makeVennDiagram produces undesired console output about chippeakanno HOT 6 CLOSED

Hi @drighelli, we will test the disable.logging = TRUE option soon. Meanwhile, you can set {r, results = "hide"} in your R markdown code chunk to hide the logging info.

from chippeakanno.

This message is from upstream package. Could you please try suppressMessage or {r messages=FALSE, warnings=FALSE}

from chippeakanno.

Thanks, but both solutions don't work, I think it's a log print to console from the venn.diagram function.

I think you can easily disable, or manage it, by setting the disable.logging=TRUE

venn.diagram(x, filename, disable.logging = FALSE, height = 3000, 
    width = 3000, resolution = 500, imagetype = "tiff", 
    units = "px", compression = "lzw", na = "stop", main = NULL, 
    sub = NULL, main.pos = c(0.5, 1.05), main.fontface = "plain",
    main.fontfamily = "serif", main.col = "black",
    main.cex = 1, main.just = c(0.5, 1), sub.pos = c(0.5,
    1.05), sub.fontface = "plain", sub.fontfamily =
    "serif", sub.col = "black", sub.cex = 1, sub.just =
    c(0.5, 1), category.names = names(x), force.unique =
    TRUE, print.mode = "raw", sigdigs = 3, direct.area =
    FALSE, area.vector = 0, hyper.test = FALSE, total.population = NULL, 
    lower.tail = TRUE, ...)
...
disable.logging
Boolean to disable log file output and print to console instead
...

from chippeakanno.

That will create a local log file without permission which is forbidden in Bioconductor package. I will consider to output the parameter.

from chippeakanno.

oh yeah, you're right, yep I think using a parameter would be the best solution.

Thanks!

from chippeakanno.

Thanks @hukai916, I didn't see your answer before! It worked!
@jianhong you can close this issue for me!

from chippeakanno.