PS Same error ("Conda dependency seemingly installed but failed to build job environment.”) running Estimate parameters tool on our Jetstream instance.
On Jul 7, 2019, at 3:06 PM, ide <ide@cs.vassar.edu> wrote:
Hi all
Now that GCC is over I wonder if we could resolve the problem from our discussion below. We have tried everything but nothing helps. We really need to get this solved...
On another note, I have a local Galaxy instance that cannot run certain of the machine learning tools from the tool shed because they require a certain module (imblearn in this case), but I get this error:
ERROR: Could not find a version that satisfies the requirement scikit-learn>=0.21 (from imbalanced-learn) (from versions: 0.9, 0.10, 0.11, 0.12, 0.12.1, 0.13, 0.13.1, 0.14, 0.14.1, 0.15.0b1, 0.15.0b2, 0.15.0, 0.15.1, 0.15.2, 0.16b1, 0.16.0, 0.16.1, 0.17b1, 0.17, 0.17.1, 0.18rc2, 0.18, 0.18.1, 0.18.2, 0.19b2, 0.19.0, 0.19.1, 0.19.2, 0.20rc1, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.21rc2) ERROR: No matching distribution found for scikit-learn>=0.21 (from imbalanced-learn)
scikit-learn is installed in python2.7 but it is version .20.3 (pip install -U scikit-learn gives Requirement already up-to-date: scikit-learn in ./.venv/lib/python2.7/site-packages (0.20.3)
I assume that Python 2.7 does not work with version .21.
Interestingly, the tools requiring imblearn work on our development Galaxy instance at jetstream.galaxy.org <http://jetstream.galaxy.org/>. There, Python 2.7 has a similarly old (.20.2) version of scikit-learn, and no version installed for Python3.
In any case, I have googled this error and discovered that there has never been a good answer on forums such as stackoverflow. So if you have an idea I'd be most grateful.
Thanks!
Begin forwarded message:
From: Keith Suderman <suderman@cs.vassar.edu <mailto:suderman@cs.vassar.edu>> Subject: Re: [galaxy-dev] Error Date: June 27, 2019 at 4:23:06 PM EDT To: Pietro Mandreoli <pietro.mandreoli@studenti.unimi.it <mailto:pietro.mandreoli@studenti.unimi.it>>, Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> Cc: Ide Nancy <ide@cs.vassar.edu <mailto:ide@cs.vassar.edu>>, galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org>
Hi Pietro,
I suspect the package is broken. The anaconda.org <http://anaconda.org/> server is available, but the libgcc-ng file is not where the package expects it to be.
I followed your suggestion and it worked... sort of. At least it exposed another error, actually the same problem but with numpy... So I applied the same solution and that worked... sort of. Now the error is:
Traceback (most recent call last): File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/_vendor/auxlib/entity.py", line 411, in __get__ val = instance.__dict__[self.name] KeyError: 'size'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/exceptions.py", line 1043, in __call__ return func(*args, **kwargs) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/main.py", line 84, in _main exit_code = do_call(args, p) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 82, in do_call exit_code = getattr(module, func_name)(args, parser) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/main_create.py", line 37, in execute install(args, parser, 'create') File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/install.py", line 304, in install handle_txn(unlink_link_transaction, prefix, args, newenv) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/install.py", line 320, in handle_txn unlink_link_transaction.print_transaction_summary() File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/core/link.py", line 877, in print_transaction_summary change_report_str = self._change_report_str(change_report) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/core/link.py", line 926, in _change_report_str size = prec.size File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/_vendor/auxlib/entity.py", line 417, in __get__ raise AttributeError("A value for {0} has not been set".format(self.name)) AttributeError: A value for size has not been set
The full Galaxy log is attached.
Cheers, Keith
On Jun 26, 2019, at 7:31 AM, Pietro Mandreoli <pietro.mandreoli@studenti.unimi.it <mailto:pietro.mandreoli@studenti.unimi.it>> wrote:
Hi, probably the package is broken see https://anaconda.org/conda-forge/libgcc-ng/files <https://anaconda.org/conda-forge/libgcc-ng/files> . Try to install the previous version manually, activating conda and then the conda environment of the tool.
commands: source _conda/bin/activate to activate CONDA cd _conda/envs
source activate <name of the tool env>
then conda install <package> -c <channel>
Best regards,
PM <signaturebeforequotedtext></signaturebeforequotedtext> Il 25/06/19 22:59, Nancy Ide <ide@cs.vassar.edu <mailto:ide@cs.vassar.edu>> ha scritto:
I get this error when trying to run "Plot confusion matrix, precision, recall and ROC and AUC curves":
CondaError: CondaHTTPError: HTTP 404 NOT FOUND for url <https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-7.3.0-hdf63c60_0.t... <https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-7.3.0-hdf63c60_0.tar.bz2> <https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-7.3.0-hdf63c60_0.t... <https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-7.3.0-hdf63c60_0.tar.bz2>>>
as the file libgcc-ng-7.3.0-hdf63c60_0.tar.bz2 does not exist in https://conda.anaconda.org/conda-forge/linux-64/ <https://conda.anaconda.org/conda-forge/linux-64/> <https://conda.anaconda.org/conda-forge/linux-64/ <https://conda.anaconda.org/conda-forge/linux-64/>>
Please help!
Thanks -----------------------------------------------------
Nancy Ide Professor of Computer Science
Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA
tel: (+1 845) 437 5988 fax: (+1 845) 437 7498 email: ide@cs.vassar.edu <mailto:ide@cs.vassar.edu> http://www.cs.vassar.edu/~ide
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Nancy Ide Professor of Computer Science
Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA
tel: (+1 845) 437 5988 fax: (+1 845) 437 7498 email: ide@cs.vassar.edu <mailto:ide@cs.vassar.edu> http://www.cs.vassar.edu/~ide
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----------------------------------------------------- Nancy Ide Professor of Computer Science Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA tel: (+1 845) 437 5988 fax: (+1 845) 437 7498 email: ide@cs.vassar.edu http://www.cs.vassar.edu/~ide -----------------------------------------------------