fabio [debian] erros and warning during the build in buildd

Hello here you can find the buildlog from i386 and it seems that there is some problems during the doc generation

https://buildd.debian.org/status/fetch.php?pkg=python-fabio&arch=i386&ver=0.5.0%2Bdfsg-1&stamp=1505210681&raw=0

reading sources... [100%] tutorials/index

/<<BUILDDIR>>/python-fabio-0.5.0+dfsg/.pybuild/pythonX.Y_2.7/build/fabio/numpyimage.py:docstring of fabio.numpyimage.NumpyImage:6: SEVERE: Unexpected section title.

Format Specification: Version 1.0
=================================
/<<BUILDDIR>>/python-fabio-0.5.0+dfsg/.pybuild/pythonX.Y_2.7/build/fabio/numpyimage.py:docstring of fabio.numpyimage.NumpyImage:51: SEVERE: Unexpected section title.

Format Specification: Version 2.0
=================================
/<<BUILDDIR>>/python-fabio-0.5.0+dfsg/doc/source/getting_started.rst:246: ERROR: Error with CSV data in "csv-table" directive:
',' expected after '"'

.. csv-table:: Supported formats
   :header: "Python Module", "Detector / Format", "Extension", "Read", "Multi-image", "Write"
   :widths: 30, 30, 20, 10, 15, 10

   "ADSC", "ADSC Quantum", ".img ", "Yes", "No", "Yes"
   "Bruker86", "Bruker formats", ".sfrm ", "Yes", "No", "Yes"
   "Bruker100", "Bruker formats", ".sfrm ", "Yes", "No", "Yes"
   "CBF", "CIF binary files", ".cbf ", "Yes", "No", "Yes"
   "DM3", "Gatan Digital Micrograph ", ".dm3 ", "Yes", "No", "No"
   "EDF", "ESRF data format ", ".edf ", "Yes", "Yes ", "Yes"
   "EDNA-XML", "Used by EDNA", ".xml ", "Yes", "No", "No"
   "Eiger", "Dectris format", ".h5", "Yes", "Yes", "Yes"
   "Fit2D", "Fit2D binary format", ".f2d", "Yes", "No", "No"
   "Fit2D mask", "Fit2D mask", ".msk ", "Yes", "No", "Yes"
   "Fit2D spreadsheet", "Fit2D Ascii format", ".spr ", "Yes", "No", "Yes"
   "GE", "General Electric", "No", "Yes", "Yes ", "No"
   "JPEG", "Joint Photographic Experts Group", ".jpg", "Yes", "No", "No"
   "JPEG2k", "JPEG 2000", ".jpx", "Yes", "No", "No"
   "Hdf5", "Needs the dataset path", ".h5", "Yes", "Yes", "No"
   "HiPiC", "Hamamatsu CCD", ".tif ", "Yes", "No", "No"
   "kcd", "Nonius KappaCCD", ".kccd ", "Yes", "No", "No"
   "marccd", "MarCCD/Mar165", ".mccd ", "Yes", "No", "No"
   "mar345", "Mar345 image plate", ".mar3450 ", "Yes", "No", "Yes"
   "mpa", "Multi-wire detector", ".mpa", "yes", "No", "No"
   "numpy", "numpy 2D array", "npy ", "Yes", "No", "Yes"
   "OXD", "Oxford Diffraction", ".img ", "Yes", "No", "Yes"
   "Pixi", "pixi", ". ", "Yes", "No", "No"
   "pilatus", "Dectris Pilatus Tiff", ".tif ", "Yes", "No", "Yes"
   "PNM", "Portable aNy Map", ".pnm ", "Yes", "No", "Yes"
   "Raxis", "Rigaku Saxs format", ".img", "Yes", "No", "No"
   "spe", "Princeton instrumentation", ".spe", "Yes, "Yes", "No"
   "TIFF", "Tagged Image File Format", ".tif ", "Yes", "No", "Yes"
/<<BUILDDIR>>/python-fabio-0.5.0+dfsg/doc/source/man/fabio_viewer.rst:8: ERROR: Command u'fabio_viewer --help' failed: [Errno 2] No such file or directory
/<<BUILDDIR>>/python-fabio-0.5.0+dfsg/doc/source/tutorials/Nexus2cbf.rst:18: WARNING: Line block ends without a blank line.
looking for now-outdated files... none found

and


/<<BUILDDIR>>/python-fabio-0.5.0+dfsg/doc/source/api/modules.rst:181: WARNING: autodoc: failed to import module 'fabio.mrcimage'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc.py", line 560, in import_object
    __import__(self.modname)
  File "/<<BUILDDIR>>/python-fabio-0.5.0+dfsg/.pybuild/pythonX.Y_3.6/build/fabio/mrcimage.py", line 50, in <module>
    if sys.version_info < (3.0):
TypeError: '<' not supported between instances of 'sys.version_info' and 'float'

Sep 12 '17 10:09 picca

On Tue, 12 Sep 2017 10:13:58 +0000 (UTC) picca [email protected] wrote:

Hello here you can find the buildlog from i386 and it seems that there is some problems during the doc generation

https://buildd.debian.org/status/fetch.php?pkg=python-fabio&arch=i386&ver=0.5.0%2Bdfsg-1&stamp=1505210681&raw=0

I think Valentin fixed this recently ... https://github.com/silx-kit/fabio/pull/158

Sep 12 '17 12:09 kif

The one from the table of formats is fixed.
But i never see the one with if sys.version_info < (3.0). That's very strange. Which version of Python 3 do you use?
And i have no idea how to fix the numpy one. The docstring do not accept any titles. Maybe it is better to link an external page to the specification.

Sep 13 '17 06:09 vallsv

Hello guyes, Here the new build log

https://buildd.debian.org/status/fetch.php?pkg=python-fabio&arch=amd64&ver=0.6.0%2Bdfsg-1&stamp=1516550885&raw=0

there is still some warning during the documentation

reading sources... [100%] tutorials/index

/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/.pybuild/pythonX.Y_2.7/build/fabio/numpyimage.py:docstring of fabio.numpyimage.NumpyImage:6: WARNING: Unexpected section title.

Format Specification: Version 1.0
=================================
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/.pybuild/pythonX.Y_2.7/build/fabio/numpyimage.py:docstring of fabio.numpyimage.NumpyImage:51: WARNING: Unexpected section title.

Format Specification: Version 2.0
=================================
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/doc/source/install.rst:15: WARNING: Error in "code" directive:
1 argument(s) required, 0 supplied.

.. code::

    sudo apt-get install python-fabio
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/doc/source/install.rst:27: WARNING: Error in "code" directive:
1 argument(s) required, 0 supplied.

.. code::

   python get-pip.py
   pip install fabio
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/doc/source/install.rst:136: WARNING: Error in "code" directive:
1 argument(s) required, 0 supplied.

.. code::

    sudo pip install fabio
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/doc/source/man/fabio_viewer.rst:8: WARNING: Command u'fabio_viewer --help' failed: [Errno 2] No such file or directory
looking for now-outdated files... none found
pickling environment... done

And still the python3 problem.

Jan 21 '18 16:01 picca

There is also a bunch of C compiler warning.

Jan 21 '18 16:01 picca

The C warnings can't be fixed unfortunately. That's from Cython file with openmp support.

It can be fixed using an extra initialization of the variable, which are anyway initialized by the algorithm later. Then it should not be needed.

Jan 22 '18 13:01 vallsv

I was more refering about the libccp4 part and not necessarely the cython generated files :)

Jan 22 '18 14:01 picca

On debian 8, I only found that, plus numpy deprecations

fabio/ext/src/columnfile.c: In function ‘cf_read_ascii’:
fabio/ext/src/columnfile.c:180:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line,2048,(FILE *)fp);
   ^

Jan 22 '18 14:01 vallsv

Sorry, I wxill put the relevant messages here :)

x86_64-linux-gnu-gcc: fabio/ext/src/ccp4_pack.c
fabio/ext/src/ccp4_pack.c: In function 'pack_chunk':
fabio/ext/src/ccp4_pack.c:816:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   { for (i = nmbr, j = 0; i > 1; i /= 2, ++j);
     ^~~
fabio/ext/src/ccp4_pack.c:817:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
     descriptor[0] = j;
     ^~~~~~~~~~
At top level:
fabio/ext/src/ccp4_pack.c:83:27: warning: 'CCP4_PCK_MASK_16' defined but not used [-Wunused-const-variable=]
 static const unsigned int CCP4_PCK_MASK_16[]={0x00,
                           ^~~~~~~~~~~~~~~~

/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/.pybuild/pythonX.Y_2.7/build/fabio/numpyimage.py:docstring of fabio.numpyimage.NumpyImage:6: WARNING: Unexpected section title.

Format Specification: Version 1.0
=================================
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/.pybuild/pythonX.Y_2.7/build/fabio/numpyimage.py:docstring of fabio.numpyimage.NumpyImage:51: WARNING: Unexpected section title.

Format Specification: Version 2.0
=================================
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/doc/source/install.rst:15: WARNING: Error in "code" directive:
1 argument(s) required, 0 supplied.

.. code::

    sudo apt-get install python-fabio
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/doc/source/install.rst:27: WARNING: Error in "code" directive:
1 argument(s) required, 0 supplied.

.. code::

   python get-pip.py
   pip install fabio
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/doc/source/install.rst:136: WARNING: Error in "code" directive:
1 argument(s) required, 0 supplied.

.. code::

    sudo pip install fabio
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/doc/source/man/fabio_viewer.rst:8: WARNING: Command u'fabio_viewer --help' failed: [Errno 2] No such file or directory
looking for now-outdated files... none found

and this one

/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/doc/source/api/modules.rst:181: WARNING: autodoc: failed to import module 'fabio.mrcimage'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc.py", line 658, in import_object
    __import__(self.modname)
  File "/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/.pybuild/pythonX.Y-dbg_3.6/build/fabio/mrcimage.py", line 50, in <module>
    if sys.version_info < (3.0):
TypeError: '<' not supported between instances of 'sys.version_info' and 'float'
/<<BUILDDIR>>/python-fabio-0.6.0+dfsg/.pybuild/pythonX.Y-dbg_3.6/build/fabio/numpyimage.py:docstring of fabio.numpyimage.NumpyImage:6: WARNING: Unexpected section title.

where is seems thaht version_info is not a float.

Jan 22 '18 14:01 picca

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[debian] erros and warning during the build in buildd

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