Wednesday, February 5, 2014

Geomorph 1.1-6 Now Available!

Geomorph users,

We have uploaded version 1.1-6 to CRAN. The windows and mac binaries have been compiled and the tarball is available.

The issue of the Mac OS X installers has been resolved. The problem stemmed from a dependancy (to JPEG), which was lagging behind for Mac binaries. We thank the curators for helping us with this issue.

Version 1.1-6 does not contain any new functions. It fixes a few small inconsistencies in the code and helpfiles (listed below). The most important update deals with two functions missing from the NAMESPACE in 1.1-5. We apologize for any problems this may have caused.
  • Minor I/O enhancements in readmulti.nts()
  • Minor I/O enhancements in define.sliders.3d() to allow sliders to be in any order
  • Simplified pPsup (original code from J. Claude) to not include size re-scaling by beta (underlying function used in trajectory.analysis() only)
  • Added name.check for groups in compare.evol.rates()


  1. Thanks for the update!
    I installed it on my Mac this afternoon and all of a sudden the functions for define.sliders.2d and define.sliders.3d are missing:

    > define.sliders.3d()
    Error: could not find function "define.sliders.3d"
    > define.sliders.3d
    Error: object 'define.sliders.3d' not found

    All of the other commands that I tried seem to work well, and reinstalling didn't help. I'm not sure what happened.


  2. Samantha,
    Hmm that is odd, because I also installed the new version on my Mac and those two functions are there. Please can you make sure you have the dependant packages all updated too? Particularly JPEG.


  3. Still nothing. I just checked that all of the dependent packages were up to date and they are. I'm still running OS 10.8 because my university does not yet support 10.9, if that makes any difference...


  4. The version of Mac shouldn't make a different but please make sure your R is the latest version. I need to know if this is just your mac or all other macs (except for mine) so troubleshooting may take a few days.


  5. Thanks for your help, Emma, I really appreciate it!

    For lack of anything else to try, I rebooted R about 10 times and the missing commands appeared! But now, when I try to define 3D sLMs, I get this error after clicking the first three points for the first sLM:

    > define.sliders.3d(gsnarray[,,1], 28, surfsliders=F)
    semi-landmark Error in cat(list(...), file, sep, fill, labels, append) :
    argument 2 (type 'list') cannot be handled by 'cat'

    If I close the rgl window and try to run it again, R crashes and gives me this:

    > define.sliders.3d(gsnarray[,,1], 28, surfsliders=F)

    *** caught segfault ***
    address 0x0, cause 'unknown'

    1: .C(rgl_clear, success = as.integer(FALSE), idata)
    2: rgl.clear(type)
    3: clear3d()
    4: define.sliders.3d(gsnarray[, , 1], 28, surfsliders = F)

    Possible actions:
    1: abort (with core dump, if enabled)
    2: normal R exit
    3: exit R without saving workspace
    4: exit R saving workspace


    1. Samantha.

      So in answer to your first question, there appears to be an issue in the CRAN repositories. The "update" wasn't actually fetching the new version 1.1-6, it was trying to install 1.1-3, which doesn't have those two functions. And so that's why you wouldn't have seen them.

      Please check to make sure you have actually got 1.1-6. You can download the mac binary itself from the website.

      Second, please make sure that when you select a point, you right-click and drag a box around it to select it. The first error may be coming from not selecting the points correctly.

  6. I installed 1.1-6 from the binary because I noticed that the "update" was only 1.1-3 when I was checking to make sure the new version had actually installed.

    For the other, I use the right-click, drag the box around each point, it connects them and the middle one turns red, and then I get the error.


    1. Please email me and we will take it from there. sherratt[at]iastate[dot]edu

  7. Thanks Emma. Geomorph helped me a lot. I have almost finishing a manuscript mainly with the help of Geomorph.

    But I still have a lot of trouble using the function plotGMPhyloMorphoSpace. I could be very useful to me but I have no idea how to construct the phy argumant... Can you help me with that?

  8. The phy argument is a phylogenetic tree object of the class phylo - use read.tree() in ape library to read in your nexus file. More on inputting trees here:

  9. Hello,
    New geomorph() user here. I've tried out most of the functions now on my old .tps files and it is great to have an all inclusive package!
    However I am having some problems with the digitize2d() function
    I'm consistently getting the following error

    Error in basename(file) : a character vector argument expected

    not only with my own data but with one of the tuturial datasets as well
    >diged.imgs <- lapply(specs, digitize2d.multi, nlandmarks=3, scale=1)
    Error in basename(file) : a character vector argument expected

    R, geomorph and all dependent packages are updated...
    ps. working on windows
    Any thoughts?

    Thank you

  10. Andrew. That is a known problem with the function. Please email me for a fix. The function will be updated in the new version coming this spring.

  11. Having the same problem with the digitize2d function as Andrew Smith. How could I fix it?

  12. Send me an email and I'll send you a source file. sherratt[at]iastate[dot]edu