Hi guys, I'am trying to run a DE analysis for my PhD thesis. Trying to install 'DeSeq2' package in Rstudio server (Ubuntu 18.04.4 LTS). After update version 3.6 to 4.0, I am having several error messages when installing new packages. The messages is always something like "Package ‘#####’ was installed before R 4.0.0: please re-install it". I tried to add a new path to the new version 4.0, as shown in the output and sessionInfo(). When I tried to install Biocmanager again, I have the same massage "...please re-install it", after chosse "a" to update all packages.

Can someone help me?

'

> .libPaths()
    [1] "/home/XXXX/R/x86_64-pc-linux-gnu-library/4.0"
    [2] "/home/XXXX/R/x86_64-pc-linux-gnu-library/3.6"
    [3] "/usr/local/lib/R/site-library"                   
    [4] "/usr/lib/R/site-library"                         
    [5] "/usr/lib/R/library"                              

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.10

loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3    grid_4.0.3

> if (!requireNamespace("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install(version = "3.12")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installation path not writeable, unable to update packages: foreign, spatial
Old packages: 'AnnotationDbi', 'BiocFileCache', 'biomaRt', 'Biostrings', 'GenomicFeatures',
  'lubridate', 'recipes', 'Rsamtools', 'Rsubread', 'waldo'
Update all/some/none? [a/s/n]:

You shouldn't point to the old 3.6 library dir, because, well, it's from an old version of R. Do you have something like a .Renviron that is setting all those library paths? By default you should only have the site-wide library (and why are there three of them?) and your personal library path. So that's the first thing to fix. Without knowing your setup it's difficult to say much more than that.

Then my usual go-to move is to do something like

library(BiocManager)
z <- dir("/home/XXXX/R/x86_64-pc-linux-gnu-library/3.6")
install(z, ask = FALSE)

Which will then replicate what you had for R-3.6 in your new R-4.0 library dir.