@rcannood taking a look!

[rcannood]

Thanks @johnkerl !

[johnkerl]

@rcannood the issue seems to be errors of the form:

/tmp/TileDB-SOMA/build/externals/install/include/spdlog/fmt/bundled/core.h:1872:38:
required from ‘std::string fmt::v8::format(format_string<T ...>, T&& ...)
[with T = {std::basic_string_view<char, std::char_traits<char> >, long int}; std::string =
std::__cxx11::basic_string<char>; format_string<T ...> = basic_format_string<char,
std::basic_string_view<char, std::char_traits<char> >, long int>]’

-- we do use some known-good fmt versions within our Conda-feedstock builds, and IIRC have used v9 at some point in the past. I do believe v8 has always been "too old" for us.

The versions that are known-good for our Conda feedstock are

• fmt 9 spdlog 1.11
• fmt 11 spdlog 1.14

I'm a little puzzled here since with docker run of fedora40 I see

# dnf list | grep spdlog
spdlog.i686         1.12.0-4.fc40 updates
spdlog.x86_64       1.12.0-4.fc40 updates
spdlog-devel.i686   1.12.0-4.fc40 updates
spdlog-devel.x86_64 1.12.0-4.fc40 updates

and 1.12 is In between 1.11 and 1.14. And I get the same build error after dnf install spdlog.

And the v8 is from here:

/tmp/TileDB-SOMA/build/externals/install/include/spdlog/fmt/bundled/core.h

At any rate -- I'll check with the team and circle back to see what recommendations we have.

[johnkerl]

@rcannood here is the issue. We are using some third-party code (which we don't control) and yet for our own code we want to compile with -Werror. It turns out that in that third-party code, there are some things that some compilers warn about & others don't. In this case the Fedora 40 compiler is emitting a warning, which is then fatal.

Here is a quick workaround for kick-the-tires mode:

• cd /tmp
• git clone https://github.com/single-cell-data/TileDB-SOMA
• Apply this diff:

diff --git a/libtiledbsoma/CMakeLists.txt b/libtiledbsoma/CMakeLists.txt
index 5d3d6d90..36361825 100644
--- a/libtiledbsoma/CMakeLists.txt
+++ b/libtiledbsoma/CMakeLists.txt
@@ -200,7 +200,8 @@ else()
   set(TILEDBSOMA_COMPILE_OPTIONS -Wall -Wextra)

   if(TILEDBSOMA_ENABLE_WERROR)
-    set(TILEDBSOMA_WERROR_OPTION -Werror)
+    ####set(TILEDBSOMA_WERROR_OPTION -Werror)
+    set(TILEDBSOMA_WERROR_OPTION "")
   else()
     set(TILEDBSOMA_WERROR_OPTION "")
   endif()

• pip install apis/python

This worked for me in a docker run of fedora:40.

We do need this to work out of the box, though, on a plain-vanilla pip install. I'll keep you posted.

[johnkerl]

@rcannood your previous two comments were IMO completely on-topic! :)

My apologies, indeed I should have mentioned checking out tag 1.14.2, rather than the default which gave you tip of main.

[johnkerl]

cc @jp-dark @nguyenv using docker-run as above with fedora:40 I applied the following test-patch:

diff --git a/libtiledbsoma/CMakeLists.txt b/libtiledbsoma/CMakeLists.txt
index 5d3d6d90..e85f67a7 100644
--- a/libtiledbsoma/CMakeLists.txt
+++ b/libtiledbsoma/CMakeLists.txt
@@ -200,7 +200,7 @@ else()
   set(TILEDBSOMA_COMPILE_OPTIONS -Wall -Wextra)

   if(TILEDBSOMA_ENABLE_WERROR)
-    set(TILEDBSOMA_WERROR_OPTION -Werror)
+    set(TILEDBSOMA_WERROR_OPTION "")
   else()
     set(TILEDBSOMA_WERROR_OPTION "")
   endif()
diff --git a/scripts/bld b/scripts/bld
index 5008e188..19bb9568 100755
--- a/scripts/bld
+++ b/scripts/bld
@@ -11,7 +11,7 @@ arg() { echo "$1" | sed "s/^${2-[^=]*=}//" | sed "s/:/;/g"; }
 build="Release"
 prefix=""
 tiledb=""
-cmake_verbose="false"
+cmake_verbose="true"
 no_tiledb_deprecated="false"

 while test $# != 0; do

and got a successful pip install -e apis/python

[root@629d17eb941a TileDB-SOMA]# uname -a
Linux 629d17eb941a 6.8.0-1016-aws #17-Ubuntu SMP Mon Sep  2 13:48:07 UTC 2024 x86_64 GNU/Linux
[root@629d17eb941a TileDB-SOMA]# python
bash: python: command not found
[root@629d17eb941a TileDB-SOMA]# python3
Python 3.12.6 (main, Sep  9 2024, 00:00:00) [GCC 14.2.1 20240801 (Red Hat 14.2.1-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import tiledbsoma
>>> tiledbsoma.show_package_versions()
tiledbsoma.__version__              1.15.0rc0.post12.dev3893317782
TileDB core version (libtiledbsoma) 2.26.2
python version                      3.12.6.final.0
OS version                          Linux 6.8.0-1016-aws

While the above test-patch is of course not the final solution, it does prove that -Werror on third-party source is indeed the issue.

This suggests that our work on #2408 #2664 #2763 was not complete.