bug#49477: [core-updates] python-pyyaml fails on sanity-check

[Julien Lepiller]

Le 8 juillet 2021 23:55:30 GMT-04:00, John Kehayias via Bug reports for GNU 
Guix <bug-guix@gnu.org> a écrit :
>Perhaps due to recent addition/changes for python sanity-check?
>
>Here is the relevant portion of the log from running ./pre-inst-env
>guix build python-pyyaml on core-updates:
>
>warning: build_py: byte-compiling is disabled, skipping.
>
>running build_ext
>building 'yaml._yaml' extension
>creating build/temp.linux-x86_64-3.9
>creating build/temp.linux-x86_64-3.9/yaml
>gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3
>-Wall -fno-semantic-interposition -fPIC
>-I/gnu/store/4nrih35yjsz2kwhr4pwxnkdzjmkgxxfq-python-3.9.5/include/python3.9
>-c yaml/_yaml.c -o build/temp.linux-x86_64-3.9/yaml/_yaml.o
>gcc: error: yaml/_yaml.c: No such file or directory
>gcc: fatal error: no input files
>compilation terminated.
>Error compiling module, falling back to pure Python
>phase `build' succeeded after 0.3 seconds
>starting phase `install'
>running "python setup.py" with command "install" and parameters
>("--prefix=/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1"
>"--no-compile" "--single-version-externally-managed" "--root=/")
>running install
>running build
>running build_py
>warning: build_py: byte-compiling is disabled, skipping.
>
>running build_ext
>building 'yaml._yaml' extension
>gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3
>-Wall -fno-semantic-interposition -fPIC
>-I/gnu/store/4nrih35yjsz2kwhr4pwxnkdzjmkgxxfq-python-3.9.5/include/python3.9
>-c yaml/_yaml.c -o build/temp.linux-x86_64-3.9/yaml/_yaml.o
>gcc: error: yaml/_yaml.c: No such file or directory
>gcc: fatal error: no input files
>compilation terminated.
>Error compiling module, falling back to pure Python
>running install_lib
>creating
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1
>creating
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib
>creating
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9
>creating
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages
>creating
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/_yaml
>copying build/lib.linux-x86_64-3.9/_yaml/__init__.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/_yaml
>creating
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/__init__.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/composer.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/constructor.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/cyaml.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/dumper.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/emitter.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/error.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/events.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/loader.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/nodes.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/parser.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/reader.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/representer.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/resolver.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/scanner.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/serializer.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>copying build/lib.linux-x86_64-3.9/yaml/tokens.py ->
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml
>warning: install_lib: byte-compiling is disabled, skipping.
>
>running install_egg_info
>running egg_info
>writing lib3/PyYAML.egg-info/PKG-INFO
>writing dependency_links to lib3/PyYAML.egg-info/dependency_links.txt
>writing top-level names to lib3/PyYAML.egg-info/top_level.txt
>warning: the 'license_file' option is deprecated, use 'license_files'
>instead
>adding license file 'LICENSE' (matched pattern 'LICENSE')
>reading manifest file 'lib3/PyYAML.egg-info/SOURCES.txt'
>reading manifest template 'MANIFEST.in'
>writing manifest file 'lib3/PyYAML.egg-info/SOURCES.txt'
>Copying lib3/PyYAML.egg-info to
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/PyYAML-5.4.1-py3.9.egg-info
>running install_scripts
>Listing
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1'...
>Listing
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib'...
>Listing
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9'...
>Listing
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages'...
>Listing
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/PyYAML-5.4.1-py3.9.egg-info'...
>Listing
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/_yaml'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/_yaml/__init__.py'...
>Listing
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/__init__.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/composer.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/constructor.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/cyaml.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/dumper.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/emitter.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/error.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/events.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/loader.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/nodes.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/parser.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/reader.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/representer.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/resolver.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/scanner.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/serializer.py'...
>Compiling
>'/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/yaml/tokens.py'...
>phase `install' succeeded after 0.5 seconds
>starting phase `add-install-to-pythonpath'
>phase `add-install-to-pythonpath' succeeded after 0.0 seconds
>starting phase `add-install-to-path'
>phase `add-install-to-path' succeeded after 0.0 seconds
>starting phase `wrap'
>find-files:
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/bin: No
>such file or directory
>find-files:
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/sbin:
>No such file or directory
>phase `wrap' succeeded after 0.0 seconds
>starting phase `check'
>running "python setup.py" with command "test" and parameters ()
>running test
>running build_py
>warning: build_py: byte-compiling is disabled, skipping.
>
>running build_ext
>building 'yaml._yaml' extension
>gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3
>-Wall -fno-semantic-interposition -fPIC
>-I/gnu/store/4nrih35yjsz2kwhr4pwxnkdzjmkgxxfq-python-3.9.5/include/python3.9
>-c yaml/_yaml.c -o build/temp.linux-x86_64-3.9/yaml/_yaml.o
>gcc: error: yaml/_yaml.c: No such file or directory
>gcc: fatal error: no input files
>compilation terminated.
>Error compiling module, falling back to pure Python
>........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
>===========================================================================
>TESTS: 1288
>phase `check' succeeded after 4.3 seconds
>starting phase `sanity-check'
>validating 'PyYAML'
>/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages
>...checking requirements: OK
>...trying to load module _yaml: ERROR:
>Traceback (most recent call last):
>File "/gnu/store/slim8x2ppjhici2iiabmyvg9lxyikiwy-sanity-check.py",
>line 69, in <module>
>    importlib.import_module(name)
>File
>"/gnu/store/4nrih35yjsz2kwhr4pwxnkdzjmkgxxfq-python-3.9.5/lib/python3.9/importlib/__init__.py",
>line 127, in import_module
>    return _bootstrap._gcd_import(name[level:], package, level)
>  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
>  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
>File "<frozen importlib._bootstrap>", line 986, in
>_find_and_load_unlocked
>  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
>File "<frozen importlib._bootstrap_external>", line 855, in exec_module
>File "<frozen importlib._bootstrap>", line 228, in
>_call_with_frames_removed
>File
>"/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages/_yaml/__init__.py",
>line 14, in <module>
>    raise exc("No module named '_yaml'")
>ModuleNotFoundError: No module named '_yaml'
>...trying to load module yaml: OK
>error: in phase 'sanity-check': uncaught exception:
>%exception #<&invoke-error program: "python" arguments:
>("/gnu/store/slim8x2ppjhici2iiabmyvg9lxyikiwy-sanity-check.py"
>"/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages")
>exit-status: 1 term-signal: #f stop-signal: #f>
>phase `sanity-check' failed after 0.2 seconds
>command "python"
>"/gnu/store/slim8x2ppjhici2iiabmyvg9lxyikiwy-sanity-check.py"
>"/gnu/store/i9aqd2hcrfc68ykd24nnjw1nzrdyazrs-python-pyyaml-5.4.1/lib/python3.9/site-packages"
>failed with status 1
>builder for
>`/gnu/store/m9vvvh5qpkrcd0hra3dpri1yqns9m36w-python-pyyaml-5.4.1.drv'
>failed with exit code 1
>build of
>/gnu/store/m9vvvh5qpkrcd0hra3dpri1yqns9m36w-python-pyyaml-5.4.1.drv
>failed
>View build log at
>'/var/log/guix/drvs/m9/vvvh5qpkrcd0hra3dpri1yqns9m36w-python-pyyaml-5.4.1.drv.bz2'.
>guix build: error: build of
>`/gnu/store/m9vvvh5qpkrcd0hra3dpri1yqns9m36w-python-pyyaml-5.4.1.drv'
>failed

I found the solution: add cython to the inputs. I'll push the fix shortly, 
thanks for reporting!