[Bioc-devel] philr recent build fail

[Justin Silverman]

Hi All, 
	I just checked on the status of philr build/check report. It had been clear as of 2 weeks ago but when I just checked it appears to be failing to build on all platforms.  (included built report from malbec1 below). I tried R CMD check and BiocCheck on my local machine without issues. I notice that ggtree is also having some issues (which I make use of in philr), perhaps this is what is causing philr to fail? Do I need to do anything?

Any help or advice appreciated, 
Justin Silverman

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data philr
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* checking for file ‘philr/DESCRIPTION’ ... OK
* preparing ‘philr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

If you use ggtree in published research, please cite:

Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.
Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628



Attaching package: 'ggtree'

The following object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:ape':

    rotate


Attaching package: 'dplyr'

The following object is masked from 'package:ggtree':

    collapse

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Found more than one class "phylo" in cache; using the first, from namespace 'ggtree'
Quitting from lines 218-230 (philr-intro.Rmd) 
Error: processing vignette 'philr-intro.Rmd' failed with diagnostics:
unused argument (check.aes = FALSE)
Execution halted


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