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itsmeludo / PhylOligo

Bioinformatics / Explore oligonucleotide composition similarity between assembly contigs or scaffolds to detect contaminant DNA.
GNU General Public License v3.0
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X11 phyloselect.R #2

Closed T-B-F closed 8 years ago

T-B-F commented 8 years ago

If phyloselect.R is used remotely, ex. through ssh without X forwarding, the script crash with the error message: Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11cairo Calls: X11 In addition: Warning message: In X11(width = 12, height = 10) : unable to open connection to X11 display '' Execution halted

I guess the culprit is this line: X11(width=12,height=10) # external display when script is launched with Rscript command

Could it be passed as an option and if not set dump the plots in a folder?

itsmeludo commented 8 years ago

in short, no. :/ X11 is needed by the function from ape to dynamically select a clade on the plot with the mouse. X11 is a dependency then. I will add it to the list and will add a description if Phyloselect need to be run remotely over ssh.