Check and install R packages
Usage
check_r(packages, lib = .libPaths()[1], force = FALSE, verbose = TRUE)Arguments
- packages
Package to be installed. Package source can be CRAN, Bioconductor or Github. By default, the package name is extracted according to the
packagesparameter.- lib
The location of the library directories where to install the packages.
- force
Whether to force the installation of packages. Default is
FALSE.- verbose
Whether to print the message. Default is
TRUE.
Examples
check_r(c("Seurat", "reticulate"))
#> ◌ [2025-11-13 12:44:21] Installing: Seurat...
#>
#> → Will install 26 packages.
#> → All 26 packages (0 B) are cached.
#> + ROCR 1.0-11
#> + Seurat 5.3.1
#> + SeuratObject 5.2.0
#> + caTools 1.18.3
#> + deldir 2.0-4
#> + dotCall64 1.2
#> + fastDummies 1.7.5
#> + fitdistrplus 1.2-4
#> + goftest 1.2-3
#> + gplots 3.2.0
#> + gtools 3.9.5
#> + ica 1.0-3
#> + leidenbase 0.1.35
#> + miniUI 0.1.2
#> + progressr 0.18.0
#> + scattermore 1.2
#> + sctransform 0.4.2
#> + spam 2.11-1
#> + spatstat.data 3.1-9
#> + spatstat.explore 3.5-3
#> + spatstat.geom 3.6-0
#> + spatstat.random 3.4-2
#> + spatstat.sparse 3.1-0
#> + spatstat.univar 3.1-4
#> + spatstat.utils 3.2-0
#> + tensor 1.5.1
#> ✔ All system requirements are already installed.
#>
#> ℹ No downloads are needed, 26 pkgs are cached
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install libcurl4-openssl-dev libssl-dev make zlib1g-dev libglpk-dev libxml2-dev pandoc libpng-dev python3 libicu-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libcurl4-openssl-dev is already the newest version (8.5.0-2ubuntu10.6).
#> libssl-dev is already the newest version (3.0.13-0ubuntu3.6).
#> make is already the newest version (4.3-4.1build2).
#> zlib1g-dev is already the newest version (1:1.3.dfsg-3.1ubuntu2.1).
#> libglpk-dev is already the newest version (5.0-1build2).
#> libxml2-dev is already the newest version (2.9.14+dfsg-1.3ubuntu3.6).
#> pandoc is already the newest version (3.1.3+ds-2).
#> libpng-dev is already the newest version (1.6.43-5build1).
#> python3 is already the newest version (3.12.3-0ubuntu2.1).
#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> 0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
#> ✔ Installed caTools 1.18.3 (78ms)
#> ✔ Installed deldir 2.0-4 (92ms)
#> ✔ Installed dotCall64 1.2 (110ms)
#> ✔ Installed fastDummies 1.7.5 (145ms)
#> ✔ Installed fitdistrplus 1.2-4 (73ms)
#> ✔ Installed goftest 1.2-3 (72ms)
#> ✔ Installed gplots 3.2.0 (108ms)
#> ✔ Installed gtools 3.9.5 (76ms)
#> ✔ Installed ica 1.0-3 (71ms)
#> ✔ Installed leidenbase 0.1.35 (71ms)
#> ✔ Installed miniUI 0.1.2 (74ms)
#> ✔ Installed progressr 0.18.0 (71ms)
#> ✔ Installed ROCR 1.0-11 (73ms)
#> ✔ Installed scattermore 1.2 (103ms)
#> ✔ Installed sctransform 0.4.2 (76ms)
#> ✔ Installed Seurat 5.3.1 (82ms)
#> ✔ Installed SeuratObject 5.2.0 (87ms)
#> ✔ Installed spam 2.11-1 (81ms)
#> ✔ Installed spatstat.data 3.1-9 (87ms)
#> ✔ Installed spatstat.explore 3.5-3 (85ms)
#> ✔ Installed spatstat.geom 3.6-0 (111ms)
#> ✔ Installed spatstat.random 3.4-2 (74ms)
#> ✔ Installed spatstat.sparse 3.1-0 (76ms)
#> ✔ Installed spatstat.univar 3.1-4 (76ms)
#> ✔ Installed spatstat.utils 3.2-0 (75ms)
#> ✔ Installed tensor 1.5.1 (46ms)
#> ✔ 1 pkg + 135 deps: kept 108, added 26 [7.5s]
#> ✔ [2025-11-13 12:44:29] Seurat and reticulate installed successfully