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I've been trying to install DESeq2 via bioconductor. however when i try do download anything via bioconductor I get an error:

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install:
'DESeq2'Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.2/library
packages:
boot, class, codetools, foreign, MASS, Matrix, nlme, spatial, survival
Old packages: 'DelayedArray', 'utf8', 'xfun'
Update all/some/none? \[a/s/n\]:

using 'force = TRUE' doesn't get me anywhere. I think i need to update the 'DelayedArray', 'utf8', 'xfun' packages. Since I receive:

              binary  source   needs_compilation
DelayedArray  0.23.2  0.24.0   TRUE
utf8          1.2.2   1.2.3    TRUE
xfun          0.36    0.37     TRUE

However, when I then say i want to update all, by typing 'a'. I get the following message:

Warning: installation of package ‘utf8’ had non-zero exit status\*

same thing for xfun.

Does anyone know how to fix this problem?

I do have to add that when then it goes to update the xfun and utf8 package, i do click 'no' when the pop up shows that asks whether i want to install packages from sources the packages which need compilation. i've also tried clicking yes to this question. the error that it then gives when i say no is:

package ‘utf8’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘utf8’Warning: problem copying C:\Users\famvi\AppData\Local\R\win-library\4.2\00LOCK\utf8\libs\x64\utf8.dll to C:\Users\famvi\AppData\Local\R\win-library\4.2\utf8\libs\x64\utf8.dll: Permission deniedWarning: restored ‘utf8’package ‘xfun’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘xfun’Warning: problem copying C:\Users\famvi\AppData\Local\R\win-library\4.2\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\famvi\AppData\Local\R\win-library\4.2\xfun\libs\x64\xfun.dll: Permission deniedWarning: restored ‘xfun’
The downloaded binary packages are in
    C:\Users\famvi\AppData\Local\Temp\RtmpG86c1M\downloaded_packages
MrFlick
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maritos
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  • Could you check this and try the solutions proposed ? : https://stackoverflow.com/questions/42807247/installing-package-cannot-open-file-permission-denied – Basti Feb 03 '23 at 11:01
  • additional info: I just tried reinstalling xfun and now i get the following message: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘xfun’ – maritos Feb 03 '23 at 11:07

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