Path: csiph.com!eternal-september.org!reader02.eternal-september.org!aioe.org!bofh.it!news.nic.it!robomod From: Andreas Tille Newsgroups: linux.debian.maint.python Subject: Placement of *.so files to be found by Python modules (Was: ont-fast5-api) Date: Thu, 27 May 2021 15:10:02 +0200 Message-ID: References: X-Original-To: Debian Python X-Mailbox-Line: From debian-python-request@lists.debian.org Thu May 27 13:08:26 2021 Old-Return-Path: X-Amavis-Spam-Status: No, score=-4.98 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, DIGITS_LETTERS=1, LDO_WHITELIST=-5, MD5_SHA1_SUM=-1, MEDS2=2, MURPHY_DRUGS_REL8=0.02] autolearn=no autolearn_force=no X-Policyd-Weight: using cached result; rate:hard: -4.6 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.10.1 (2018-07-13) X-Mailing-List: archive/latest/19198 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/20210527130809.GD18307@an3as.eu Approved: robomod@news.nic.it Lines: 73 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: debian-med@lists.debian.org X-Original-Date: Thu, 27 May 2021 15:08:09 +0200 X-Original-Message-ID: <20210527130809.GD18307@an3as.eu> X-Original-References: <243e5b57-1c3e-8432-46bf-1a34381b3370@gmx.de> <20210522071046.GC8962@an3as.eu> <20210522212431.GF8962@an3as.eu> <20210523083600.GH8962@an3as.eu> <20210523210438.GI8962@an3as.eu> <117ff77a-5330-530f-c578-79e060e5d2dc@nileshpatra.info> Xref: csiph.com linux.debian.maint.python:13410 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 -- http://fam-tille.de