Question

Kmergenie: R script cannot output png files

1

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10.1 years ago

dlepp ▴ 10

Just trying this out, and while the plots are generated and best k predicted, the report is not generated. RScript seems to be working and I have ghostscript v9.05. Running on Biolinux 7 system (Ubuntu 12.04).

Full error message is:

R cannot output png files; testing if ghostscript is present.. HTML report not generated (Kmergenie is probably running on a cluster): neither R can create png files, nor ghostscript is installed

KmerGenie • 3.8k views

ADD COMMENT • link updated 2.8 years ago by Ram 44k • written 10.1 years ago by dlepp ▴ 10

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Hello dlepp!

We believe that this post does not fit the main topic of this site.

This is not really a bioinformatics question but a R installation and support one. You should post this on R forums or StackExchange.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLY • link 10.1 years ago by Istvan Albert 101k

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Hi Istvan,

I believe this was a kmergenie question, so it does fit the topic of this forum. (the user probably should have mentioned Kmergenie in the title..)

dlepp: can you paste the output of the following command? (Maybe ghostscript isn't found on your system when the shell environment is not loaded.)

python -c "import subprocess; subprocess.Popen(['gs','--version'])"

ADD REPLY • link updated 2.8 years ago by Ram 44k • written 10.1 years ago by Rayan Chikhi ★ 1.5k

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actually yes, it is a valid question, apologies for closing it

it just was not clear from the content if this was simply an R question or a script packaged with a bioinformatics tool, I actually missed the kmergenie mention

ADD REPLY • link updated 2.8 years ago by Ram 44k • written 10.1 years ago by Istvan Albert 101k

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no worries!

ADD REPLY • link updated 2.8 years ago by Ram 44k • written 10.1 years ago by Rayan Chikhi ★ 1.5k

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Can you do:

png(); plot(1:10); dev.off();
bitmap(file="bitmap.png"); plot(1:10); dev.off();

and tell us what the output is? There should be an Rplot.png and a bitmap.png file with a plot.

ADD REPLY • link updated 2.8 years ago by Ram 44k • written 10.1 years ago by Michael 55k

score 0 · Answer 1 · 2014-09-23

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10.1 years ago

ALchEmiXt ★ 1.9k

Are you on a headless server? If so you should most likely fix output for png for all R scripts. The answer of Michael should help you test that.

This might seem trivial and I may be mistaken.... but isn't kmergenie outputting by default these images as base64 embedded code inside the html output? Then you don't get saved along the html file... as far as I remember.

Look for these tags in the html output:

<img  src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAeAA blablabla etc">

ADD COMMENT • link 10.1 years ago by ALchEmiXt ★ 1.9k

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Kmergenie checks if R can generate png. If not, it falls back to ghostscript to do the pdf->png conversion. I've noticed that for many clusters R doesn't support png output due to no X server

ADD REPLY • link 10.1 years ago by Rayan Chikhi ★ 1.5k