Installation

r BiocManager::install("Bioconductor/BiocAddins")

Utility functions

Installing BiocManager

Bioconductor uses BiocManager to distribute packages and manage Bioconductor versions. It is important for users to make use of BiocManager instead of install.packages in order to ensure proper package versioning.

The RStudio Addin makes it easy for users to obtain and install BiocManager from CRAN.

r useBiocManager()

After installation of BiocManager, users may install a package via the install function:

r BiocManager::install("Biobase")

Developer section

Run BiocCheck

Developers can run BiocCheck quite easily with the RStudio Addin from the dropdown menu. It essentially runs:

r BiocCheck::BiocCheck()

We recommend using the following keyboard shortcut:

Ctrl / ⌘ (Mac) + shift + C

Version Bumps

BiocAddins makes it easy to bump your package’s version by running the bumpVersion function:

r bumpVersion()

Note that this will increase the Z version of the package by 1, a.k.a, the patch version.

Installing devel

Developers who wish to install the development version of Bioconductor can do so after installing BiocManager:

r BiocManager::install(version = "devel")

Developers must ensure that the correct version of R is being used. For more information, please review the BiocManager package vignette.

Session Info

``` r sessionInfo()

> R Under development (unstable) (2023-11-17 r85547)

> Platform: x86_64-pc-linux-gnu

> Running under: Ubuntu 22.04.3 LTS

>

> Matrix products: default

> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0

> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

>

> locale:

> [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8 LCMONETARY=en_US.UTF-8

> [6] LCMESSAGES=enUS.UTF-8 LCPAPER=enUS.UTF-8 LCNAME=C LCADDRESS=C LC_TELEPHONE=C

> [11] LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

>

> time zone: America/New_York

> tzcode source: system (glibc)

>

> attached base packages:

> [1] stats graphics grDevices utils datasets methods base

>

> other attached packages:

> [1] colorout_1.2-2

>

> loaded via a namespace (and not attached):

> [1] miniUI0.1.1.1 compiler4.4.0 BiocManager1.30.22 BiocBaseUtils1.5.0 promises1.2.1 Rcpp1.0.11 stringr_1.5.1

> [8] later1.3.2 yaml2.3.8 fastmap1.1.1 mime0.12 R62.5.1 BiocAddins0.99.19 knitr_1.45

> [15] htmlwidgets1.6.4 tibble3.2.1 desc1.4.3 profvis0.3.8 shiny1.8.0 pillar1.9.0 rlang_1.1.2

> [22] utf81.2.4 cachem1.0.8 stringi1.8.3 xfun0.41 httpuv1.6.13 fs1.6.3 pkgload_1.3.3

> [29] memoise2.0.1 cli3.6.2 magrittr2.0.3 digest0.6.33 rstudioapi0.15.0 xtable1.8-4 remotes_2.4.2.1

> [36] devtools2.4.5 lifecycle1.0.4 vctrs0.6.5 evaluate0.23 glue1.6.2 urlchecker1.0.1 codetools_0.2-19

> [43] sessioninfo1.2.2 pkgbuild1.4.3 fansi1.0.6 rmarkdown2.25 purrr1.0.2 pkgconfig2.0.3 tools_4.4.0

> [50] usethis2.2.2 ellipsis0.3.2 htmltools_0.5.7

```