Hi All

Environment: Windows 8.1, R-3.6.3

First time user of packages from Bioconductor. I was able to change the BiocManager to the correct R version (3.6.3, BiocManager 3.10) and install the packages. However,it appears the process did not install all the packages in the Bioconductor.

I was practicing some test runs in Bioinformatics and when I tried to execute the "library(Biostrings)",I got an error stating the package was not installed.

Does the command "BiocManager::install()" not automatically install all packages? Are there any branches / forks that are distinct from Bioconductor that I'm not accessing and should be accessing?

Any clarification provided will be very helpful.

Thanks

Dutta

Hi Dutta - BiocManager::install() does multiple things - here are those that I am aware of:

• it will check that the R and Bioconductor versions match
• it will install BiocVersion if not already available (for example for a new R installation)
• it will also check if CRAN and Bioconductor packages need to be updated (if there is a newer version available on the Bioconductor server)
• it will also check if packages need to be downgraded (if a too recent version is installed locally)

To install specific packages and their dependencies, you need to name them. For example:

BiocManager::install("SummarizedExperiment") ## one package
BiocManager::install(c("SummarizedExperiment", "MultiAssayExperiment")) ## several at once

Does the command "BiocManager::install()" not automatically install all packages?

No, that certainly will not install every single package in bioconductor. Why would anyone want that?

Just install what you need as you need it.