Hi everyone, I just installed the new R (4.4.1) and now I get the error message "paths not writable" when I try to install any Bioconductor package. See below

    BiocManager::install("LEA")
    getOption("repos") replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager") for details.
    Replacement repositories:
        CRAN: http://cran.rstudio.com/
    Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14 ucrt)
    Installing package(s) BiocVersion, LEA
    trying URL https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/BiocVersion_3.19.1.zip
    Content type application/zip length 8382 bytes
    downloaded 8382 bytes

    trying URL https://bioconductor.org/packages/3.19/bioc/bin/windows/contrib/4.4/LEA_3.16.0.zip
    Content type application/zip length 978685 bytes (955 KB)
    downloaded 955 KB

    package BiocVersion successfully unpacked and MD5 sums checked
    package LEA successfully unpacked and MD5 sums checked

    The downloaded binary packages are in
        C:\Users\scatag\AppData\Local\Temp\RtmpsbWNRe\downloaded_packages
    Installation paths not writeable, unable to update packages
      path: C:/Program Files/R/R-4.4.1/library
      packages:
        boot, foreign, MASS, nlme, survival

However, when I try to load the library with library(LEA) it loads it without problem or error message (I haven't tested if the function of this package work though).

I have the same problem with another Bioconductor package SeqArray. I also tried to install the package in another folder with BiocManager::install("LEA", lib.loc = "C:/path") but it doesn't work. It says it cant' re-write the package:

The downloaded binary packages are in
    C:\Users\scatag\AppData\Local\Temp\RtmpsbWNRe\downloaded_packages
Warning message:
In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\scatag\AppData\Local\R\win-library\4.4\00LOCK\LEA\libs\x64\LEA.dll to C:\Users\scatag\AppData\Local\R\win-library\4.4\LEA\libs\x64\LEA.dll: Permission denied

What is happening? Why I have this problem with all Bioconductor packages?? I can install CRAN packages without any problem...

Would really appreciate some help! Thanks! Best, Gabry

sessionInfo( )
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_Australia.utf8  LC_CTYPE=English_Australia.utf8    LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C                       LC_TIME=English_Australia.utf8    

time zone: Australia/Brisbane
tzcode source: internal

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

other attached packages:
[1] devtools_2.4.5 usethis_3.0.0 

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5         cli_3.6.3           rlang_1.1.4         purrr_1.0.2         pkgload_1.4.0       promises_1.3.0      shiny_1.9.1         xtable_1.8-4        glue_1.8.0         
[10] htmltools_0.5.8.1   httpuv_1.6.15       pkgbuild_1.4.4      ellipsis_0.3.2      fastmap_1.2.0       lifecycle_1.0.4     memoise_2.0.1       BiocManager_1.30.25 compiler_4.4.1     
[19] miniUI_0.1.1.1      fs_1.6.4            sessioninfo_1.2.2   LEA_3.16.0          htmlwidgets_1.6.4   Rcpp_1.0.13         rstudioapi_0.16.0   urlchecker_1.0.1    later_1.3.2        
[28] digest_0.6.37       R6_2.5.1            parallel_4.4.1      magrittr_2.0.3      tools_4.4.1         mime_0.12           profvis_0.4.0       cachem_1.1.0        remotes_2.5.0

You have installed the packages you wanted:

package BiocVersion successfully unpacked and MD5 sums checked
    package LEA successfully unpacked and MD5 sums checked

But there are some packages (the recommended packages) that are installed in a different location that you don't have write privileges, and that are not updated:

Installation paths not writeable, unable to update packages
      path: C:/Program Files/R/R-4.4.1/library
      packages:
        boot, foreign, MASS, nlme, survival

As a general rule that's not a problem, but if you want to update the recommended packages you have to run R as an administrator and then use BiocManager::install. But I would caution against doing anything else with R as administrator. After installing the recommended packages, close R and restart with your regular privileges.