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| -rw-r--r-- | issues/genenetwork2/broken-collections-features.gmi | 6 | ||||
| -rw-r--r-- | issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip | bin | 0 -> 143152 bytes | |||
| -rw-r--r-- | issues/genenetwork3/ctl-maps-error.gmi | 45 |
3 files changed, 51 insertions, 0 deletions
diff --git a/issues/genenetwork2/broken-collections-features.gmi b/issues/genenetwork2/broken-collections-features.gmi index 12baf69..129c3e9 100644 --- a/issues/genenetwork2/broken-collections-features.gmi +++ b/issues/genenetwork2/broken-collections-features.gmi @@ -35,3 +35,9 @@ There are some features in the search results page, and/or the collections page * The "CTL" and "WCGNA" features have a failure mode that might have been caused by recent changes making use of AJAX calls, rather than submitting the form manually. * The "MultiMap" and "Generate Heatmap" features raise exceptions that need to be investigated and resolved * The "Partial Correlations" feature seems to run forever + +## Break-out Issues + +We break-out the issues above into separate pages to track the progress of the fixes for each feature separately. + +=> /issues/genenetwork3/ctl-maps-error diff --git a/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip b/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip Binary files differnew file mode 100644 index 0000000..7681b88 --- /dev/null +++ b/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip diff --git a/issues/genenetwork3/ctl-maps-error.gmi b/issues/genenetwork3/ctl-maps-error.gmi new file mode 100644 index 0000000..c919d92 --- /dev/null +++ b/issues/genenetwork3/ctl-maps-error.gmi @@ -0,0 +1,45 @@ +# CTL Maps Error + +## Tags + +* type: bug +* status: open +* priority: high +* assigned: zachs, fredm +* keywords: CTL, CTL Maps, gn3, genetwork3, genenetwork 3 + +## Description + +Trying to run the CTL Maps feature in the collections page as described in +=> /issues/genenetwork2/broken-collections-feature + +We get an error in the results page of the form: + +``` +{'error': '{\'code\': 1, \'output\': \'Loading required package: MASS\\nLoading required package: parallel\\nLoading required package: qtl\\nThere were 13 warnings (use warnings() to see them)\\nError in xspline(x, y, shape = 0, lwd = lwd, border = col, lty = lty, : \\n invalid value specified for graphical parameter "lwd"\\nCalls: ctl.lineplot -> draw.spline -> xspline\\nExecution halted\\n\'}'} +``` + +on the CLI the same error is rendered: +``` +Loading required package: MASS +Loading required package: parallel +Loading required package: qtl +There were 13 warnings (use warnings() to see them) +Error in xspline(x, y, shape = 0, lwd = lwd, border = col, lty = lty, : + invalid value specified for graphical parameter "lwd" +Calls: ctl.lineplot -> draw.spline -> xspline +Execution halted +``` + +On my local development machine, the command run was +``` +Rscript /home/frederick/genenetwork/genenetwork3/scripts/ctl_analysis.R /tmp/01828928-26e6-4cad-bbc8-59fd7a7977de.json +``` + +=> /issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip Here is a zipped version of the json file. + +Troubleshooting a while, I suspect +=> https://github.com/genenetwork/genenetwork3/blob/27d9c9d6ef7f37066fc63af3d6585bf18aeec925/scripts/ctl_analysis.R#L79-L80 this is the offending code. + +=> https://cran.r-project.org/web/packages/ctl/ctl.pdf The manual for the ctl library +indicates that our call above might be okay, which might mean something changed in the dependencies that the ctl library used. |