Hi,
there is a problem with ont-fast5-api[0]
On Wed, May 26, 2021 at 03:22:21AM +0530, Nilesh Patra wrote:
> However, one problem - I'm being verbose so we are in loop:
>
> - This package had .so files vendored in ont_fast5_api/vbz_plugin/* -- this
> is a violation, and hence you repacked it - see this[1]
> - The so files it had, are basically the shared object files that
> libvbz-hdf-plugin vendors, and that was why we packaged it
> - *Now*, we need to somehow tell this package to find the .so files at the
> right location
>
> I did not manage to do that, so I simply ended up symlinking the .so vendored
> by libvbz-hdf-plugin in that directory. This looks like a bad workaround,
> and hence if you have some way to fixup paths, please have a look.
> The bad change I'm talking about is this one[2]
I can confirm if I disable Nilesh's patch[2] than the build time
tests are failing like:
======================================================================
ERROR: test_add_read_from_multi (test.test_compress_fast5.TestVbzConvert)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/ont-fast5-api-3.1.5+dfsg/.pybuild/cpython3_3.9_ont_fast5_api/build/ont_fast5_api/fast5_read.py",
line 104, in add_raw_data
self.handle[self.raw_dataset_group_name].create_dataset('Signal',
data=data, dtype='i2',
File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/group.py",
line 136, in create_dataset
dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
File
"/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/dataset.py", line
137, in make_new_dset
dcpl = filters.fill_dcpl(
File
"/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/filters.py", line
234, in fill_dcpl
raise ValueError("Unknown compression filter number: %s" % compression)
ValueError: Unknown compression filter number: 32020
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/build/ont-fast5-api-3.1.5+dfsg/.pybuild/cpython3_3.9_ont_fast5_api/build/test/test_compress_fast5.py",
line 98, in test_add_read_from_multi
output_f5.add_existing_read(input_read, target_compression)
File
"/build/ont-fast5-api-3.1.5+dfsg/.pybuild/cpython3_3.9_ont_fast5_api/build/ont_fast5_api/multi_fast5.py",
line 80, in add_existing_read
self._add_read_from_multi(read_to_add, target_compression)
File
"/build/ont-fast5-api-3.1.5+dfsg/.pybuild/cpython3_3.9_ont_fast5_api/build/ont_fast5_api/multi_fast5.py",
line 97, in _add_read_from_multi
output_read.add_raw_data(raw_data, raw_attrs,
compression=target_compression)
File
"/build/ont-fast5-api-3.1.5+dfsg/.pybuild/cpython3_3.9_ont_fast5_api/build/ont_fast5_api/fast5_read.py",
line 107, in add_raw_data
raise_missing_vbz_error_read(e)
File
"/build/ont-fast5-api-3.1.5+dfsg/.pybuild/cpython3_3.9_ont_fast5_api/build/ont_fast5_api/compression_settings.py",
line 73, in raise_missing_vbz_error_read
raise IOError(VBZ_ERROR_MESSAGE.format(register_plugin())) from err
OSError: Failed to read compressed raw data. VBZ compression filter (id=32020)
may be missing from expected path:
'/build/ont-fast5-api-3.1.5+dfsg/.pybuild/cpython3_3.9_ont_fast5_api/build/ont_fast5_api/vbz_plugin'
======================================================================
ERROR: test_compress_read_from_single (test.test_compress_fast5.TestVbzConvert)
----------------------------------------------------------------------
...
I wonder if there is some trick to point the code to the proper
location of the plugins. Just a warning: The plugins are currently
in new[3] as well as its precondition libstreamvbyte[4].
Kind regards
Andreas.
[0] https://salsa.debian.org/med-team/ont-fast5-api
> [1]:
> https://salsa.debian.org/med-team/ont-fast5-api/-/commit/097a79d489062b82c6b3abfc45a970bee59893de
> [2]:
> https://salsa.debian.org/med-team/ont-fast5-api/-/commit/eb74a43929768ab0455f549919df2c5a6607525d
[3] https://ftp-master.debian.org/new/libvbz-hdf-plugin_1.0.1-1.html
[4] https://ftp-master.debian.org/new/libstreamvbyte_0.4.1-1.html
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