Hi,

I tried to install DESeq2 in an renv managed environment. I kept getting the following error:

> BiocManager::install("DESeq2")                                                                                                                                                                              
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)                                                                                                                                         
Installing package(s) 'DESeq2'                                                                                                                                                                                
Warning: dependency ‘foreign’ is not available                                                                                                                                                                
also installing the dependency ‘Hmisc’                                                                                                                                                                        

trying URL 'https://cloud.r-project.org/src/contrib/Hmisc_4.4-0.tar.gz'                                                                                                                                       
Content type 'application/x-gzip' length 744545 bytes (727 KB)                                                                                                                                                
==================================================                                                                                                                                                            
downloaded 727 KB                                                                                                                                                                                             

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz'                                                                                                                     
Content type 'application/x-gzip' length 2060061 bytes (2.0 MB)                                                                                                                                               
==================================================                                                                                                                                                            
downloaded 2.0 MB                                                                                                                                                                                             

ERROR: dependency ‘foreign’ is not available for package ‘Hmisc’
ERROR: dependency ‘Hmisc’ is not available for package ‘DESeq2’

The problem seems to be that foreign requires R>= 4.0.0 and I'm using R 3.6.2. I fixed the issue by installing foreign version 0.8-76 from source:

install.packages(<path_to_.tar.gz>, repos = NULL, type="source")

and then repeating the normal installation process. The thing is that foreign is a dependency of Hmisc and I do not know if this issue can be fixed by the DESeq2 maintainers directly via the dependencies of the DESeq2 package. I'm writing this post to point out this issue, make my solution available to the public and to ask if there is something the DESeq2 maintainers can do to fix this.

Thank you.

The current version of DESeq2 doesn’t depend on Hmisc.