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cschwan / sage-on-gentoo

(Unofficial) Gentoo Overlay for Sage- and Sage-related ebuilds
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[dev-python/cython] permission denied when building doc #354

Closed Alessandro-Barbieri closed 9 years ago

Alessandro-Barbieri commented 9 years ago

Installation fails at documentation. Maybe sandbox violation?

If you need more info, I will provide.

make -C docs html 
make: Entering directory '/var/tmp/portage/dev-python/cython-0.22-r2/work/Cython-0.22/docs'
sphinx-build -b html -d build/doctrees -D latex_paper_size=a4  . build/html
Making output directory...
Running Sphinx v1.2.2
loading pickled environment... not yet created
loading intersphinx inventory from http://docs.python.org/3/objects.inv...
building [html]: targets for 51 source files that are out of date
updating environment: 51 added, 0 changed, 0 removed
reading sources... [  1%] index
reading sources... [  3%] src/quickstart/build
reading sources... [  5%] src/quickstart/cythonize
reading sources... [  7%] src/quickstart/index
reading sources... [  9%] src/quickstart/install
reading sources... [ 11%] src/quickstart/overview
reading sources... [ 13%] src/reference/compilation
reading sources... [ 15%] src/reference/directives
reading sources... [ 17%] src/reference/extension_types
reading sources... [ 19%] src/reference/index
reading sources... [ 21%] src/reference/interfacing_with_other_code
reading sources... [ 23%] src/reference/language_basics
reading sources... [ 25%] src/reference/limitations
reading sources... [ 27%] src/reference/special_mention
reading sources... [ 29%] src/reference/special_methods_table
reading sources... [ 31%] src/tutorial/appendix
reading sources... [ 33%] src/tutorial/array
reading sources... [ 35%] src/tutorial/caveats
reading sources... [ 37%] src/tutorial/cdef_classes
reading sources... [ 39%] src/tutorial/clibraries
reading sources... [ 41%] src/tutorial/cython_tutorial
reading sources... [ 43%] src/tutorial/external
reading sources... [ 45%] src/tutorial/index
reading sources... [ 47%] src/tutorial/memory_allocation
reading sources... [ 49%] src/tutorial/numpy
reading sources... [ 50%] src/tutorial/profiling_tutorial
reading sources... [ 52%] src/tutorial/pure
reading sources... [ 54%] src/tutorial/pxd_files
reading sources... [ 56%] src/tutorial/readings
reading sources... [ 58%] src/tutorial/related_work
reading sources... [ 60%] src/tutorial/strings
reading sources... [ 62%] src/userguide/buffer
reading sources... [ 64%] src/userguide/debugging
reading sources... [ 66%] src/userguide/early_binding_for_speed
reading sources... [ 68%] src/userguide/extension_types
reading sources... [ 70%] src/userguide/external_C_code
reading sources... [ 72%] src/userguide/fusedtypes
reading sources... [ 74%] src/userguide/index
reading sources... [ 76%] src/userguide/language_basics
reading sources... [ 78%] src/userguide/limitations
reading sources... [ 80%] src/userguide/memoryviews
reading sources... [ 82%] src/userguide/numpy_tutorial
reading sources... [ 84%] src/userguide/parallelism
reading sources... [ 86%] src/userguide/pxd_package
reading sources... [ 88%] src/userguide/pypy
reading sources... [ 90%] src/userguide/pyrex_differences
reading sources... [ 92%] src/userguide/sharing_declarations
reading sources... [ 94%] src/userguide/source_files_and_compilation
reading sources... [ 96%] src/userguide/special_methods
reading sources... [ 98%] src/userguide/wrapping_CPlusPlus
reading sources... [100%] welcome

/var/tmp/portage/dev-python/cython-0.22-r2/work/Cython-0.22/docs/src/quickstart/install.rst:59: WARNING: duplicate citation Sage, other instance in /var/tmp/portage/dev-python/cython-0.22-r2/work/Cython-0.22/docs/src/quickstart/build.rst
/var/tmp/portage/dev-python/cython-0.22-r2/work/Cython-0.22/docs/src/tutorial/related_work.rst:44: WARNING: duplicate citation Pyrex, other instance in /var/tmp/portage/dev-python/cython-0.22-r2/work/Cython-0.22/docs/src/quickstart/overview.rst
looking for now-outdated files... none found
pickling environment... done
checking consistency... /var/tmp/portage/dev-python/cython-0.22-r2/work/Cython-0.22/docs/src/userguide/numpy_tutorial.rst:: WARNING: document isn't included in any toctree
/var/tmp/portage/dev-python/cython-0.22-r2/work/Cython-0.22/docs/src/userguide/pxd_package.rst:: WARNING: document isn't included in any toctree
/var/tmp/portage/dev-python/cython-0.22-r2/work/Cython-0.22/docs/welcome.rst:: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  1%] index
writing output... [  3%] src/quickstart/build
writing output... [  5%] src/quickstart/cythonize
writing output... [  7%] src/quickstart/index
writing output... [  9%] src/quickstart/install
writing output... [ 11%] src/quickstart/overview
writing output... [ 13%] src/reference/compilation
writing output... [ 15%] src/reference/directives
writing output... [ 17%] src/reference/extension_types
writing output... [ 19%] src/reference/index
writing output... [ 21%] src/reference/interfacing_with_other_code
writing output... [ 23%] src/reference/language_basics
writing output... [ 25%] src/reference/limitations
writing output... [ 27%] src/reference/special_mention
writing output... [ 29%] src/reference/special_methods_table
writing output... [ 31%] src/tutorial/appendix
writing output... [ 33%] src/tutorial/array
writing output... [ 35%] src/tutorial/caveats
writing output... [ 37%] src/tutorial/cdef_classes
writing output... [ 39%] src/tutorial/clibraries
writing output... [ 41%] src/tutorial/cython_tutorial
writing output... [ 43%] src/tutorial/external
writing output... [ 45%] src/tutorial/index
writing output... [ 47%] src/tutorial/memory_allocation
writing output... [ 49%] src/tutorial/numpy
writing output... [ 50%] src/tutorial/profiling_tutorial
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writing output... [ 52%] src/tutorial/pure
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>>> Failed to emerge dev-python/cython-0.22-r2, Log file:

>>>  '/var/tmp/portage/dev-python/cython-0.22-r2/temp/build.log'

 * Messages for package sys-devel/llvm-3.5.1:

 * The C++ compiler -g option is known to increase the size of the package
 * considerably. If you run out of space, please consider removing it.
 * 

 * Regenerating GNU info directory index...
 *      used by /usr/lib/python2.7/site-packages/PyQt4/QtOpenGL.so (dev-python/PyQt4-4.11.1)

F: mkdir
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F: mkdir
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C: mkdir ././var/cache/fonts/pk 

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A: /var/cache/fonts/pk
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C: mkdir ././var/cache/fonts/pk * --------------------------------------------------------------------------------

>>> Failed to emerge dev-python/cython-0.22-r2, Log file:

>>>  '/var/tmp/portage/dev-python/cython-0.22-r2/temp/build.log'

 * Messages for package sys-devel/llvm-3.5.1:

 * The C++ compiler -g option is known to increase the size of the package
 * considerably. If you run out of space, please consider removing it.
 * 

 * Regenerating GNU info directory index...
 * Processed 203 info files.

F: mkdir
S: deny
P: ././var/cache/fonts/pk
A: /var/cache/fonts/pk
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C: mkdir ././var/cache/fonts/pk 

F: mkdir
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C: mkdir ././var/cache/fonts/pk 

F: mkdir
S: deny
P: ././var/cache/fonts/pk
A: /var/cache/fonts/pk
R: /var/cache/fonts/pk
C: mkdir ././var/cache/fonts/pk * --------------------------------------------------------------------------------

>>> Failed to emerge dev-python/cython-0.22-r2, Log file:

>>>  '/var/tmp/portage/dev-python/cython-0.22-r2/temp/build.log'
kiwifb commented 9 years ago

Definitely sandbox violation. I will look into it further. It is curious that it wasn't spotted in the main tree before, I'll have to check the patches.

kiwifb commented 9 years ago

OK, I cannot reproduce it here. If I remember correctly you have a hardened profile, so it is probably linked to that. You will likely get the same problem if you install cython-0.22 from the main tree so we'll need to open a matching bug in gentoo's bugzilla.

One thing I would like you to try is in the ebuild to replace

 use doc && unset XDG_CONFIG_HOME && emake -C docs html

by 

use doc && unset XDG_CONFIG_HOME && export VARTEXFONTS="${T}"/fonts && emake -C docs html
Alessandro-Barbieri commented 9 years ago

Changed and worked. Thanks.

kiwifb commented 9 years ago

Can you confirm that you are using a hardened profile? I will fix it in the overlay but the main Gentoo tree should also be affected, so someone will have to open a bug in bugzilla to get it fixed there.

Alessandro-Barbieri commented 9 years ago

I confirm the hardened profile.