Errors when installing bioconductor packages in RStudio installed in Ubuntu 24.04

General
, ,
1

Hello,

I installed Ubuntu 24.04 and started preparing the machine for data analysis. I started installing R and RStudio using the following commands:
https://cran.r-project.org/bin/linux/ubuntu/fullREADME.html

sudo apt-get update
sudo apt-get install r-base

Then,

choose ubuntu

Then,

sudo apt update -qq

sudo apt install --no-install-recommends software-properties-common dirmngr

wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

Then,
sudo apt-get install r-base-dev

Then,

download RStudio for Ubuntu 24.04
$cd Download

$sudo dpkg -i rstudio-2024.09.0-375-amd64.deb

sudo apt install -f

I am able to successfully install packages from CRAN but encounter errors when attempting to install packages from Bioconductor.

Example of errors:
ERROR: dependencies ‘systemfonts’, ‘textshaping’ are not available for package ‘ragg’

  • removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.4/ragg’

Then, I ran

$sudo apt-get install libcurl4-openssl-dev r-base

Are there any specific libraries or dependencies that need to be installed on Ubuntu beforehand?

I have updates:
$sudo apt install r-cran-curl
Then, I installed devtools to install DADA2

install.packages("devtools")
library("devtools")
devtools::install_github("benjjneb/dada2", ref="v1.26")

but I got the error below:

ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘ShortRead’

  • removing ‘/home/raizada/R/x86_64-pc-linux-gnu-library/4.4/ShortRead’

Thanks!

2

Do you have the R packages systemfonts and textshaping installed? If not, what happens if you try to install them?

3

Hello,

Thanks for your suggestion.
I did the followings:

I did the following:

$sudo apt install libharfbuzz-dev libfribidi-dev

install.packages("textshaping", dependencies = TRUE)

$sudo apt install libfontconfig1-dev

install.packages("systemfonts", dependencies = TRUE)

but this did not help to install dada2

Then I tried this since it requires installing ShortRead package

BiocManager::install("ShortRead")
then dada2 was installed successfully

Thanks again!

4

You could give pak a go, it'll install system requirements automatically, and it'll also instal Bioconductor packages without any other package needed.
See All about installing pak. — Installing pak • pak

You can also use it to check the system requirements of packages:

❯ pak::pkg_sysreqs("ragg", sysreqs_platform="ubuntu-2404")
── Install scripts ──────────────────────────────────── Ubuntu 2404 ──
apt-get -y update
apt-get -y install libfreetype6-dev libjpeg-dev libpng-dev \
  libtiff-dev libfontconfig1-dev libfribidi-dev libharfbuzz-dev

── Packages and their system dependencies ────────────────────────────
ragg        – libfreetype6-dev, libjpeg-dev, libpng-dev, libtiff-dev
systemfonts – libfontconfig1-dev, libfreetype6-dev
textshaping – libfreetype6-dev, libfribidi-dev, libharfbuzz-dev
5

Thanks so much for your answer.
Yesterday, I installed devtools, and a few packages from bioconductor for metagenomic data analysis.
I wonder if I ran the code provided int the link:

install.packages("pak", repos = sprintf(
  "https://r-lib.github.io/p/pak/stable/%s/%s/%s",
  .Platform$pkgType,
  R.Version()$os,
  R.Version()$arch
))

, there will be any issue or redundancy in package installation?
Again, thanks!