Tuesday, 23 May 2017

GCDkit for OS X ? Yes, but...

One of the most common complains regarding GCDkit is that it is platform-specific, i.e. Windows only (and it's not too fond of win 10, either...). Well the latest version (GCDkit 4.1) is, at long last, able to operate on Linux and OS X.

Ok, hold your horses -- it is still very clunky and not fully functional. But indeed, it can load and start. The reason I'm bringing this up today is, I just had a colleague visiting, and we managed to install and start GCDkit on his Mac, using normal, publicly released versions. It may, or may not, work for you. Good luck.

Short instructions for users familiar with R:

  • Install R (the current version of GCDkit is known to work under R 3.2.1, we offer no guarantee with any other version).
  • Install the following packages : R2HTML, RODBC and sp
  • Download the zip version of GCDkit and install it as a "local binary package"

Longer instructions

  • Download R for OS X, version 3.2.1, from this page
  • Install it, keep all the default options.
  • Before installing GCDkit, you must install three additional packages. Start R, and then either 

(1) in the console, type the following commandinstall.packages(R2HTML)
A dialog should pop up, showing a list of "mirrors" in different countries (sites from which you can download the package). Select the one closer to you. the ones that are labelled "https" may not work behind a proxy.
Some information should appear in the console. If R ask whether it should "install from sources and compile", say "no".
Repeat the procedure for the other two packages: install.packages(RODBC) and install.packages(sp)

(2) from "packages and data" in the menu bar, select "package installer". There is a tutorial video here. Select "cran-binaries" from the top menu, then "get list". Find the mirror nearer to you (again) and then scroll the list until you reach R2HTML, RODBC and sp. Install all three of them.

  • Now you can install GCDkit. First, go to gcdkit.org and download the zip file of GCDkit 4.1. Install it as a "local package", following the instructions on this page: go to the package installer again, this time select "local binary package", and navigate to the zip file that contains GCDkit. This morning we had issues with the package manager and had to restart R, this happens, don't worry.

And now ? 

 Now GCDkit is installed, together with all the relevant libraries, so it is able to run. However, what is not there is the GUI: no menus or dialogs for you, sorry.

To launch GCDkit: start R, and then from the console type library(GCDkit).  This will load GCDkit, and you should see all the familiar instructions, ending with


Geochemical Data Toolkit (GCDkit) 4.1,
built R 3.2.1; ; 2016-02-05 16:12:23 UTC; windows

Please support our efforts and cite the package 'GCDkit' in publications
using the reference below. Type 'citation("GCDkit")' for BibTex version.

Vojtech Janousek, Colin M. Farrow and Vojtech Erban (2006).
Interpretation of whole-rock geochemical data in igneous geochemistry:
introducing Geochemical Data Toolkit (GCDkit).
Journal of Petrology 47(6): 1255-1259.
doi: 10.1093/petrology/egl013

Ready 2 Go - Enjoy!

GCDkit->

Now you can (and have to) type GCDkit commands from the R console. In the next post I'll give a couple of examples.

Linux ?

Well, probably. None of us is a Linux user but we got it running on an (emulated) Ubuntu (virtual) machine.
If you're using Linux, you probably know what to do, so follow the "short" instructions above.


But I want a platform-independent GUI !

Well, so do I... Stay tuned, maybe one day...

(gWidgets2 + RGtk2)

2 comments:

  1. Great manual how to use. I was searching for similar post for http://essayguard.com/services/darwinessay Darwinessay prices cause I've had some difficulties with installing this toolkit.

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