Geomorph update 2.1.7 Now Available!

September 28, 2015
By

(This article was first published on geomorph, and kindly contributed to R-bloggers)

Geomorph users,

We have uploaded version 2.1.7 of geomorph to CRAN. The windows binaries have been compiled and the tarball is available. 

However, subsequent to this, we found that under certain input scenarios, some of the changes we made to underlying support code had undesirable outcomes. We have corrected these issues in version 2.1.7-1. The corrected version is found in our GitHub repository (see below for installation information).

Also, because of a recurring issue with rgl (see here for details), the mac binaries continue to not be updated on CRAN. Please read below about what to do if you are a mac user.


CRAN policies do not permit frequent updates to packages, and 2.1.7 was just released last week. As a consequence, we recommend that going forward, all geomorph users should install the latest version from our Github repository.  Beginning immediately, we will maintain the current version of geomorph on the ‘Stable’ branch in our GitHub repository. This version represents the most recent release to CRAN plus any necessary bug fixes. See the ReadMe file in Git for more information.

To install geomorph directly from GitHub, go to R and type the following two commands:

> install.packages(“devtools”)
> devtools::install_github(“EmSherratt/geomorph”, ref=”Stable”)

NOTE: that to install from source using GitHub users must have followed the instructions to install the necessary compilers on the Installation Page.

New Features in 2.1.7-1:

  • New function compare.multi.evol.rates() for comparing rates of evolution among traits
  • plotGMPhyloMorphoSpace() now plots 3D phylomorphospaces and chronophylomorphospaces
  • Added ShowPlot option to bilat.symmetry(), compare.modular.partitions(), globalIntegration(), morphol.integr(), and phylo.pls()

Other Changes for 2.1.7-1:

Details of other changes can be found in the NEWS file.

Mac Users:

Due to dependancy on the rgl package, and a problem at their end with compiling binaries for OSX (see here for details), the most current version of geomorph available on CRAN for mac users in 2.1.5. This is now 2 versions behind the most recent. We suggest that mac users install geomorph from source, using the github repository. Please read and follow these instructions:

1) Go to the Mac App store and download Xcode Development Tools and follow install instructions.
For OS10.6, follow the instructions here.

2) Install the gcc and gfortran compilers.

For OS 10.8 and below: go to CRAN website here and download the GNU Fortran compiler (gfortran-4.2.3.pkg) and follow install instructions.
   
For OS 10.9 and above:
    Open Terminal (Applications/Utilities) and type in
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2

This will download the installer. Then type
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

This will install the compilers into the /usr/local/lib/ folder. The command sudo will ask for your password. Type it in, but note it will not appear on the line. Press return. The terminal window will fill with all the files being written.
(This information is thanks to the The Coatless Professor who troubleshooted R with Mavericks).

3) If it is not already on your Mac, install XQuartz (X11). It will be installed in the Utilities folder. This program must be running every time you use geomorph (required by rgl).


Emma

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