Check error message appearing in assessment reports

[gothub]

Assessment reports created after Nov 21, 2021 one or both of the following messages in the check output.

• "Error in library(jsonlite, quietly = TRUE) : there is no package called ‘jsonlite’ Execution halted"
• "ImportError: library metadig not found"

For example:

[gothub]

The first error "Error in library(jsonlite, quietly = TRUE) : there is no package called ‘jsonlite’ Execution halted" is a result of a CRAN mirror not being available. This mirror was referenced in the Docker file that builds the metadig-worker container. The solution is to change the current, inactive mirror with '(repos = c(CRAN = "http://cran.rstudio.com"', which uses a content delivery network, fronted by Amazon CloudFlare (https://www.rstudio.com/blog/rstudio-cran-mirror/).

The second error is due to updating to Jython v2.7.2, which no longer inspects the environment variable 'JYTHONPATH' to determine the location of the NCEAS metadig Python library. Jython v2.7.2 uses a command line argument to communication this value now. This is specified in the Java command from the metadig-worker Docker file. The new Dockerfile command specified the search path like this:

CMD java  -Dpython.path=/opt/local/metadig/metadig-py edu.ucsb.nceas.mdqengine.Worker