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carissalow / rapids

Reproducible Analysis Pipeline for Data Streams
http://www.rapids.science/
GNU Affero General Public License v3.0
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CalledProcessError #77

Closed IanLiu0313 closed 4 years ago

IanLiu0313 commented 4 years ago

Hi, I have been experiencing this issue after running the command "snakemake -j1" The error says "CalledProcessError in line 8 of /home/ianliu/rapids/rules/preprocessing.snakefile:".

I've followed all the steps as the documentation instructs.

CalledProcessError

JulioV commented 4 years ago

@IanLiu0313 can you paste your .env file without your password and the first 35 lines of you config.yaml, please?

JulioV commented 4 years ago

@IanLiu0313 The problem is Ubuntu wide when trying to connect to an old MySQL server (in this case api.awareframework.com) with MySQL client 8.0. You will get the same error message if you try to connect from the command line. There you can add the option --ssl-mode=DISABLED but we can't do this from the R connector.

I talked to Denzil and it is not feasible to update api.awareframework.com at the moment as it's meant mostly for testing. The quickest solution would be to import your database to another server or to a local environment. Alternatively, you could replace mysql-client and libmysqlclient-dev with mariadb-client and libmariadbclient-devinstall and reinstall renv, in theory it should work but I have not tested it.

More info about this issue here https://bugs.launchpad.net/ubuntu/+source/mysql-8.0/+bug/1872541

IanLiu0313 commented 4 years ago

That's very helpful! Thank you so much Julio!