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Fix R dependencies for gsl and reticulate in the METviewer Docker image. #226

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JohnHalleyGotway opened this issue Nov 30, 2020 · 0 comments · Fixed by #228 or #229
Closed
19 of 21 tasks

Fix R dependencies for gsl and reticulate in the METviewer Docker image. #226

JohnHalleyGotway opened this issue Nov 30, 2020 · 0 comments · Fixed by #228 or #229
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priority: high High Priority reporting: DTC NOAA BASE NOAA Office of Atmospheric Research DTC Project requestor: NCAR/RAL NCAR Research Applications Laboratory type: bug Fix something that is not working

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JohnHalleyGotway commented Nov 30, 2020

Describe the Problem

This issue arose via MET-Help:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=97638

The user reported that when running the METviewer container, the plot fails whenever aggregation methods are requested. I replicated this behavior and produced the following R-script error message:

RunningRscript /opt/tomcat/webapps/metviewer//R_work/include/agg_stat.R
==== Start Rscript error ====
Error in library(gsl) : there is no package called 'gsl'
Execution halted
==== End Rscript error ====
Rscript time 0:00:00.212

So debugging reveals that both the gsl and reticulate libraries are missing from the installation of R inside the container. Both are included by at least one of the METviewer R-scripts.

The issue with GSL is that yum install gsl-devel installs GSL version 1.15. However, the R GSL package requires GSL version 2.1 or higher. So fix the system level installation of GSL and add one line to also install the missing reticulate package.

Expected Behavior

The aggregation methods should work inside the container.

Environment

Describe your runtime environment:
1. METviewer Docker image

To Reproduce

Describe the steps to reproduce the behavior:
*1. Follow the METplus Training video: https://dtcenter.github.io/METplus-Training/modules/METviewer/docker.html
2. Launch METviewer and load sample data.
3. Make any plot that uses aggregation.
4. Note the error in the Rscript log tab.
Post relevant sample data following these instructions:
https://dtcenter.org/community-code/model-evaluation-tools-met/met-help-desk#ftp

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Consider the impact to the other METplus components.

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@JohnHalleyGotway JohnHalleyGotway added type: bug Fix something that is not working priority: high High Priority requestor: NCAR/RAL NCAR Research Applications Laboratory labels Nov 30, 2020
@JohnHalleyGotway JohnHalleyGotway added this to the METviewer 4.0 milestone Nov 30, 2020
@JohnHalleyGotway JohnHalleyGotway added this to To do in METviewer-4.0-beta2 (12/09/20) via automation Nov 30, 2020
@JohnHalleyGotway JohnHalleyGotway self-assigned this Nov 30, 2020
@JohnHalleyGotway JohnHalleyGotway added this to To do in METplus Version 3.1 Support via automation Nov 30, 2020
JohnHalleyGotway added a commit that referenced this issue Dec 1, 2020
…will install correctly. Also, install the reticulate R package.
This was linked to pull requests Dec 1, 2020
METplus Version 3.1 Support automation moved this from To do to Done Dec 2, 2020
METviewer-4.0-beta2 (12/09/20) automation moved this from To do to Done Dec 2, 2020
@TaraJensen TaraJensen added the reporting: DTC NOAA BASE NOAA Office of Atmospheric Research DTC Project label Dec 21, 2020
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Labels
priority: high High Priority reporting: DTC NOAA BASE NOAA Office of Atmospheric Research DTC Project requestor: NCAR/RAL NCAR Research Applications Laboratory type: bug Fix something that is not working
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