GCDkit 6.1 has been released!

On July 8, 2022 has been released a new version of GCDkit 6.1. It was developed in R 4.1.3 and code-named, in support of a struggle for democracy and freedom, Invincible tractor. There are no revolutionary changes, but rather bug fixes and performance improvements. The main aim was to optimize the whole system for speed. Most important features are summarised below.

Performance improvements

• Quicker start up with several options.
• Normative calculations have been further optimized for speed. 
• Quicker routine enabling overplotting datasets.
• Many functions can be newly called in the batch mode: e.g., addLegend(), cluster(), mergeDataRows(), mergeDataCols().
• trendTicks() was modified, so that it can be used also in cases  when only [x,y] coordinate pairs along the trend are known. In this case, a fourth-order polynomial  is fitted to the data.  Also, the function trendTicks() can be called just to perform the underlaying calculations, returning all the parameters of the fitted trend invisibly (plot = FALSE).
• Optional offline installation, if no live Internet connection is available.  
• Several parameters of a plate can be changed at the same time, using the brand new function plateUser(). It is simply a wrapper to the modified function figUser, invoked to modify each individual slot.
• New function diagramWithCircles() - the same like plotWithCircles() but plotting a diagram (stand-alone Figaro template) on the background.
• New functions contourAll, chullAll outlining the whole dataset  (analogous to the already existing contourGroups, chullGroups).
• contourAll, contourGroups use now much improved algorithm; contouring is based on kernel density estimates.
• Reprogrammed were many of the functions in the SrNd.r plugin.
• Error bars plotting (obtained by the function fousy()) were improved significantly.

Bug fixes

• profiler()redesigned completely, updated were especially colour handling and legends;  this function can work also with a variable different from WR.
• EarthChem() thoroughly checked/tested, including documentation and examples. It was redirected to http://portal.earthchem.org/restsearchservice.
• Spiderplots and profiles did not zoom up correctly.
• CIPW() was slow, and its repeated use further slowed down the whole system (thanks to Sergio Esteve for suggesting a remedy for this problem). Analogous issue has been fixed also in CIPWhb() and Catanorm() normative calculations.
• isocon() function did not return results, both slopes were swapped in the output and the examples with atomic=TRUE did not work correctly.
• plateLabelSlots() fixed, was causing unpredictable behaviour when followed by overplotDataset, plateAddReservoirs etc.
• Patches were not loaded due to namespace conflicts. The whole patching code was revised.
• Some functions of GCDkit did not work correctly in RStudio under Windows.
• Whalen() did not plot some of the average A-type compositions correctly.
• Manual pages for some of the geotectonic diagrams were not linked to the HTML help system.
• Many doi links were added/updated/fixed in the help system.
• figMulti() did not produce correctly all spiderplots if one or more groups were empty (e.g., when lacking the REE data).
• User-defined Ta/Yb - K2O/Yb (Pearce 1982) plot [PearceDestructive1.r] fixed.
• HTML output is newly produced in temporary directory, where a writing permission should be always guaranteed.
• plotWithCircles(): sizing of smallest circles improved, the colours can be newly semitransparent.
• After invoking peekDataset(), lists of available classification and geotectonic plots are built afresh to match the data available in the given dataset.
• Frost(), Frost_2008(), Maniar(), Cann(), Whalen() and MullerKternary() functions did not allow overplotting on some of their panels.
• [Win] r2clipboard() did not work on Windows systems.
• [Win]  save.data() was appending to preexisting files instead of overwriting them.
• [Mac]  HTML web system was malfunctioning in the Safari browser on Mac.
• [Mac] Rudimentary functionality for the Plate() function, instead of an error message.

New geotectonic/general purpose diagrams

• Plotting scatterplot with smoothed densities (smoothed two-dimensional histogram) after Eilers & Goeman (2004)  (courtesy of Paul Eilers).
• New binary geotectonic diagram ThN-NbN for basaltic rocks of Saccani (2015) based on NMORB-normalized compositions.
• New CIPW-normative classification diagram for plutonic rocks of Enrique (2018).

Known GCDkit 6.0 installation problems and how to solve them

We have been  receiving reports recently of failed installations on both Mac and Windows. If you have the same problem, please:

• Check once more all the instructions at http://www.gcdkit.org/download
• In particular, make sure that you install R first, in appropriate version (that is 3.6.0 for GCDkit  6.0)
• If you are behind a proxy, select Internet2  option during Custom R installation
• Check that you are online before installing the supporting libraries

On Windows:

• For installation, run R with admin privileges
• If you receive a message saying that RODBC is not available for R 3.6.0:
  [1] Download the zipped version of the RODBC library from https://cran.r-project.org/bin/windows/contrib/3.6/RODBC_1.3-16.zip.
  [2] Go to RGUI menu Packages>Install package(s) from local zip files... and browse for this downloaded file on your disc. DO NOT unzip it beforehand. 
• In case you are missing any other R libraries, their appropriate zipped version can be found at  https://cran.r-project.org/bin/windows/contrib/3.6/, downloaded and installed analogously to the case of RODBC.

We do apologise for the inconvenience - the fact that  RODBC library is not correctly configured on the CRAN server is unfortunately beyond our control.

I am pleased to announce that we are just finishing a GCDkit version 6.1 that should fix a few known bugs and feature, among other things, also offline installer.

Vojtech 

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)

Troubles with Windows 10

We have been recently flooded by  email reports of those of you who could not start the GCDkit installer on Windows 10. Strangely, the other versions of the system seem unaffected. We have examined the problem and, as it seems, it consists in the sudden change in security policy of Microsoft, requiring all installation programs to have a valid security certificate.

While we are working on the remedy, the only way on Win 10 seems to use the "advanced" setup taking advantage of the R library mechanism.  

There is no need to be afraid of this,  The procedure is as follows:

• download and install the R 3.2.1 for Windows
• download the GCDkit_4.1.zip library
• run the R console in a SDI mode
• install the library from the R console (Menu Packages > Install package(s) from local zip files...)
• install the R2HTML, RODBC and sp libraries (Menu Packages > Install package(s)...) [working Internet connection is required]
• load the GCDkit library (Menu Packages > Load package > GCDkit or type library(GCDkit) into the R Console)
  

The last step is to be repeated every time you start R GUI a new. 

Alternatively, you can make an shortcut at your Desktop with a text similar to mine (do take care of the correct path):

"C:\R\R-3.2.1\bin\i386\Rgui.exe" --silent --no-save --sdi

Please do note the quotation marks, they should be there.

Setting the directory to that with R libraries. In my case it is:

C:\R\R-3.2.1\library\GCDkit

I hope that this will help. Please let us know if there are any further problems. 


Vojtech