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ndcn / omicser

The NDCN omics browser app for browsing and sharing general omics data.
https://ndcn.github.io/omicser
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github actions stop #182

Closed ricoderks closed 2 years ago

ricoderks commented 2 years ago

The github actions are not fnishing. They stop on the error the that package ComplexHeatmap can not be installed due to depency circlize.

I tried to install ComplexHeatmap (via github) locally to see if I can get some more information on the error. The error I get locally is:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘circlize’ 0.4.13 is being loaded, but >= 0.4.14 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ricoderks commented 2 years ago

I noticed that there was a change in ComplexHeatmap 6 days ago which causes this. The requirement for circlize changed from 0.4.5 to 0.4.14. The CRAN version is 0.4.13. Maybe we should wait a few days to see if CRAN get's updated.

ergonyc commented 2 years ago

I started looking into this when it first failed. For now waiting to see if there's a CRAN update. Having the error in the actions is not critical since we don't have updated documentation being pushed... In the longer term I think we may want to pin ComplexHeatmap to a stable version.

Also probably should open an issue / dialog with @jokergoo for advice. He maintains both ComplexHeatmap and Circlize... and might have some interest in what we are doing.

jokergoo commented 2 years ago

Hi, I will submit circlize 0.4.14 to CRAN today :)

jokergoo commented 2 years ago

Now 0.4.14 is on CRAN https://cran.r-project.org/web/packages/circlize/index.html It may take several days to be available on other mirrors.

ricoderks commented 2 years ago

Should be fixed know.