bmbroom/rstudio-ngchm

rstudio with preinstalled NGCHM R library

rstudio-ngchm's Issues

Error : export to ngchm failed

Hi,

I am getting this error while trying to run NGCHM!

Here's the console output :

INFO [2020-09-24 14:41:12] Creating NGCHM as infercnv.ngchm
INFO [2020-09-24 14:41:12] Initializing new NGCHM InferCNV Object.
INFO [2020-09-24 14:44:53] Saving new NGCHM object
Thu Sep 24 02:44:54 PM 2020 PROGRESS :Writing specification: 50 creating specification directory
Thu Sep 24 02:44:54 PM 2020 PROGRESS :Writing specification: 80 writing extra support files
Sep 24, 2020 2:44:56 PM org.apache.pdfbox.pdmodel.font.PDType1Font
WARNING: Using fallback font LiberationSans for base font Symbol
Sep 24, 2020 2:44:56 PM org.apache.pdfbox.pdmodel.font.PDType1Font
WARNING: Using fallback font LiberationSans for base font ZapfDingbats
Warning: No heat map description provided in properties : chm.info.caption.
Warning: Column label type (axisTypes where = col or both) not specified. Will use generic linkouts menu
Warning: Row label type (axisTypes where = row or both) not specified. Will use generic linkouts menu

START Data Generator Heat Map Generation: Thu Sep 24 14:45:01 KST 2020
Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using ':0' as the value of the DISPLAY variable.
at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
at sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:65)
at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:115)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:74)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:103)
at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:82)
at java.awt.image.BufferedImage.createGraphics(BufferedImage.java:1181)
at mda.ngchm.datagenerator.HeatmapDataGenerator.buildTnThumbnail(Unknown Source)
at mda.ngchm.datagenerator.HeatmapDataGenerator.processHeatMap(Unknown Source)
at mda.ngchm.datagenerator.ShaidyRMapGen.main(Unknown Source)
Error in NGCHM::chmExportToFile(hm, file_path, overwrite = TRUE, shaidyMapGen = path_to_shaidyMapGen) :
export to ngchm failed

I saw in some other comments that this could be a Java version problem, and could be taken care of by installing the right version - 1.8. Unfortunately, I've checked for the Java version and it seems to be correct, so what else do you think could be wrong?

Thanks.

chmViewer() not working

Hi, Is the chmViewer() command still working? I can't open the viewer using this command.