# Known issues in EasyBuild 5.0.0

## General

### Re-download of sources from git repos

The format of archives generated by EasyBuild 5.0.0 for sources from git repos (_i.e._ `git_config`) has changes from `.tar.gz` to `.tar.xz`. Therefore you might experience that EasyBuild downloads again sources of packages that were already in your system.

_Solution:_ you can set the `filename` parameter for that source file in the easyconfig back to the name of the archive you already have locally with a `.tar.gz` extension.

**TODO:** document this as expected behaviour

---

### Bad magic number errors due to removed EasyBlocks

Several easyblocks have been removed in EasyBuild 5.0.0. If you upgrade from version 4.9 to 5.0 by pulling the new release into an existing local repo of 4.9, then you might experience unexpected errors about _bad magic numbers_.

The cause of this issue are leftover `.pyc` and `.pyo` files from non-existent easyblocks, which can interfere with the operation of EasyBuild 5.0 and generate so-called _bad magic number_ errors.

_Solution:_ remove all `.pyc` and `.pyo` files from the easyblocks repo that belong to non-existent easyblocks.

TODO:
- document this as known issue including workaround
- improve logic used by EB to query for existing easyblocks to avoid this problem?

### All Ruby packages broken

All installations in Ruby fail. The base installation of `Ruby/3.3.0-GCCcore-12.3.0` provides its own `openssl.so` which has linking issues:

== 2025-03-16 04:18:09,293 run.py:500 INFO Running shell command 'gem install --bindir /user/brussel/101/vsc10122/easybuild/install/zen2/software/colorize/0.7.7-GCC-12.3.0/bin --local /user/brussel/101/vsc10122/easybuild/install/zen2/build/colorize/0.7.7/GCC-12.3.0/colorize-0.7.7.gem' in /rhea/scratch/brussel/vo/000/bvo00005/vsc10122/easybuild/install/zen2/build/colorize/0.7.7/GCC-12.3.0
== 2025-03-16 04:18:09,897 run.py:598 INFO Output of 'gem ...' shell command (stdout + stderr): <internal:/rhea/scratch/brussel/vo/000/bvo00005/vsc10122/easybuild/install/zen2/software/Ruby/3.3.0-GCCcore-12.3.0/lib/ruby/3.3.0/rubygems/core_ext/kernel_require.rb>:127:in `require': /rhea/scratch/brussel/vo/000/bvo00005/vsc10122/easybuild/install/zen2/software/Ruby/3.3.0-GCCcore-12.3.0/lib/ruby/3.3.0/x86_64-linux/openssl.so: undefined symbol: EC_GROUP_new_curve_GF2m, version OPENSSL_1_1_0 - /rhea/scratch/brussel/vo/000/bvo00005/vsc10122/easybuild/install/zen2/software/Ruby/3.3.0-GCCcore-12.3.0/lib/ruby/3.3.0/x86_64-linux/openssl.so (LoadError)

## EasyConfigs

### AOCC-4.2.0-GCCcore-13.3.0.eb

Installation fails with linking errors about unrecognized symbols to symbols that are part of the C++ standard library. Flang is broken as well

Failure is caused by the recent change in `keepsymlinks` default. Setting `keepsymlinks=False` solves the issue.

Fix in [PR#3659](https://github.com/easybuilders/easybuild-easyblocks/pull/3659)

### gemmi-0.6.5-GCCcore-12.3.0.eb

CMake needed at runtime

== 2025-03-13 14:50:12,728 build_log.py:226 ERROR EasyBuild encountered an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Sanity check failed: command "/user/brussel/101/vsc10122/easybuild/install/zen2/software/Python/3.11.3-GCCcore-12.3.0/bin/python -c "import gemmi"" failed; output:
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1140, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1080, in _find_spec
  File "/user/brussel/101/vsc10122/easybuild/install/zen2/software/gemmi/0.6.5-GCCcore-12.3.0/lib/python3.11/site-packages/_gemmi_editable.py", line 49, in find_spec
    self.rebuild()
  File "/user/brussel/101/vsc10122/easybuild/install/zen2/software/gemmi/0.6.5-GCCcore-12.3.0/lib/python3.11/site-packages/_gemmi_editable.py", line 77, in rebuild
    result = subprocess.run(
             ^^^^^^^^^^^^^^^
  File "/user/brussel/101/vsc10122/easybuild/install/zen2/software/Python/3.11.3-GCCcore-12.3.0/lib/python3.11/subprocess.py", line 548, in run
    with Popen(*popenargs, **kwargs) as process:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/user/brussel/101/vsc10122/easybuild/install/zen2/software/Python/3.11.3-GCCcore-12.3.0/lib/python3.11/subprocess.py", line 1024, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/user/brussel/101/vsc10122/easybuild/install/zen2/software/Python/3.11.3-GCCcore-12.3.0/lib/python3.11/subprocess.py", line 1917, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'cmake'

Fix in [PR#22572](https://github.com/easybuilders/easybuild-easyconfigs/pull/22572)

### libStatGen-1.0.15-GCCcore-12.3.0.eb

Another victim of `keepsymlinks`.

ERROR: Installation of libStatGen-1.0.15-GCCcore-12.3.0.eb failed: "Sanity check failed: no file found at 'include/VcfFile.h' in /user/brussel/101/vsc10122/easybuild/install/zen2/software/libStatGen/1.0.15-GCCcore-12.3.0\nno file found at 'include/SamFile.h' in /user/brussel/101/vsc10122/easybuild/install/zen2/software/libStatGen/1.0.15-GCCcore-12.3.0\nno file found at 'include/BamIndex.h' in /user/brussel/101/vsc10122/easybuild/install/zen2/software/libStatGen/1.0.15-GCCcore-12.3.0\nno file found at 'include/Cigar.h' in /user/brussel/101/vsc10122/easybuild/install/zen2/software/libStatGen/1.0.15-GCCcore-12.3.0"

Fix in [PR#22565](https://github.com/easybuilders/easybuild-easyconfigs/pull/22565)

### MATSim-15.0-GCCcore-12.3.0-Java-17.eb

Sanity check fails, proably due to `CLASSPATH` not being expanded in fake module.

== 2025-03-13 14:40:29,158 run.py:500 INFO Running shell command 'java org.matsim.run.ReleaseInfo' in /dev/shm/vsc10122/eb-698r4rc0/eb-sanity-check-9jtbpvq5
== 2025-03-13 14:40:29,461 run.py:598 INFO Output of 'java ...' shell command (stdout + stderr):
Error: Could not find or load main class org.matsim.run.ReleaseInfo
Caused by: java.lang.ClassNotFoundException: org.matsim.run.ReleaseInfo

== 2025-03-13 14:40:29,462 run.py:603 WARNING Shell command FAILED (exit code 1, see output above): java org.matsim.run.ReleaseInfo
== 2025-03-13 14:40:29,462 easyblock.py:3883 WARNING Sanity check: sanity check command java org.matsim.run.ReleaseInfo failed with exit code 1 (output: Error: Could not find or load
 main class org.matsim.run.ReleaseInfo
 Caused by: java.lang.ClassNotFoundException: org.matsim.run.ReleaseInfo)
>> result for command 'java org.matsim.run.ReleaseInfo': FAILED

### MPICH-4.2.2-GCC-13.3.0.eb

Build fails due to changes in EB5 related to unknown configuration options.

== Results of the build can be found in the log file(s) /user/brussel/101/vsc10122/easybuild/install/zen4/log/easybuild-MPICH-4.2.2-20250313.025805.axOEo.log
   2 == 2025-03-13 03:03:02,367 build_log.py:226 ERROR EasyBuild encountered an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Found unrecognized co
     nfigure options: --with-devices, --with-thread-package, --enable-sharedlibs, --enable-fc (at easybuild/easybuild-framework/easybuild/main.py:140 in build_and_install_software)
   1 == 2025-03-13 03:03:02,370 build_log.py:226 ERROR EasyBuild encountered an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Installation of MPICH
     -4.2.2-GCC-13.3.0.eb failed: 'Found unrecognized configure options: --with-devices, --with-thread-package, --enable-sharedlibs, --enable-fc' (at easybuild/easybuild-framework/easybuil
     d/main.py:178 in build_and_install_software)
3663 ERROR: Installation of MPICH-4.2.2-GCC-13.3.0.eb failed: 'Found unrecognized configure options: --with-devices, --with-thread-package, --enable-sharedlibs, --enable-fc'

Fix in [PR#3663](https://github.com/easybuilders/easybuild-easyblocks/pull/3663)

### OpenSSL-1.1.eb with Mamba-23.11.0-0.eb

The conda environment of Mamba messes up the wrapper for OpenSSL:

== 2025-03-15 19:05:45,357 run.py:500 INFO Running shell command 'openssl version -d' in /rhea/scratch/brussel/101/vsc10122/easybuild/easybuild-easyconfigs/easybuild/easyconfigs
== 2025-03-15 19:05:45,459 run.py:563 DEBUG Captured stdout: OPENSSLDIR: "/vscmnt/brussel_pixiu_apps/_apps_brussel/RL8/skylake-ib/software/Mamba/23.11.0-0/ssl"
== 2025-03-15 19:05:45,460 run.py:598 INFO Output of 'openssl ...' shell command (stdout + stderr): OPENSSLDIR: "/vscmnt/brussel_pixiu_apps/_apps_brussel/RL8/skylake-ib/software/Mamba/23.11.0-0/ssl"
== 2025-03-15 19:05:45,460 run.py:601 INFO Shell command completed successfully (see output above): openssl version -d
== 2025-03-15 19:05:45,460 openssl.py:92 INFO OPENSSLDIR determined from system openssl: /vscmnt/brussel_pixiu_apps/_apps_brussel/RL8/skylake-ib/software/Mamba/23.11.0-0/ssl
== 2025-03-15 19:05:45,460 openssl.py:104 DEBUG SSL certificates directory: /vscmnt/brussel_pixiu_apps/_apps_brussel/RL8/skylake-ib/software/Mamba/23.11.0-0/ssl/certs
== 2025-03-15 19:05:45,460 openssl_wrapper.py:93 DEBUG Requiring minimum OpenSSL version: 1.1.1
== 2025-03-15 19:05:45,461 openssl_wrapper.py:102 DEBUG Restricting maximum OpenSSL version: 1.2
== 2025-03-15 19:05:45,462 openssl_wrapper.py:135 INFO Matrix of version library names: [['libssl.so.1.1', 'libcrypto.so.1.1']]
== 2025-03-15 19:05:45,462 filetools.py:561 WARNING Could not find command 'openssl11' (with permissions to read/execute it) in $PATH (['/user/brussel/101/vsc10122/.local/venv/eb.py36/bin', '/user/brussel/101/vsc10122/.local/bin', '/vscmnt/brussel_pixiu_apps/_apps_brussel/RL8/skylake-ib/software/Mamba/23.11.0-0/bin', '/vscmnt/brussel_pixiu_apps/_apps_brussel/RL8/skylake-ib/software/Mamba/23.11.0-0/condabin', '/user/brussel/101/vsc10122/.local/bin', '/usr/local/bin', '/usr/bin', '/usr/local/sbin', '/usr/sbin'])

### Paraver-4.12.0-GCC-13.3.0.eb

There is a linking issue between Cairo and Pixman:

/user/brussel/101/vsc10122/easybuild/install/zen4/software/binutils/2.42-GCCcore-13.3.0/bin/ld: /user/brussel/101/vsc10122/easybuild/install/zen4/software/cairo/1.18.0-GCCcore-13.3.0/lib/../lib64/libcairo.so.2: undefined reference to `pixman_image_set_dither'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:445: wxparaver.bin] Error 1
make[3]: Leaving directory '/rhea/scratch/brussel/vo/000/bvo00005/vsc10122/easybuild/install/zen4/build/Paraver/4.12.0/GCC-13.3.0/wxparaver-4.12.0/src/wxparaver/src'
make[2]: *** [Makefile:399: install-recursive] Error 1
make[2]: Leaving directory '/rhea/scratch/brussel/vo/000/bvo00005/vsc10122/easybuild/install/zen4/build/Paraver/4.12.0/GCC-13.3.0/wxparaver-4.12.0/src/wxparaver'
make[1]: *** [Makefile:583: install] Error 2
make[1]: Leaving directory '/rhea/scratch/brussel/vo/000/bvo00005/vsc10122/easybuild/install/zen4/build/Paraver/4.12.0/GCC-13.3.0/wxparaver-4.12.0/src'
make: *** [Makefile:778: install] Error 2

### PDT-3.25.2-GCCcore-13.3.0.eb

Fetching of sources fails. This issue is not related to EasyBuild, the download server of this software is currently unreachable.

Fix in [PR#22523](https://github.com/easybuilders/easybuild-easyconfigs/pull/22523)

### polars-0.20.2-gfbf-2023a.eb

This easyconfig is currently not usable due to recent changes in the `Cargo` easyblock.

Fix in [PR#3654](https://github.com/easybuilders/easybuild-easyblocks/pull/3654)

TODO:
- try and get `Cargo` PR merged
- doesn't necessarily need to block EasyBuild 5.0

### Qt6-6.7.2-GCCcore-13.3.0.eb

Usual file name too long errors:

ninja: error: WriteFile(__services_network_public_mojom_mojom_shared_dictionary_shared_cpp_sources__jumbo_merge__rhea_scratch_brussel_vo_000_bvo00005_vsc10122_easybuild_install_zen4_
      build_Qt6_6.7.2_GCCcore-13.3.0_easybuild_obj_qtwebengine_src_core_target_toolchain_target__rule.rsp): Unable to create file. File name too long
    1 ninja: build stopped: .

Related bug reports upstream:
* https://bugreports.qt.io/browse/QTBUG-59769
* https://bugs.gentoo.org/911715

Fix in [PR#22570](https://github.com/easybuilders/easybuild-easyconfigs/pull/22570)

### Rust-1.81.0-GCCcore-13.3.0, Rust-1.83.0-GCCcore-13.3.0

Installations with RPATH enabled fail on the sanity checks of the binaries:

Sanity check failed: No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/miri
No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/cargo-clippy
No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/cargo-fmt
No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/cargo-miri
No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/rustdoc
No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/rustfmt
No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/rust-analyzer
No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/rustc
No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/cargo
No '(RPATH)' found in 'readelf -d' output for /user/brussel/101/vsc10122/easybuild/install/zen4/software/Rust/1.83.0-GCCcore-13.3.0/bin/clippy-driver" (at easybuild/easybuild-framework/easybuild/main.py:178 in build_and_install_software)

These binaries have RUNPATHs instead of RPATH. The Rust easyblock converts RUNPATHS on RPATHS for the libraries, but not the executables.

Fix in [PR#3660](https://github.com/easybuilders/easybuild-easyblocks/pull/3660)

### Scalene-1.5.26-GCCcore-12.3.0.eb

== 2025-03-13 14:03:00,251 run.py:598 INFO Output of '/user/brussel/101/vsc10122/easybuild/install/zen2/software/Python/3.11.3-GCCcore-12.3.0/bin/python ...' shell command (stdout + stderr):
Processing /rhea/scratch/brussel/vo/000/bvo00005/vsc10122/easybuild/install/zen2/build/Scalene/1.5.26/GCCcore-12.3.0/Scalene/scalene-1.5.26
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [18 lines of output]
      /user/brussel/101/vsc10122/easybuild/install/zen2/software/Python/3.11.3-GCCcore-12.3.0/lib/python3.11/site-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
      !!

              ********************************************************************************
              Requirements should be satisfied by a PEP 517 installer.
              If you are using pip, you can try `pip install --use-pep517`.
              ********************************************************************************

      !!
        dist.fetch_build_eggs(dist.setup_requires)
      running egg_info
      make vendor-deps
      rm -fr vendor/
      mkdir -p vendor && cd vendor && git clone https://github.com/emeryberger/Heap-Layers
      Cloning into 'Heap-Layers'...
      /usr/libexec/git-core/git-remote-https: symbol lookup error: /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b
      make: *** [GNUmakefile:57: vendor/Heap-Layers] Error 128
      error: command '/usr/bin/make' failed with exit code 2
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

This one downloads vendored packages with git, but it lacks a build dependency on git.

Fix in [PR#22567](https://github.com/easybuilders/easybuild-easyconfigs/pull/22567)

### XML-LibXML-2.0210-GCCcore-13.3.0.eb

Installation fails due to missing `Alien::Build::MM`: this can be fixed by converting from `Bundle` to `PerlBundle`

Installation fails due to failed test on `Alien::Base`: fixed by adding missing `FFI::CheckLib`

Fix in [PR#22521](https://github.com/easybuilders/easybuild-easyconfigs/pull/22521)

TODO: open framework PR to not expand glob patterns for fake module file