Error In X11 Unable To Start Device Png
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R Unable To Open Connection To X11 Display
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Capabilities X11 False
4.7 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up R unable to start device PNG - capabilities() has TRUE for PNG? up vote 0 down vote favorite no png support in this version of r I am working with a R script within a wider pipeline that seems to not work with some versions of Rscript but with others. The call fails due to being unable to connect to X11, which is understandable because this is on a server. But my local installation of Rscript is able to handle this fine? My local installation is version 3.0.1, while the one that other users that are reporting this unable to start device x11cairo problem are on 3.0.2. Here is a simple test case - first the .R file: #!/usr/bin/env Rscript capabilities() png("abc") dev.off() Run with my local env: -bash-4.1$ ./test.R jpeg png tiff tcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE libxml fifo cledit iconv NLS profmem cairo TRUE TRUE FALSE TRUE TRUE FALSE TRUE null device 1 Run on the installation of Rscript others are trying to use: jpeg png tiff tcltk X11 aqua http/ftp sockets TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE libxml fifo cledit iconv NLS profmem cairo TRUE TRUE FALSE TRUE TRUE FALSE TRUE Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width, : unable to start device PNG Calls: png In addition: Warning message: In png("abc") : unable to open connection to X11 display '' Execution halted r share|improve this question asked Jul 28 '14 at 16:39 Ian Fiddes 838923 add a comment| 4 Answers 4 active oldest votes up vote 6 down vote accepted In case anyone ever finds this on google, the solution is png("abc", type="cairo") share|improve this answer answered Jul 31 '14 at 16:46 Ian Fiddes 838923 Just a quick note, this didn't work for me, but i found another solution: Use the much more forgiving bitmap() function. Despite the name, it
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X11 Is Not Available R
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Unable To Start Png() Device Ggsave
answers are voted up and rise to the top Why is R having trouble rendering plots to a PNG file? up vote 1 down vote favorite I am trying to get R to do some very basic plotting and such in UNIX, but am http://stackoverflow.com/questions/24999983/r-unable-to-start-device-png-capabilities-has-true-for-png getting a weirdo error relating to X11, when as far as I can tell I'm not even needing X11. I have a matrix name d and want to save an image of a heatmap of this matrix without ever actually displaying the image (since I don't want to use X11). Here is my code: png(file="my_image.png") heatmap(d) dev.off() The problem is I am getting the following error: Error in X11(paste("png::", filename, sep = ""), g$width, g$height, pointsize, : unable to start device PNG In addition: Warning message: In png(file http://superuser.com/questions/603744/why-is-r-having-trouble-rendering-plots-to-a-png-file = "interative_hen.png") : unable to open connection to X11 display '' I don't know this is happening, since I don't see how R is needing X11, and even if it does, X11 is installed and working properly for every application I tested it with. linux unix png x11-forwarding r share|improve this question edited Jun 5 '13 at 15:14 Breakthrough 29k882128 asked Jun 4 '13 at 20:05 jake9115 1721516 Are you doing this remotely over SSH? –Breakthrough Jun 4 '13 at 20:08 Yes, I am SSHing into a cluster –jake9115 Jun 4 '13 at 20:12 I'm going to assume there's no X11 server on the cluster... If that's the case, you need to set an X11 server up on your computer, and configure your SSH client to allow X11 forwarding. This should allow you to generate the PNG files (some newsgroups mention that the X11 composter is required to render images from R). –Breakthrough Jun 4 '13 at 20:18 Thanks for the idea, but I already have an X11 server and client. From the same SSH window, I can type 'firefox' and fire up an X11 display of firefox, so I don't see why R is having a problem! –jake9115 Jun 4 '13 at 20:20 Can you add the output of calling the capabilities() function in R? See this Stack Overflow question (and more specifically, How to run R scripts on servers without X11) regarding starting R with a virtual framebuffer. If you're comfortable, you might also want to try compiling R from source witho
• rss Community Log In Sign Up Add New Post Question: Making PNG figures from plots in R from toolshed https://biostar.usegalaxy.org/p/9170/ (without X11) 0 2.0 years ago by y.hoogstrate • 270 Netherlands y.hoogstrate • 270 wrote: Hi everyone, I'm encountering problems when I want to export a plot from https://bitbucket.org/young_computation/rose/pull-requests/1 R into a PNG, using several R packages from the toolshed(s). This problem is probably related to the following issue: http://dev.list.galaxyproject.org/package-r-xx-problem-X11-is-not-available-td4663344.html Therefore, I'm using the package: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_2 When unable to I run R code of the following structure: png(output_PValue_distribution_plot) plot(x_var,y_var) dev.off() R crashes with the following error: Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width, : unable to start device PNG Calls: png In addition: Warning message: In png(output_PValue_distribution_plot) : unable to open connection to X11 display '' Execution halted How I interpret this is that unable to start in order to produce PNG's, R needs to be compiled with the X11 library. Because the installer from the toolshed uses the compilation argument " --without-x", it doesn't compile with X11 and so it is not possible to produce PNGs, correct? I also tried another solution; installation of R with X from the following repository: https://testtoolshed.g2.bx.psu.edu/repository?repository_id=5f7d83aa4f577607 . However, the repository requires several other dependencies which are not programmed within the installer: libx11-dev libxt-dev (and some more, because after all it still work out). So, what would be the best way to create a PNG figure from my plot(s) within an R instance from a toolshed? Does it require R to be compiled with X11 or are there ways to overcome this (I am not sure but I thought I read something about Cairo)? Or would somebody recommend to use a non-R program to convert from e.g. PDF/SVG to PNG? I think this is awckward since R should be the perfect tool to produce PNG figures. Thanks in advance,
cloning? Learn how to clone a repository. Clone in SourceTree Atlassian SourceTree is a free Git and Mercurial client for Windows. Atlassian SourceTree is a free Git and Mercurial client for Mac. young_computation Untitled project ROSE Pull requests Pull requests #1 Open Source Repository dyndna Branch dyndna/-suggest-fix-for-error-unable-to-start-d-1452109589398 Destination Repository young_computation Branch master ### Suggest fix for error: unable to start device PNG Bitbucket cannot automatically merge this request. The commits that make up this pull request have been removed. Bitbucket cannot automatically merge this request due to conflicts. Review the conflicts on the Overview tab. You can then either decline the request or merge it manually on your local system using the following commands: git checkout master git remote add dyndna/rose https://bitbucket.org/dyndna/rose.git git fetch dyndna/rose git merge --no-ff -m 'Merged in dyndna/rose/dyndna/-suggest-fix-for-error-unable-to-start-d-1452109589398 (pull request #1)' remotes/dyndna/rose/dyndna/-suggest-fix-for-error-unable-to-start-d-1452109589398 Overview Commits Activity Author Samir Amin Reviewers Description Suggest fix for error: unable to start device PNG Reproduce error: On headless machines like cluster computing environment, default png command expects X11 device and throws following error: Running ROSE_main.py with required arguments gives following error: > png(filename=plotFileName,height=600,width=600) Error in .External2(C_X11, paste("png::", filename, sep = ""), g$width, : unable to start device PNG Calls: png In addition: Warning message: In png(filename = plotFileName, height = 600, width = 600) : unable to open connection to X11 display '' Execution halted` Suggested fix: Replace libpng device requirement with cairo device in line 166 of file: ROSE_callSuper.R png(filename=plotFileName,height=600,width=600, type="cairo") END Learn about pull requests Comments (0) Pull request updated. Reload Blog Support Plans & pricing Documentation API Site status Version info Terms of service Privacy policy English Git 2.7.4.1.g5468f9e Mercurial 3.6.3 Django 1.7.11 Python 2.7.3 4729d131423b / 4729d131423b @ app-124 JIRA Software Confluence Bamboo SourceTree HipChat Atlassian Help Online help Learn Git Keyboard shortcuts Latest features Bitbucket tutorials Site status Support