This is a problem with ggtree not with your package. You should be okay.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Justin
Silverman <jsilv...@gmail.com>
Sent: Wednesday, October 12, 2016 11:26:41 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] philr recent build fail
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
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs
--no-resave-data philr
###
##############################################################################
##############################################################################
* 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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