makeVennDiagram produces undesired console output

[drighelli]

Hi,

I'm using the makeVennDiagram function as in the following code, but together with the plot, it prints lots of output in console.

This is not ideal because it makes it difficult to read the output when including the function in a rmakrdown.

Is there a sort of verbose argument to remove this annoying output?

mol <- findOverlapsOfPeaks(gr1, gr2)
makeVennDiagram(mol, NameOfPeaks=names(mrrplist), by="region",
    fill=c(colors[2], colors[7]), # circle fill color
    col=c(colors[4], colors[3]), #circle border color
    cat.col=c(colors[4], colors[3]))

This is a screenshot of the output:

Thanks, Dario

[jianhong]

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

[drighelli]

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
...

[hukai916]

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.

[jianhong]

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

[drighelli]

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

Thanks!

[drighelli]

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