tag:blogger.com,1999:blog-8499895524521663926.post1708790056269034027..comments2024-03-27T07:13:39.236-04:00Comments on Phylogenetic Tools for Comparative Biology: "Alpha" version of phytools package now availableLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-8499895524521663926.post-65819265995842188262011-06-02T16:11:28.917-04:002011-06-02T16:11:28.917-04:00Thanks for the fix. Seems to be a Mac/Linux vs. P...Thanks for the fix. Seems to be a Mac/Linux vs. PC issue. I will have to try and figure this one out!Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-13747963479075138462011-06-02T15:23:46.818-04:002011-06-02T15:23:46.818-04:00Thanks for posting this Liam. This is great.
I am...Thanks for posting this Liam. This is great.<br /><br />I am on a Mac and had similar problems as people mentioned above. I got the package to install by doing the following:<br /><br />1) unarchiving the tar.gz folder<br /><br />2) in the terminal, I moved to the folder where the phytools was and typed the command<br /> R CMD INSTALL phytools_0.0-1<br /><br />3) Then in the R-terminal, I just typed library(phytools)<br /><br />cheers,<br />mattmwpennellhttps://www.blogger.com/profile/02523892313236801738noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-41656845556518437222011-06-02T15:06:01.477-04:002011-06-02T15:06:01.477-04:00Thanks for letting me know.Thanks for letting me know.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-44133068429923822072011-06-02T10:44:32.284-04:002011-06-02T10:44:32.284-04:00Installed fine on my PC.
-DaveInstalled fine on my PC.<br />-Davedwbapsthttps://www.blogger.com/profile/17606476387441191531noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-50868470356082012912011-06-01T22:57:56.628-04:002011-06-01T22:57:56.628-04:00just a quick follow-up, I tried reinstalling it wh...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. <br /><br />However, 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). <br /><br />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!Rafael Maiahttps://www.blogger.com/profile/02395303011366399867noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-85819860313487191312011-06-01T22:02:13.279-04:002011-06-01T22:02:13.279-04:00BTW, this is what I get when I install to my netbo...BTW, this is what I get when I install to my netbook:<br /><br />> install.packages("phytools_0.0-1.tar.gz", type="source")<br />inferring 'repos = NULL' from the file name<br />WARNING: omitting pointless dependence on 'R' without a version requirement<br />* installing *source* package 'phytools' ...<br />** R<br />** preparing package for lazy loading<br />Loading required package: quadprog<br />Loading required package: igraph<br />Loading required package: rgl<br />** help<br />No man pages found in package 'phytools' <br />*** installing help indices<br />** building package indices ...<br />** testing if installed package can be loaded<br /><br />* DONE (phytools)<br />> sessionInfo()<br />R version 2.11.1 (2010-05-31) <br />i386-pc-mingw32 <br /><br />locale:<br />[1] LC_COLLATE=English_United States.1252 <br />[2] LC_CTYPE=English_United States.1252 <br />[3] LC_MONETARY=English_United States.1252<br />[4] LC_NUMERIC=C <br />[5] LC_TIME=English_United States.1252 <br /><br />attached base packages:<br />[1] stats graphics grDevices utils datasets methods baseLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-78646858986448395332011-06-01T21:54:20.584-04:002011-06-01T21:54:20.584-04:00Thanks for the feedback guys. Not sure what the p...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. - LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-25867686590928021542011-06-01T21:26:16.692-04:002011-06-01T21:26:16.692-04:00I got somewhat the same error:
> sessionInfo()...I got somewhat the same error:<br /><br />> sessionInfo()<br />R version 2.13.0 (2011-04-13)<br />Platform: i386-apple-darwin9.8.0/i386 (32-bit)<br /><br />locale:<br />[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8<br /><br />attached base packages:<br />[1] stats graphics grDevices utils datasets methods base <br /><br />loaded via a namespace (and not attached):<br />[1] tools_2.13.0<br /><br />> install.packages('/Users/RMaia/Downloads/phytools_0.0-1.tar.gz',type='source')<br />inferring 'repos = NULL' from the file name<br />Warning in file(name, "wb") :<br /> cannot open file 'phytools_0.0-1/DESCRIPTION': Permission denied<br />Error in file(name, "wb") : cannot open the connection<br />Warning message:<br />In install.packages("/Users/RMaia/Downloads/phytools_0.0-1.tar.gz", :<br /> installation of package '/Users/RMaia/Downloads/phytools_0.0-1.tar.gz' had non-zero exit <br /><br />#and if I try using the Package Installer:<br /><br />Warning in file(name, "wb") :<br /> cannot open file 'phytools_0.0-1/DESCRIPTION': Permission denied<br />Error in file(name, "wb") : cannot open the connection<br /><br /><br />BUT... then I tried uncompressing the file, and I started getting more specific errors:<br /><br />> install.packages("/Users/RMaia/Desktop/phytools_0.0-1",repos=NULL,type="source")<br />WARNING: omitting pointless dependence on 'R' without a version requirement<br />* installing *source* package ‘phytools’ ...<br />** R<br />** preparing package for lazy loading<br />Loading required package: quadprog<br />Warning message:<br />In install.packages("/Users/RMaia/Desktop/phytools_0.0-1", repos = NULL, :<br /> installation of package '/Users/RMaia/Desktop/phytools_0.0-1' had non-zero exit status<br />Loading required package: igraph<br />Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :<br /> there is no package called 'igraph'<br />Error : package 'igraph' could not be loaded<br />ERROR: lazy loading failed for package ‘phytools’<br />* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/phytools’<br /><br /><br />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!<br /><br />> install.packages("/Users/RMaia/Desktop/phytools_0.0-1",repos=NULL,type="source")<br />WARNING: omitting pointless dependence on 'R' without a version requirement<br />* installing *source* package ‘phytools’ ...<br />** R<br />** preparing package for lazy loading<br />Loading required package: quadprog<br />Loading required package: igraph<br />Loading required package: rgl<br />** help<br />No man pages found in package ‘phytools’ <br />*** installing help indices<br />** building package indices ...<br />** testing if installed package can be loaded<br /><br />* DONE (phytools)<br /><br />> library(phytools)<br />Loading required package: ape<br />Loading required package: phangorn<br />Loading required package: igraph<br />Loading required package: rgl<br /><br />> help(package="phytools") #works fine<br />> branching.diffusion(time.stop=10) #quick test of a function, works fine as well!<br /><br /><br />Hope that helps! Thanks for putting this together!Rafael Maiahttps://www.blogger.com/profile/02395303011366399867noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-13017231972431922302011-06-01T21:24:57.880-04:002011-06-01T21:24:57.880-04:00Up and running on a PC!! (Windows 7)
My Mac is...Up and running on a PC!! (Windows 7) <br /><br />My Mac is at work, so I can't try that till tomorrow, but I've run a couple functions without problems on the PC. <br /><br />Congrats on getting this up!Luke Mahlernoreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-2885925635732548032011-06-01T20:39:09.779-04:002011-06-01T20:39:09.779-04:00> install.packages("phytools_0.0-1.tar.gz&...> install.packages("phytools_0.0-1.tar.gz",type="source")<br />Installing package(s) into ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library’<br />(as ‘lib’ is unspecified)<br />inferring 'repos = NULL' from the file name<br />Warning in file(name, "wb") :<br /> cannot open file 'phytools_0.0-1/DESCRIPTION': Permission denied<br />Error in file(name, "wb") : cannot open the connection<br />Warning in install.packages :<br /> installation of package 'phytools_0.0-1.tar.gz' had non-zero exit status<br /><br /><br /><br />> sessionInfo()<br />R version 2.13.0 (2011-04-13)<br />Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)<br /><br />locale:<br />[1] C/en_US.UTF-8/C/C/C/C<br /><br />attached base packages:<br />[1] stats graphics grDevices utils datasets methods base <br /><br />other attached packages:<br />[1] infochimps_0.3 RJSONIO_0.7-1 stringr_0.4 RCurl_1.5-0 bitops_1.0-4.1<br /><br />loaded via a namespace (and not attached):<br />[1] plyr_1.5.1 tools_2.13.0Anonymoushttps://www.blogger.com/profile/01944150859555101169noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-22052171226585420322011-06-01T20:14:57.493-04:002011-06-01T20:14:57.493-04:00Hi Scott. Yes, it does work on my machine with no...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! - LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-2608046758206986422011-06-01T19:41:31.839-04:002011-06-01T19:41:31.839-04:00Unfortunately,
install.packages("phytools_0....Unfortunately, <br />install.packages("phytools_0.0-1.tar.gz",type="source")<br /><br />didn't work for me after downloading your tarball. Does it work on your machine?Anonymoushttps://www.blogger.com/profile/01944150859555101169noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-57483865577551460812011-06-01T17:32:29.137-04:002011-06-01T17:32:29.137-04:00In the first version of this post I claimed:
"...In the first version of this post I claimed:<br />"I believe one could also load the source directly from the hosting URL, i.e.:<br />> install.packages("http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/phytools_0.0-1.tar.gz",type="source")"<br />Unfortunately, I didn't seem to be able to get that to work, so I have removed the suggestion.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.com