Problems installing brainGraph package

[Jessica Bartley]

Hello! I'm trying to install the brainGraph package to run some graph theory on my fMRI data in R.  I am encountering a problem with dependencies when downloading -- specifically, I'm receiving the error: 

gtk.c:7:10: fatal error: 'gdk/gdkx.h' file not found

#include <gdk/gdkx.h>

I'm using Rstudio (with R version 3.3.1) on Mac OSX 10.9.5 (Mavericks). I've been doing some research on this and it looks like GDK requires X11 (but not XQuarts?) and this causes some problems on Macs.

Does anyone run into this issue before and know how to get around this?

Thank you!

Jessica

[Chris Watson]

Does this error appear when you try to install RGtk2, or were you successful in installing that package? (cairoDevice, too)

I will try to search around for answers. I do not have a Mac so unfortunately I cannot test it myself. Initial googling returned the following, please try the command listed in the answer: http://apple.stackexchange.com/questions/202501/how-to-install-rgtk2-on-os-x-10-10-5

Chris

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[Jessica Bartley]

Hi Chris, 

Thanks for your help! Yes, the error occurs when I attempt to install RGtk2 or cairoDevice independently from brainGraph. As in that link, I have attempted to install the binary version of RGtk2 but that version apparently doesn't contain gdk.h, so install.packages('brainGraph') generates the same error:

#include <gdk/gdkx.h>

         ^

1 error generated.

make: *** [gtk.o] Error 1

ERROR: compilation failed for package ‘cairoDevice’

* removing ‘/usr/local/lib/R/3.3/site-library/cairoDevice’

So far I have attempted to download these packages in Rstudio as well as in terminal via homebrew. None have worked thus far.  After much googling I'm a bit stuck and am considering either downgrading my R version or updating my OSX, just to see if that changes anything.

Your help is greatly appreciated! Thanks!

Jessica

On Thursday, October 13, 2016 at 2:18:32 PM UTC-4, Chris Watson wrote:

Does this error appear when you try to install RGtk2, or were you successful in installing that package? (cairoDevice, too)

I will try to search around for answers. I do not have a Mac so unfortunately I cannot test it myself. Initial googling returned the following, please try the command listed in the answer: http://apple.stackexchange.com/questions/202501/how-to-install-rgtk2-on-os-x-10-10-5

Chris

On Thu, Oct 13, 2016 at 12:47 PM, Jessica Bartley <jessica....@gmail.com> wrote:

Hello! I'm trying to install the brainGraph package to run some graph theory on my fMRI data in R.  I am encountering a problem with dependencies when downloading -- specifically, I'm receiving the error: 

gtk.c:7:10: fatal error: 'gdk/gdkx.h' file not found

#include <gdk/gdkx.h>

I'm using Rstudio (with R version 3.3.1) on Mac OSX 10.9.5 (Mavericks). I've been doing some research on this and it looks like GDK requires X11 (but not XQuarts?) and this causes some problems on Macs.

Does anyone run into this issue before and know how to get around this?

Thank you!

Jessica

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[Chris Watson]

I don't know if upgrading your OS is necessary, as the package has been downloaded for darwin13.4.0 (which corresponds to OSX 10.9.5). Same with the R version. However, I guess it couldn't hurt.
Have you seen this link, it is listed in the User Guide: https://gist.github.com/sebkopf/9405675#macos

Please try the suggestions there and let me know. I am not sure how out-of-date the information in that link is, though. I am eager to get the appropriate info in the User Guide for other users.

Chris

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[Chris Watson]

You may want to try this out, as well, and see other answers in that thread: http://stackoverflow.com/a/16886757

[Chris Watson]

This may be the first thing to follow: http://stackoverflow.com/a/17998459

[Chris Watson]

Hi Jessica, I also want to point out that the CRAN check on Mavericks passed, see the following link: https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64-mavericks/brainGraph-00check.html

They checked it on R 3.3.0 and OS X 10.9.2

[Chris Watson]

Hi Jessica, I just wanted to follow-up to see if you had any luck installing. Did you try any of the links I shared?

Chris

[Sean Ma]

Following up on this thread, I had to download the binary GTK .pkg from https://r.research.att.com/ to finish my install on OSX Yosemite (10.10.5).

Sean

[Chris Watson]

Thanks Sean! This is really helpful and I will add this to the "Installation" chapter in the User Guide.

Chris

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[Sean Ma]

Just a followup if you have Mac OS greater than 10.13 (High Sierra), Github user sebkopf has an excellent gist post describing in detail the necessary steps needed to get 'RGtk2' installed on the system. Highly recommended!

https://gist.github.com/sebkopf/9405675

Sean

[Chris Watson]

That's great! I will add it to the User Guide.

Chris

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[Chris Watson]

Actually, that link was already included in the User Guide. But I will write that it works for OS X >= 10.13.

[Maria Luisa Mandelli]

Hi Chris and Sean,

I have OS Yosemite 10.10.5, I installed the binary GTK but still have problem on installing brainGraph in R studio. it keeps looking for the dependency ‘RGtk2’. Do you have some suggestions?

thank you

[Sean Ma]

Hi Maria, 

If you have installed the AT&T binary GTK on your Yosemite machine, what happens if you first install `RGtk2` before installing `brainGraph`? Does this help solve your problem?

Sean