BiocManager

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Problem with BiocManager connection to Internet under Windows: problem solved

5

For all, whom it may concern - I found the solution what to do, if your R is writing something like: ``` > BiocManager::install(version="3.14") Error: Bioconductor version cannot be validated;...

lokapal

Proof-of-concept for the proposal in Issue #190 .

HenrikBengtsson

I'm creating this issue to have a place to discuss [CRANhaven](https://www.cranhaven.org/) that I presented to the Bioconductor Technical Advisor Board (TAB) on 2024-03-07. # Background The gist is that CRANhaven...

HenrikBengtsson

Version map cannot be validated - not mapping to new bioconductor website

9

Submitting the basic installation command for Bioconductor: `if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.18")` in R (version 4.3.0) returns the following error: `Error: Bioconductor version cannot be validated;...

aehrenberg

Provide exported function to determine BioC version for R version

8

I know of at least two packages that have had to implement this themselves, so it would be useful for BiocManager to provide an exported interface.

hadley

Reported via email ```{r} .libPaths(tempfile()) BiocManager::install('phangorn') # installs phangorn ``` So far so good, but ```{r} > BiocManager::install('phangorn', dependencies = TRUE) Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)...

mtmorgan

Installation problem in Bioconductor packages in R. BiocManager::intall() not working.

3

``` > BiocManager::install("ChIPseeker") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) Warning message: package(s) not installed when...

bakshiasif

BiocManager::valid() does not check for 'missing' dependencies

1

Suppose Package A depends on B depends on C. The user installs A (hence B & C) then removes B. BiocManager::valid() does not detect this situation, because A and C...

mtmorgan

WISH: Clarify "BiocManager.check_repositories" message and silence it in more cases?

1

# Issue It is not always clear why the following message appear: ```r 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org ``` For instance, it...

HenrikBengtsson

Some packages cannot be installed with BiocManager 3.22 despite the website stating it

11

When I tried to install PCAtools and CRISPRball (and a little earlier DESeq2) I get the message `Warning message: package ‘XXX’ is not available for Bioconductor version '3.22'`. These packages...

gernophil