All code for this document is located at here.
Overall, RStudio provides a fantastic tutorial and discussion on installing devtools. Please consult this before the rest of the document. If you have errors, please see below.
As Neuroconductor is GitHub-based, we will need a way for R to install packages directly from GitHub. The devtools package provides this functionality. In this tutorial, we will go through the steps of installing devtools, and some common problems. You must have devtools installed to install from GitHub in subsequent tutorials on installing Neuroconductor packages.
There are other packages that will do this and are more lightweight (see remotes and ghit), but we will focus on devtools.
You need to install Command Line Tools, aka the command line tools for Xcode, if you have not already. http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/ is a great tutorial how.
If you already have devtools installed great! (Why are you in this section?) You can always reinstall the most up to date version from the steps below.
packages = installed.packages()
packages = packages[, "Package"]
if (!"devtools" %in% packages) {
install.packages("devtools")
}remotes and ghit packagesIf you want a lighter-weight package that has the install_github functionality that devtools provides, but not all the “development” parts of devtools, the remotes package exists just for that:
packages = installed.packages()
packages = packages[, "Package"]
if (!"remotes" %in% packages) {
install.packages("remotes")
}The ghit package is the lightest-weight package I have seen which has a install_github function, but may have some limited functionality compared to remotes in the functionality of installing package with dependencies in other systems, such as BitBucket.
In any subsequent tutorial, when you see devtools::install_github, just insert remotes::install_github and it should work just the same.
In the install_github function, there are additional options to pass to the install function from devtools. One of those arguments is upgrade_dependencies, which default is set to TRUE. So if you want to install a package from GitHub, but not update any of the dependencies, then you can use install_github(..., upgrade_dependencies = FALSE).
If you cannot install devtools, many times it is due to git2r. You should look at the installation logs and if you see something like:
The OpenSSL library that is required to
build git2r was not found.
Please install:
libssl-dev (package on e.g. Debian and Ubuntu)
openssl-devel (package on e.g. Fedora, CentOS and RHEL)
openssl (Homebrew package on OS X)Then run sudo apt-get libssl-dev or sudo yum install openssl-devel on your respective Linux machine. Try to re-install devtools.
For Mac, you have to install Homebrew which the tutorial is located in the link. After Homebrew is installed you should be able to type in the Terminal:
brew update
brew install opensslThen try to re-install devtools.
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.2 (2020-06-22)
## os macOS Catalina 10.15.7
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2021-02-16
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
## assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.0.0)
## cachem 1.0.4 2021-02-13 [1] CRAN (R 4.0.2)
## callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2)
## cli 2.3.0 2021-01-31 [1] CRAN (R 4.0.2)
## colorout * 1.2-2 2020-06-01 [2] Github (jalvesaq/colorout@726d681)
## crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.2)
## desc 1.2.0 2020-06-01 [2] Github (muschellij2/desc@b0c374f)
## devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
## digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
## ellipsis 0.3.1 2020-05-15 [2] CRAN (R 4.0.0)
## evaluate 0.14 2019-05-28 [2] CRAN (R 4.0.0)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.2)
## fs 1.5.0 2020-07-31 [2] CRAN (R 4.0.2)
## glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
## htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
## knitr 1.31 2021-01-27 [1] CRAN (R 4.0.2)
## lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.2)
## magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
## memoise 2.0.0 2021-01-26 [1] CRAN (R 4.0.2)
## pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.2)
## pkgload 1.1.0 2020-05-29 [2] CRAN (R 4.0.0)
## prettyunits 1.1.1 2020-01-24 [2] CRAN (R 4.0.0)
## processx 3.4.5 2020-11-30 [1] CRAN (R 4.0.2)
## ps 1.5.0 2020-12-05 [1] CRAN (R 4.0.2)
## purrr 0.3.4 2020-04-17 [2] CRAN (R 4.0.0)
## R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
## remotes 2.2.0 2020-07-21 [2] CRAN (R 4.0.2)
## rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.2)
## rmarkdown 2.6 2020-12-14 [1] CRAN (R 4.0.2)
## rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2)
## rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.2)
## sessioninfo 1.1.1 2018-11-05 [2] CRAN (R 4.0.0)
## stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
## stringr 1.4.0 2019-02-10 [2] CRAN (R 4.0.0)
## testthat 3.0.2 2021-02-14 [1] CRAN (R 4.0.2)
## usethis 2.0.1 2021-02-10 [1] CRAN (R 4.0.2)
## withr 2.4.1 2021-01-26 [1] CRAN (R 4.0.2)
## xfun 0.21 2021-02-10 [1] CRAN (R 4.0.2)
## yaml 2.2.1 2020-02-01 [2] CRAN (R 4.0.0)
##
## [1] /Users/johnmuschelli/Library/R/4.0/library
## [2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library