[Bioc-devel] philr recent build fail

[Shepherd, Lori]

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-bounces at r-project.org> on behalf of Justin Silverman <jsilve24 at gmail.com>
Sent: Wednesday, October 12, 2016 11:26:41 AM
To: bioc-devel at 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


        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]