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 packages parameter.
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"))
#> ℹ [2025-09-20 14:01:57] Installing: Seurat...
#>  
#> → Will install 40 packages.
#> → All 40 packages (0 B) are cached.
#> + ROCR               1.0-11 
#> + RcppHNSW           0.6.0  
#> + RcppTOML           0.2.3  
#> + Seurat             5.3.0  
#> + SeuratObject       5.2.0  
#> + caTools            1.18.3 
#> + deldir             2.0-4  
#> + dotCall64          1.2    
#> + fastDummies        1.7.5  
#> + fitdistrplus       1.2-4  
#> + future             1.67.0 
#> + future.apply       1.20.0 
#> + globals            0.18.0 
#> + goftest            1.2-3  
#> + gplots             3.2.0  
#> + gtools             3.9.5  
#> + here               1.0.2  
#> + ica                1.0-3  
#> + leidenbase         0.1.35 
#> + listenv            0.9.1  
#> + lmtest             0.9-40 
#> + miniUI             0.1.2  
#> + parallelly         1.45.1 
#> + pbapply            1.7-4  
#> + progressr          0.16.0 
#> + reticulate         1.43.0  + ✔ python3
#> + rprojroot          2.1.1  
#> + scattermore        1.2    
#> + sctransform        0.4.2  
#> + sp                 2.2-0  
#> + spam               2.11-1 
#> + spatstat.data      3.1-8  
#> + spatstat.explore   3.5-2  
#> + spatstat.geom      3.5-0  
#> + spatstat.random    3.4-1  
#> + spatstat.sparse    3.1-0  
#> + spatstat.univar    3.1-4  
#> + spatstat.utils     3.1-5  
#> + tensor             1.5.1  
#> + zoo                1.8-14 
#> ✔ All system requirements are already installed.
#>   
#> ℹ No downloads are needed, 40 pkgs are cached
#> ✔ Got deldir 2.0-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (278.91 kB)
#> ✔ Got fastDummies 1.7.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (41.76 kB)
#> ✔ Got dotCall64 1.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (31.26 kB)
#> ✔ Got caTools 1.18.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (205.11 kB)
#> ✔ Got globals 0.18.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (158.33 kB)
#> ✔ Got lmtest 0.9-40 (x86_64-pc-linux-gnu-ubuntu-24.04) (403.49 kB)
#> ✔ Got future 1.67.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (965.33 kB)
#> ✔ Got gplots 3.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (496.91 kB)
#> ✔ Got zoo 1.8-14 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.03 MB)
#> ✔ Got ROCR 1.0-11 (x86_64-pc-linux-gnu-ubuntu-24.04) (465.58 kB)
#> ✔ Got future.apply 1.20.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (191.24 kB)
#> ✔ Got tensor 1.5.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (13.96 kB)
#> ✔ Got ica 1.0-3 (x86_64-pc-linux-gnu-ubuntu-24.04) (85.54 kB)
#> ✔ Got SeuratObject 5.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.08 MB)
#> ✔ Got RcppTOML 0.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (244.01 kB)
#> ✔ Got Seurat 5.3.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.68 MB)
#> ✔ Got fitdistrplus 1.2-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.96 MB)
#> ✔ Got goftest 1.2-3 (x86_64-pc-linux-gnu-ubuntu-24.04) (58.64 kB)
#> ✔ Got listenv 0.9.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (106.26 kB)
#> ✔ Got spam 2.11-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.75 MB)
#> ✔ Got parallelly 1.45.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (571.86 kB)
#> ✔ Got leidenbase 0.1.35 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.33 MB)
#> ✔ Got spatstat.geom 3.5-0 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.16 MB)
#> ✔ Got reticulate 1.43.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.97 MB)
#> ✔ Got spatstat.sparse 3.1-0 (x86_64-pc-linux-gnu-ubuntu-24.04) (213.31 kB)
#> ✔ Got gtools 3.9.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (361.11 kB)
#> ✔ Got RcppHNSW 0.6.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (217.19 kB)
#> ✔ Got miniUI 0.1.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (35.20 kB)
#> ✔ Got spatstat.utils 3.1-5 (x86_64-pc-linux-gnu-ubuntu-24.04) (398.60 kB)
#> ✔ Got sctransform 0.4.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (565.94 kB)
#> ✔ Got spatstat.univar 3.1-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (324.92 kB)
#> ✔ Got rprojroot 2.1.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (113.23 kB)
#> ✔ Got pbapply 1.7-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (100.53 kB)
#> ✔ Got scattermore 1.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (339.10 kB)
#> ✔ Got sp 2.2-0 (x86_64-pc-linux-gnu-ubuntu-24.04) (5.31 MB)
#> ✔ Got spatstat.random 3.4-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.21 MB)
#> ✔ Got spatstat.data 3.1-8 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.17 MB)
#> ✔ Got spatstat.explore 3.5-2 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.50 MB)
#> 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:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates 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 python3 libcurl4-openssl-dev libssl-dev make zlib1g-dev libglpk-dev libxml2-dev pandoc libpng-dev libicu-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> python3 is already the newest version (3.12.3-0ubuntu2).
#> libcurl4-openssl-dev is already the newest version (8.5.0-2ubuntu10.6).
#> libssl-dev is already the newest version (3.0.13-0ubuntu3.5).
#> 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-1.3ubuntu3.5).
#> pandoc is already the newest version (3.1.3+ds-2).
#> libpng-dev is already the newest version (1.6.43-5build1).
#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> 0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
#> ✔ Installed caTools 1.18.3  (65ms)
#> ✔ Installed deldir 2.0-4  (110ms)
#> ✔ Installed dotCall64 1.2  (132ms)
#> ✔ Installed fastDummies 1.7.5  (166ms)
#> ✔ Installed fitdistrplus 1.2-4  (72ms)
#> ✔ Installed future 1.67.0  (74ms)
#> ✔ Installed future.apply 1.20.0  (74ms)
#> ✔ Installed globals 0.18.0  (105ms)
#> ✔ Installed goftest 1.2-3  (72ms)
#> ✔ Installed gplots 3.2.0  (75ms)
#> ✔ Installed gtools 3.9.5  (76ms)
#> ✔ Installed here 1.0.2  (76ms)
#> ✔ Installed ica 1.0-3  (69ms)
#> ✔ Installed leidenbase 0.1.35  (100ms)
#> ✔ Installed listenv 0.9.1  (71ms)
#> ✔ Installed lmtest 0.9-40  (71ms)
#> ✔ Installed miniUI 0.1.2  (72ms)
#> ✔ Installed parallelly 1.45.1  (74ms)
#> ✔ Installed pbapply 1.7-4  (74ms)
#> ✔ Installed progressr 0.16.0  (107ms)
#> ✔ Installed RcppHNSW 0.6.0  (105ms)
#> ✔ Installed RcppTOML 0.2.3  (72ms)
#> ✔ Installed reticulate 1.43.0  (76ms)
#> ✔ Installed ROCR 1.0-11  (76ms)
#> ✔ Installed rprojroot 2.1.1  (76ms)
#> ✔ Installed scattermore 1.2  (142ms)
#> ✔ Installed sctransform 0.4.2  (146ms)
#> ✔ Installed Seurat 5.3.0  (80ms)
#> ✔ Installed SeuratObject 5.2.0  (82ms)
#> ✔ Installed sp 2.2-0  (94ms)
#> ✔ Installed spam 2.11-1  (94ms)
#> ✔ Installed spatstat.data 3.1-8  (81ms)
#> ✔ Installed spatstat.explore 3.5-2  (138ms)
#> ✔ Installed spatstat.geom 3.5-0  (90ms)
#> ✔ Installed spatstat.random 3.4-1  (74ms)
#> ✔ Installed spatstat.sparse 3.1-0  (71ms)
#> ✔ Installed spatstat.univar 3.1-4  (70ms)
#> ✔ Installed spatstat.utils 3.1-5  (69ms)
#> ✔ Installed tensor 1.5.1  (67ms)
#> ✔ Installed zoo 1.8-14  (98ms)
#> ✔ 1 pkg + 134 deps: kept 94, added 40, dld 38 (40.14 MB) [12.2s]
#> ℹ [2025-09-20 14:02:09] Seurat and reticulate installed successfully