[Phylobase-devl] Urgent! problems with installing

Marguerite Butler mbutler at hawaii.edu
Wed Jul 2 18:09:51 CEST 2008


Hi Francois, Brian, and Ben,

Thank you for looking into this. But to the ape developers: has the  
code for read.nexus changed recently? Or is this a problem with the R  
version?

I installed ape from binaries each time, which is ape 2.1-3. I got  
the bug with it installed in R 2.7.1 but not R 2.6.2.

I downloaded ape 2.1-3 and ape 2.2 sources, and did a diff on the  
read.nexus.R files, and got no differences. I'm worried about what  
else will come up if I use R 2.7 for the comparative methods course.

Marguerite


On Jul 2, 2008, at 5:48 AM, François Michonneau wrote:

> Hi Marguerite
>
> I think I found the bug. I looked at that very quickly so I might  
> be wrong.
>
> It comes from the function read.nexus. Towards the end there is:
>
>     if (Ntree == 1) {
>         trees <- trees[[1]]
>         #trees$tip.label <- TRANS[, 2]
>     }
>     else {
>         if (!is.null(tree.names))
>             names(trees) <- tree.names
>         if (translation)
>             attr(trees, "TipLabel") <- TRANS[, 2]
>         class(trees) <- "multiPhylo"
>     }
>     if (length(grep("[\\/]", file)) == 1)
>         file <- paste(getwd(), file, sep = "/")
>     attr(trees, "origin") <- file
>     trees
>
>
> However, the variable TRANS is defined only if the word "translate"  
> is present (look at the beginning of read.nexus) in the nexus file.  
> Thus the error message. I haven't spent enough time to try to  
> figure out what this line was doing specifically, but if this line  
> is commented then there is no error message and it still works.
>
> Cheers,
> François
>
> Marguerite Butler wrote:
>> Hi Ben,
>> Thanks for the quick reply!
>>>
>>>      No problems here with 2.7.0.
>>>   Can you send a read.nexus example for me to try?
>>>
>> Here is the nexus file that read.nexus couldn't read under R 2.7.1  
>> yesterday (this was a problem both for macs and pc's on several  
>> people's computers -- I had a small group of students try it).  
>> When I downgraded it read in fine.
>> --------------------------------------------------------------------- 
>> ---
>> It would be great if you could give it a try.
>>>
>>>> The binaries were available on the r-forge site for a while, but  
>>>> not anymore.
>>>
>>>   It looks (?) like they're there -- I even downloaded the file
>>> and it seems to have the right bits in it, but I can't tell
>>> without trying to install it ...
>>>
>> Oops! Sorry you are right, the binaries are there. I guess I got  
>> myself confused because it is not passing the check. However, it  
>> is not possible to install the binaries unless you have 2.7. The  
>> real problem is that I can't install from source in 2.6.2.
>>> But my problem is that I can't even install from source. When I
>>>> did R CMD check on the package, I get one warning:
>>>> ====
>>>> * checking if this is a source package ... WARNING
>>>> Subdirectory 'pkg/src' contains object files.
>>>> ====
>>>> I found "phylobase.so" in pkg/src. Is this supposed to be there?  
>>>> It might be the culprit because the error I get when I try to  
>>>> load phylobase is:
>>>>  > require(phylobase)
>>>> Loading required package: phylobase
>>>> Error in dyn.load(file, ...) :
>>>>   unable to load shared library '/Library/Frameworks/R.framework/ 
>>>> Resources/library/phylobase/libs/i386/phylobase.so':   dlopen(/ 
>>>> Library/Frameworks/R.framework/Resources/library/phylobase/libs/ 
>>>> i386/phylobase.so, 6): Library not loaded: /Library/Frameworks/ 
>>>> R.framework/Versions/2.7/Resources/lib/libR.dylib
>>>>   Referenced from: /Library/Frameworks/R.framework/Resources/ 
>>>> library/phylobase/libs/i386/phylobase.so   Reason: image not found
>>>> Which doesn't make a whole lot of sense since I'm installing  
>>>> from source on R 2.6.2.
>>>
>>>   It seems it's still looking for a 2.7 library?
>> Yes, that is what it looks like to me.  Why would it be doing  
>> that? I tried trashing the phylobase directory in the location on  
>> my computer where R is installed, which is here: /Library/ 
>> Frameworks/R.framework/Resources/library/phylobase
>> before re-installing, in case there was something in there from a  
>> previous installation with 2.7 still lurking around, but it didn't  
>> seem to help. Is there anything else I should do for a "clean"  
>> install of phylobase?
>>>
>>>> So I went back and removed the "phylobase.so" from the pkg/src  
>>>> directory (the version I got from the svn repository -- revision  
>>>> 192), and tried rebuilding. It passed the check this time, so I  
>>>> installed. But when I try loading, I still get the same error  
>>>> above from my require(phylobase) command??
>>>> Has anyone else had problems?
>>>> I don't think it's entirely a 2.6.2 issue because I don't think  
>>>> it's working for the 2.7.X versions either, otherwise wouldn't  
>>>> there be binaries available?
>>>> I am preparing for the NESCENT course, so this is pretty urgent.  
>>>> Any help would be greatly appreciated.
>>>> Marguerite
>>>
>>>    I will do anything I can to help but am a little restricted
>>> since it's working fine for me and I don't have a Mac ...
>>>
>> If it turns out that we can only use ape with 2.6.2, and phylobase  
>> with 2.7, is there a way to switch between R versions on the same  
>> computer (of course in different R sessions)? I know that  the old  
>> versions are still there when you install a newer version. Has any  
>> of the other mac users had problems? Thanks,
>> Marguerite
>> ____________________________________________
>> Marguerite A. Butler
>> Department of Zoology
>> University of Hawaii
>> 2538 McCarthy Mall, Edmondson 259
>> Honolulu, HI  96822
>> Phone: 808-956-4713
>> FAX:   808-956-9812
>> Dept: 808-956-8617
>> http://www2.hawaii.edu/~mbutler
>> http://www.hawaii.edu/zoology/
>> --------------------------------------------------------------------- 
>> ---
>> _______________________________________________
>> Phylobase-devl mailing list
>> Phylobase-devl at lists.r-forge.r-project.org
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>> phylobase-devl

____________________________________________
Marguerite A. Butler
Department of Zoology
University of Hawaii
2538 McCarthy Mall, Edmondson 259
Honolulu, HI  96822

Phone: 808-956-4713
FAX:   808-956-9812
Dept: 808-956-8617
http://www2.hawaii.edu/~mbutler
http://www.hawaii.edu/zoology/

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