BiocManager

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Error: argument "update" is missing, with no default

13

I'm getting the following error in my Github Actions workflows when using Bioconductor 3.16 e.g. [here](https://github.com/grimbough/biocActionsExamples/actions/runs/3329539630/jobs/5506890568#step:3:336) ``` Error in .install_github(todo, lib = lib, lib.loc = lib.loc, repos = repos, :...

grimbough

Error: loading failed for install BiocManager packages

10

These days I installed the BiocManager in R version 4.2.0, but I am failed for it I tried lots of method, but got the same error I am appreciate it...

zhoujiaqi704

When reading your helpfiles I noticed that you had used a slightly incorrect syntax for your links. So I have fixed them with this PR. cheers Tom

remlapmot

BiocManager::repositories() Reports Missing `books` for 3.15/3.16

9

When using Bioconductor 3.15 or 3.16, the command `BiocManager::repositories()` reports that the `book` repository is available, but the repository does not appear to exist on bioconductor.org.

jonyoder

Default to Bioc devel for R-devel

9

Currently BiocManager would not work with the devel version of R. While the current Bioc works with 4.2 for release and devel, shouldn't BiocManager default to the current Bioc devel...

lshep

return value of `BiocManager::install()`

4

Having `BiocManager::install()` return the "pkgs" argument is not especially useful. Could it instead return success/error codes? Otherwise, how can you tell in a script whether the requested packages were installed...

lwaldron

BiocManager::install() not installing package if available version is lower than current

11

I have **SQLDataFrame** 1.9.1: ``` packageVersion("SQLDataFrame") # [1] ‘1.9.1’ ``` and the version of **SQLDataFrame** currently available in BioC 3.15 is 1.9.0: ``` library(BiocManager) available.packages(repos=BiocManager::repositories())["SQLDataFrame", "Version"] # [1] "1.9.0" ```...

hpages

Suppress the prompt from the remotes package

1

When installing a GitHub package, the `remotes` package will prompt the user whether to update the package dependencies, which is duplicated as `BiocManager` will also ask the user the same...

Jiefei-Wang

checking for already installed does not respect lib argument

4

So I'm testing locally and I have an environment variable set up to specify a different installation path: ``` > .libPaths() [1] "/home/shepherd/R-Libraries/4.2-Bioc3.15" [2] "/home/shepherd/R-Installs/bin/R-devel/library" ``` I need biocViews to...

lshep

These sections of the `config.yaml` need to be added so that we can have dates for both `RSPM` and `MRAN` options. ```r config

LiNk-NY