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>>
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/> 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 http://www.cs.vassar.edu/~ide -----------------------------------------------------
Hi Nancy, this looks like a timout during a download of conda packages. I assume anaconda.org had some hiccups, please try again. Those URLs should exists. Ciao, Bjoern Am 25.06.19 um 22:59 schrieb Nancy Ide:
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Unfortunately still the same error! Trying Pietro’s solution.
On Jun 26, 2019, at 5:57 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Nancy,
this looks like a timout during a download of conda packages.
I assume anaconda.org had some hiccups, please try again. Those URLs should exists.
Ciao, Bjoern
Am 25.06.19 um 22:59 schrieb Nancy Ide:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
----------------------------------------------------- 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 -----------------------------------------------------
Hi, probably the package is broken see 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> 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>>
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/>
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 http://www.cs.vassar.edu/~ide
-----------------------------------------------------
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<signatureafterquotedtext></signatureafterquotedtext>
Hi Pietro, I suspect the package is broken. The 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> wrote:
Hi, probably the package is broken see 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> 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>>
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/>
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 http://www.cs.vassar.edu/~ide
-----------------------------------------------------
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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> Subject: Re: [galaxy-dev] Error Date: June 27, 2019 at 4:23:06 PM EDT To: Pietro Mandreoli <pietro.mandreoli@studenti.unimi.it>, Björn Grüning <bjoern.gruening@gmail.com> Cc: Ide Nancy <ide@cs.vassar.edu>, 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 . 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>>
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/>
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 http://www.cs.vassar.edu/~ide
-----------------------------------------------------
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
<signatureafterquotedtext></signatureafterquotedtext> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
----------------------------------------------------- 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 -----------------------------------------------------
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
-----------------------------------------------------
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
<signatureafterquotedtext></signatureafterquotedtext> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/> <galaxy-error-log.txt>
-----------------------------------------------------
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
-----------------------------------------------------
----------------------------------------------------- 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 -----------------------------------------------------
participants (5)
-
Björn Grüning -
ide -
Keith Suderman -
Nancy Ide
-
Pietro Mandreoli