ERROR: dependency ‘treeio’ is not available for package ‘agalmar’

[Lisa K. Johnson]

Hi! Not really an issue because I was able to fix, so feel free to close. Wanted to share here in case it helps anyone. Looking forward to exploring functions in this package. Thank you!

Installing in RStudio (MacOS 10_13_3, RStudio 1.1.383, R 3.4.2) with:

install_github('caseywdunn/agalmar')

Fixed with this from recommendation:

install.packages("base64enc", type = "binary")
install.packages("jsonlite", type="binary")
install.packages("rmarkdown")
devtools::install_github("tidyverse/reprex")
source("https://bioconductor.org/biocLite.R")
biocLite("treeio")
install_github('caseywdunn/agalmar')

Error messages:

> install_github('caseywdunn/agalmar')
Downloading GitHub repo caseywdunn/agalmar@master
from URL https://api.github.com/repos/caseywdunn/agalmar/zipball/master
Installing agalmar
Downloading GitHub repo caseywdunn/hutan@master
from URL https://api.github.com/repos/caseywdunn/hutan/zipball/master
Installing hutan
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL  \
  '/private/var/folders/5m/37fhf86x0g70t9w632_f9yf80000gn/T/RtmpCHxgE5/devtools875e654ab908/caseywdunn-hutan-ff536f3'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests 

* installing *source* package ‘hutan’ ...
Warning in as.POSIXlt.POSIXct(x, tz) :
  unknown timezone 'zone/tz/2018c.1.0/zoneinfo/America/Los_Angeles'
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hutan)
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL  \
  '/private/var/folders/5m/37fhf86x0g70t9w632_f9yf80000gn/T/RtmpCHxgE5/devtools875e4bfb0cb8/caseywdunn-agalmar-33d5a33'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests 

ERROR: dependency ‘treeio’ is not available for package ‘agalmar’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/agalmar’
Installation failed: Command failed (1)

Tried biocLite("treeio") with the following error:

ERROR: dependency ‘rmarkdown’ is not available for package ‘reprex’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/reprex’

The downloaded source packages are in
	‘/private/var/folders/5m/37fhf86x0g70t9w632_f9yf80000gn/T/RtmpCHxgE5/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘reprex’ had non-zero exit status

Tried install.packages("reprex") with the following error:

ERROR: dependency ‘rmarkdown’ is not available for package ‘reprex’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/reprex’
Warning in install.packages :
  installation of package ‘reprex’ had non-zero exit status