sk-sahu / sig-bio-shiny Goto Github PK

For now, this requires at least 8GB memory to run few clusterProfiler functions.

Someway if this can hold to a lesser memory.

When a enrich function returns NULL the app disconnected

No gene set have size > 10 ...
--> return NULL...

When the input list and gene-id type doesn't match shiny app disconnection.

Error: Failed to install 'SigBio' from GitHub:
Failed to install 'DOSE' from GitHub:
(converted from warning) cannot remove prior installation of package ‘backports’

Once the input IDs detected it can be used to

• give error message for foreign IDs (other than keys)
• Can be used to auto-fill input ID type.

The RStudio example seems to crash when I try testing it. When downloading and trying this locally I ran into several issues with dependencies such as rlang, which required manual updating:

> runApp('sig-bio-shiny-app.R')
Running Sig-Bio-Shiny v0.2.3 | Sun May 17 14:47:47 2020
Checking if SigBio v0.2.3 Package is installed...
Error: package or namespace load failed for ‘SigBio’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace ‘rlang’ 0.4.5 is already loaded, but >= 0.4.6 is required
> install.packages("rlang")

Once this was resolved, I used 'Run app' to run the application per the instructions, but ran into the below. Intermittent issues with KEGG availability?

Info: Downloading xml files for NA, 1/0 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  cannot open URL 'http://rest.kegg.jp/get/NA/kgml': HTTP status was '400 Bad Request'
Warning: Download of NA xml file failed!
This pathway may not exist!
Info: 
Warning: 
Info: Downloading png files for NA, 1/0 pathways..
Warning: Download of NA png file failed!
This pathway may not exist!
Info: 
Warning: 
Warning: Failed to download KEGG xml/png files, hsa skipped!

Use this - shinymeta