I just wanted to let you know that I have just posted the first "alpha" version of my "phytools" (phylogenetic tools for comparative biology - and other things) package online at my R phylogenetics page (direct link to zipped tarball here).
To install, simply download the file, navigate to the appropriate directory, and then type:
> install.packages("phytools_0.0-1.tar.gz",type="source")
The package can then be loaded as normal, i.e.,
> require(phytools)
or
> library(phytools)
in the current or future R sessions.
Please let me know if you find any difficulties with functions loaded this way, rather than downloaded and loaded from their individual source files. (Or, of course, any difficulties in general.) I look forward to comments! (Even a report of successful installation is more than welcome.)
Unfortunately, I have not yet written man pages for these functions, so this will have to come in the first "beta" version release of "phytools" - hopefully some time soon.
In the first version of this post I claimed:
ReplyDelete"I believe one could also load the source directly from the hosting URL, i.e.:
> install.packages("http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/phytools_0.0-1.tar.gz",type="source")"
Unfortunately, I didn't seem to be able to get that to work, so I have removed the suggestion.
Unfortunately,
ReplyDeleteinstall.packages("phytools_0.0-1.tar.gz",type="source")
didn't work for me after downloading your tarball. Does it work on your machine?
Hi Scott. Yes, it does work on my machine with no problem. I am in Windows (although this should not matter, I don't think, but this is difficult for me to test). Please let me know if you can figure it out; or if other users have better luck, please speak up. Also, feel free to post the error message that is returned by R when you try to execute this. Thanks for the comment by the way! - Liam
ReplyDelete> install.packages("phytools_0.0-1.tar.gz",type="source")
ReplyDeleteInstalling package(s) into ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library’
(as ‘lib’ is unspecified)
inferring 'repos = NULL' from the file name
Warning in file(name, "wb") :
cannot open file 'phytools_0.0-1/DESCRIPTION': Permission denied
Error in file(name, "wb") : cannot open the connection
Warning in install.packages :
installation of package 'phytools_0.0-1.tar.gz' had non-zero exit status
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] C/en_US.UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] infochimps_0.3 RJSONIO_0.7-1 stringr_0.4 RCurl_1.5-0 bitops_1.0-4.1
loaded via a namespace (and not attached):
[1] plyr_1.5.1 tools_2.13.0
Up and running on a PC!! (Windows 7)
ReplyDeleteMy Mac is at work, so I can't try that till tomorrow, but I've run a couple functions without problems on the PC.
Congrats on getting this up!
I got somewhat the same error:
ReplyDelete> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.13.0
> install.packages('/Users/RMaia/Downloads/phytools_0.0-1.tar.gz',type='source')
inferring 'repos = NULL' from the file name
Warning in file(name, "wb") :
cannot open file 'phytools_0.0-1/DESCRIPTION': Permission denied
Error in file(name, "wb") : cannot open the connection
Warning message:
In install.packages("/Users/RMaia/Downloads/phytools_0.0-1.tar.gz", :
installation of package '/Users/RMaia/Downloads/phytools_0.0-1.tar.gz' had non-zero exit
#and if I try using the Package Installer:
Warning in file(name, "wb") :
cannot open file 'phytools_0.0-1/DESCRIPTION': Permission denied
Error in file(name, "wb") : cannot open the connection
BUT... then I tried uncompressing the file, and I started getting more specific errors:
> install.packages("/Users/RMaia/Desktop/phytools_0.0-1",repos=NULL,type="source")
WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package ‘phytools’ ...
** R
** preparing package for lazy loading
Loading required package: quadprog
Warning message:
In install.packages("/Users/RMaia/Desktop/phytools_0.0-1", repos = NULL, :
installation of package '/Users/RMaia/Desktop/phytools_0.0-1' had non-zero exit status
Loading required package: igraph
Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
there is no package called 'igraph'
Error : package 'igraph' could not be loaded
ERROR: lazy loading failed for package ‘phytools’
* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/phytools’
Then I installed and loaded the quadrprog package, and tried again. The installation went a bit further, but stopped when trying to load the igraph package. After installing and loading it, seems the installation was successful!
> install.packages("/Users/RMaia/Desktop/phytools_0.0-1",repos=NULL,type="source")
WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package ‘phytools’ ...
** R
** preparing package for lazy loading
Loading required package: quadprog
Loading required package: igraph
Loading required package: rgl
** help
No man pages found in package ‘phytools’
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (phytools)
> library(phytools)
Loading required package: ape
Loading required package: phangorn
Loading required package: igraph
Loading required package: rgl
> help(package="phytools") #works fine
> branching.diffusion(time.stop=10) #quick test of a function, works fine as well!
Hope that helps! Thanks for putting this together!
Thanks for the feedback guys. Not sure what the problem is exactly, but it seems to be Mac/Linux vs. PC specific. I will try to sort this out ASAP. - Liam
ReplyDeleteBTW, this is what I get when I install to my netbook:
ReplyDelete> install.packages("phytools_0.0-1.tar.gz", type="source")
inferring 'repos = NULL' from the file name
WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package 'phytools' ...
** R
** preparing package for lazy loading
Loading required package: quadprog
Loading required package: igraph
Loading required package: rgl
** help
No man pages found in package 'phytools'
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (phytools)
> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
just a quick follow-up, I tried reinstalling it while having the required quadprog, igraph and rgl packages loaded to see if that was the issue, but the installation still failed.
ReplyDeleteHowever, uncompressing the tar.gz file and using the folder as a source still worked even if those three packages weren't loaded (as long as they were installed, it would call and load them).
Don't know exactly if that'd help solve the problem, but maybe it'll at least help mac users install the package, if anyone can replicate this behavior. Cheers!
Installed fine on my PC.
ReplyDelete-Dave
Thanks for letting me know.
ReplyDeleteThanks for posting this Liam. This is great.
ReplyDeleteI am on a Mac and had similar problems as people mentioned above. I got the package to install by doing the following:
1) unarchiving the tar.gz folder
2) in the terminal, I moved to the folder where the phytools was and typed the command
R CMD INSTALL phytools_0.0-1
3) Then in the R-terminal, I just typed library(phytools)
cheers,
matt
Thanks for the fix. Seems to be a Mac/Linux vs. PC issue. I will have to try and figure this one out!
ReplyDelete