From 483d4c241152854f65dc0aeeb4e92065acafd5b8 Mon Sep 17 00:00:00 2001 From: Mary Llewellyn Date: Tue, 2 Apr 2024 13:26:07 +0100 Subject: [PATCH 1/3] update setup for system deps --- setup.md | 19 ++++--------------- 1 file changed, 4 insertions(+), 15 deletions(-) diff --git a/setup.md b/setup.md index 9f599b8d..1c70caa6 100644 --- a/setup.md +++ b/setup.md @@ -9,8 +9,10 @@ to set up for the lessons. This should take about an hour to run, depending on the speed of your computer, your internet connection, and any packages you have installed already. You'll need to install R 4.0 or later. -The following code will download the data and install the libraries -used in the current version of this lesson: +On Linux and Mac systems, R package installation often requires additional system dependencies. To ensure that you can download packages using the code below, first run the terminal commands for your Linux distribution [here](https://docs.posit.co/connect/admin/r/dependencies/). For Mac systems, you can use the Ubuntu code. Note that you will need to use root access (sudo) to install the system dependencies. Windows users can skip this step. + +All learners should then run the following code to download the data and install the libraries +used in this lesson: ```r install.packages("BiocManager") @@ -40,17 +42,4 @@ for (file in data_files) { } ``` -On Linux systems, part of the above may fail due to the **`bluster`** package and you may receive error messages after running `BiocManager::install(table[[1]])`, indicating that the package `igraph` was not installed successfully. - -Detailed installation instructions for `igraph` can be found at [https://r.igraph.org/](https://r.igraph.org/), but the following workaround code may resolve the issue: - -```r -install.packages('igraph', repos=c(igraph = 'https://igraph.r-universe.dev', - CRAN = 'https://cloud.r-project.org')) - -BiocManager::install('bluster') -``` - -Note especially the C libraries that are mentioned on the `igraph` help page for compiling from source --- these are usually available via a package manager (homebrew, apt, pacman, etc), and are required if your R installation is unable to use pre-compiled binaries from CRAN. - {% include links.md %} From 776ca638306a6d09b5f8600782226e86ded7c2c9 Mon Sep 17 00:00:00 2001 From: Mary Llewellyn Date: Tue, 2 Apr 2024 13:27:55 +0100 Subject: [PATCH 2/3] edit wording to make more generic --- setup.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.md b/setup.md index 1c70caa6..7e4fea9f 100644 --- a/setup.md +++ b/setup.md @@ -9,7 +9,7 @@ to set up for the lessons. This should take about an hour to run, depending on the speed of your computer, your internet connection, and any packages you have installed already. You'll need to install R 4.0 or later. -On Linux and Mac systems, R package installation often requires additional system dependencies. To ensure that you can download packages using the code below, first run the terminal commands for your Linux distribution [here](https://docs.posit.co/connect/admin/r/dependencies/). For Mac systems, you can use the Ubuntu code. Note that you will need to use root access (sudo) to install the system dependencies. Windows users can skip this step. +On Linux and Mac systems, R package installation often requires additional system dependencies. If you are a Linux or Mac user, to ensure that you can download packages using the code below, first run the terminal commands for your distribution [here](https://docs.posit.co/connect/admin/r/dependencies/). For Mac systems, you can use the Ubuntu code. Note that you will need to use root access (sudo) to install the system dependencies. Windows users can skip this step. All learners should then run the following code to download the data and install the libraries used in this lesson: From ce4cd0d086b7b27d97cf2cd7fdd02763a020503d Mon Sep 17 00:00:00 2001 From: Alan O'Callaghan Date: Thu, 4 Apr 2024 17:27:15 +0100 Subject: [PATCH 3/3] Update setup.md --- setup.md | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/setup.md b/setup.md index 7e4fea9f..be078dbb 100644 --- a/setup.md +++ b/setup.md @@ -9,7 +9,18 @@ to set up for the lessons. This should take about an hour to run, depending on the speed of your computer, your internet connection, and any packages you have installed already. You'll need to install R 4.0 or later. -On Linux and Mac systems, R package installation often requires additional system dependencies. If you are a Linux or Mac user, to ensure that you can download packages using the code below, first run the terminal commands for your distribution [here](https://docs.posit.co/connect/admin/r/dependencies/). For Mac systems, you can use the Ubuntu code. Note that you will need to use root access (sudo) to install the system dependencies. Windows users can skip this step. +R usually enables package downloads using pre-built binaries. Some times, this is not possible, +particularly on Linux and Mac systems. In this case, R package installation often requires additional +system dependencies. If you are a Linux user, to ensure that you can download packages using the code +below, first run the terminal commands for your distribution +[here](https://docs.posit.co/connect/admin/r/dependencies/). +Note that you will need to use root access (sudo) to install the system dependencies. +Mac users may need to use [homebrew](https://brew.sh/) to install system dependencies, +and Windows users may need to install [RTools](https://cran.r-project.org/bin/windows/Rtools/). +Ideally, installing packages will proceed without error and you can ignore these steps, +but this isn't always the case. + +Previous learners have reported issues with **`igraph`**. Installation instructions for this package can be found on [https://r.igraph.org/](https://r.igraph.org/), All learners should then run the following code to download the data and install the libraries used in this lesson: