Bug for @brj1: install GitHub fails

[richelbilderbeek]

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Hi @brj1, I wanted to use your density trees plot (as requested in #134), that has not made it yet into ggtree. Sadly, already the installation of it fails:

# Sure, we've installed tidytree
library(tidytree)

# Install @brj1's for of ggtree
devtools::install_github("brj1/ggtree")

This results in an error:

Downloading GitHub repo brj1/ggtree@master
✔  checking for file ‘/tmp/Rtmpfu4zfC/remotes19d1498b26b9/brj1-ggtree-36d4cf2/DESCRIPTION’ ...
─  preparing ‘ggtree’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘ggtree_1.13.6.tar.gz’
   
Installing package into ‘/home/richel/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
* installing *source* package ‘ggtree’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error : object ‘as_data_frame’ is not exported by 'namespace:tidytree'
ERROR: lazy loading failed for package ‘ggtree’
* removing ‘/home/richel/R/x86_64-pc-linux-gnu-library/3.4/ggtree’
* restoring previous ‘/home/richel/R/x86_64-pc-linux-gnu-library/3.4/ggtree’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/tmp/Rtmpfu4zfC/file19d1d42f5ba/ggtree_1.13.6.tar.gz’ had non-zero exit status

Apparently, the tidytree has its interface changed. I hope you, @brj1, can fix it :+1:.

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Sorry Guangchuang for using your repo for this Issue. It is just that forks do not have their own Issues...

[GuangchuangYu]

since as_data_frame is not a generic method anymore in tibble and will remove in future release, I just change the as_data_frame to as_tibble in tidytree.

I think what @brj1 need is to merge upstream from my repo.

[brj1]

I agree @GuangchuangYu . I'm trying to merge, but I am have trouble buiding the latest version of ggtree.

EDIT: in particular I get the error message:

* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ggtree’ ...
** R
Error in parse(outFile) : 
  /Users/bjones/git/ggtree/R/reexports.R:3:11: unexpected SPECIAL
2: ##' @export
3: magrittr::%>%
             ^
ERROR: unable to collate and parse R files for package ‘ggtree’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ggtree’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ggtree’

Rolling back to 9416b852753df fixes the issue.

[brj1]

Okay I pushed my merge with 9416b852753df . I was able to build it, but I haven't tested it yet.

[brj1]

Okay I got it working. The following displays correctly:

library(ape)
library(ggtree)

# Here I create two trees. In one tree, taxon 'C' is the outlier. In the other tree, taxon 'B' is the outlier
tree_1 <- ape::read.tree(text = "((A:2,B:2):1, C:3);")
tree_2 <- ape::read.tree(text = "((A:1,C:1):2, B:3);")

trees <- list(tree_1, tree_2)

# Show them overlapping
ggtree::ggdensitree(trees, layout='rectangular') + ggtree::geom_tiplab()

[GuangchuangYu]

fixed R check for previous commit :)

[brj1]

It works now.