半小时后Bioconductor更新一直更新失败

Question

I'm working with R and need to install some packages.

> BiocManager::install( c( list, of, packages) )
    Error: Bioconductor version '3.13' requires R version '4.1'; use
    `BiocManager::install(version = '3.16')` with R version 4.2; see
    https://bioconductor.org/install                                                                                                                                                                                                                                                                  

ok, so I need to update bioconductor. No problem:

BiocManager::install(version = '3.16')

At this point I get an absolute torrent of text output to my terminal for over half an hour. It ends with this:

** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
    * DONE (ggpubr)
    The downloaded source packages are in        
        ‘/tmp/Rtmpu3HGq9/downloaded_packages’
    Error in .install_github(todo, lib = lib, lib.loc = lib.loc, repos = repos,  :
        argument "update" is missing, with no default
    In addition: Warning message: 
    package(s) not installed when version(s) same as or greater than current; use  
        `force = TRUE` to re-install: 'BiocVersion'   

So I do it again with the "force" option, but the process insists on starting all over again from scratch, so I have to wait another half-hour and get the same problem. I've done this almost a dozen times now with variations on the command and environment settings and this is eating up days of work time.

I also noticed another message in the output:

Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
     cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'

Am I being blocked by some internal network? I've also tried setting a proxy with Sys.setenv(http_proxy="[proxyAddress]:[port]")

To no avail. I'm Running out of ideas and would much appreciate any help.

Answer 1

This issue is discussed here: https://github.com/Bioconductor/BiocManager/issues/142 . Basically it will be fixed in the next release of BiocManager, which is whatever comes after 1.30.19.