[Phylobase-devl] [Phylobase-commits] r180 - pkg/tests

[Peter Cowan]

Ben,

The error I got is appended below, to be honest I didn't even attempt  
to debug it.

I'm running 2.7.0 on a mac with Leopard.

I agree, it's bad form to find a problem and not at least open a  
ticket for it, I'll do that.

Peter

----
* checking examples ... OK
* checking tests ...
  Running 'misctests.R'
  Running 'nexusdata.R'
make[1]: *** [nexusdata.Rout] Error 1
make: *** [all] Error 2
ERROR
Running the tests in 'tests/nexusdata.R' failed.
Last 13 lines of output:
  Reading CHARACTERS block...
  Skipping unknown block (CHARACTERS2)
  Reading TREES block...
  Reading ASSUMPTIONS block...
  Skipping unknown block (MESQUITECHARMODELS)
  Skipping unknown block (MESQUITE)
  Skipping unknown block (brownie)
  Error in check_data(res, ...) :
    Tip data names are a subset of tree tip labels
  (missing data names: [&R],,,,,,,,,,)
  (extra data names:  
Myrmecocystuscreightoni 
,Myrmecocystusdepilis 
,Myrmecocystuskennedyi 
,Myrmecocystusmendax 
,Myrmecocystusnavajo 
,Myrmecocystusnequazcatl 
,Myrmecocystusplacodops 
,Myrmecocystustenuinodis 
,Myrmecocystustestaceus,Myrmecocystuswheeleri,Myrmecocystusyuma)
  Calls: NexusToPhylo4D -> phylo4d -> phylo4d -> .local -> check_data
  Execution halted

On Jun 1, 2008, at 6:37 AM, Ben Bolker wrote:

>  NCL tests don't fail on my system -- what happens on yours?
> Do the tests run in interactive mode but fail during testing, or is it
> just testing?  I don't necessarily have a problem with short-term
> commenting-out in either case (although obviously the former is
> less alarming), but in the long run it would be much better to try to
> fix the problem -- can you at least file a Tracker item/bug report?
>
> (off-topic: did you set up the Tracker for phylobase?  I was
> having a little trouble figuring out how to do it for a different r- 
> forge
> package ...)
>
> cheers
>  Ben
>
>
> noreply at r-forge.wu-wien.ac.at wrote:
>> Author: pdc
>> Date: 2008-06-01 11:00:51 +0200 (Sun, 01 Jun 2008)
>> New Revision: 180
>>
>> Modified:
>>  pkg/tests/nexusdata.R
>> Log:
>> committing out NCL tests, as they cause R CMD check to fail
>>
>> Modified: pkg/tests/nexusdata.R
>> ===================================================================
>> --- pkg/tests/nexusdata.R	2008-05-31 19:42:00 UTC (rev 179)
>> +++ pkg/tests/nexusdata.R	2008-06-01 09:00:51 UTC (rev 180)
>> @@ -1,17 +1,17 @@
>> ## try to read NEXUS files
>> -library(phylobase)
>> -fn <- system.file("nexusfiles/ 
>> treepluscharV01.nex",package="phylobase")
>> -td<-NexusToPhylo4D(fn)
>> -summary(td)
>> +## library(phylobase)
>> +## fn <- system.file("nexusfiles/ 
>> treepluscharV01.nex",package="phylobase")
>> +## td<-NexusToPhylo4D(fn)
>> +## summary(td)
>> ## would try plotting, but typically don't have enough room
>> ## to plot data
>> ## Error in .local(x, ...) :  ##    No room left to plot data;  
>> please try reducing ratio.tree or cex.label.
>> -plot(as(td,"phylo4"))
>> +## plot(as(td,"phylo4"))
>> ## try to read a nexus file where the newick string describing the  
>> tree is split
>> ## across several lines
>> -multiLine <- system.file("nexusfiles/ 
>> MultiLineTrees.nex",package="phylobase")
>> -multiLineTrees <-NexusToPhylo4(multiLine)
>> -summary(multiLineTrees)
>> +## multiLine <- system.file("nexusfiles/ 
>> MultiLineTrees.nex",package="phylobase")
>> +## multiLineTrees <-NexusToPhylo4(multiLine)
>> +## summary(multiLineTrees)
>>
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>