Dear members of the R geomorph Development Team, As you surely know, I am a big fan of the 'geomorph' R package, which I have been using since its inception (as part of a larger personal move to do every possible analysis, morphometric or not, using R). Several times, I have provided tentative bug reports and humble suggestions for improvements (that sometimes have been incorporated into new releases of the package).
But with due respect, today I have a few severe complaints, that I am posting here because they may have been of concern for other morphometricians working with the geomorph package. My first -- and biggest -- complaint concern the way landmark coordinates captured by the 'digitize2d' routine are stored in the latest version of geomorph. There seems to have been some change in the code (undocumented as far as I could see) which altered the scaling of the coordinates -- as a result, I lost weeks of work on a file with more than 70 fish specimens because when I opened the file in geomorph 2.17 to re-start digitizing the remaining specimens (after having digitized about 50 in geomorph 2.15), all coordinates were unexpectedly changed and the file became even unreadable by Jim Rohlf's tps programs (but before this change in geomorph I could have the tps programs read files digitized in geomorph without trouble). Well, at first I solved this by simply downgrading my version of geomorph, returning to the old 2.15 version and everything worked fine. Since I use RStudio, i just had to remember to unckeck geomorph in the list of packages to be updated. But today, to my dismay and further annoyance, when I upgraded several packages in my R installation -- even unckecking as usual the geomorphy entry -- I got a strange error message which turned geomorph (whatever the installed version) useless! Here it is: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'Biostrings' ERROR: lazy loading failed for package 'geomorph' * removing 'C:/Program Files/R/R-3.1.3/library/geomorph' The geomorph package depends on other two packages, 'ape' and 'rgl', but none of them have been upgraded recently and both load fine and without any error messages, therefore I suppose the above error is generated by geomorph itself. Right, the error message about a missing package may be a minor (and easily fixed) issue. But so is not the changes done to the digitize2d function, which lead to data loss and waste of time and resources! Even if there are some good reason (as surely does!) for changing the scaling of landmark coordinates, such change should no tbe done without at least providing users with the option of using the previous mode of operation of the routine. Besides, such change should be carefully documented (and I could not fund any mention to it in the "NEWS" file of the latest versions of geomorph). I hope you understand my reasons for complaining, and I look forward to obtaining directions on how to get out of this mess (currently, I cannot even use geomorph, whatever the version, because as a a result of the "misisng package" error, the entire package was automatically wiped out of my R installation...) Life is short (so we need R)! With best regards, -- Dr. Mauro J. Cavalcanti E-mail: mauro...@gmail.com Web: http://sites.google.com/site/maurobio -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
