Hello, unfortunately, I cannot install packages into my library under

C:R/R-4.2.2/library.

If I reply no to the question ' Do you want to install from sources the package which needs compilation?" then it does temporarily download (ex. C:\Users\MY_UNDER_NAME\AppData\Local\Temp\Rtmpc7SkRr\downloaded_packages).

I suspect this may be even an R issue, instead of a Bioconductor as well, so apologies in advance if this is the case

if (!requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install(version = "3.16")

Below is the error message in Rstudio

* installing *source* package 'DelayedArray' ...
** using staged installation
** libs
gcc  -I"C:/R/R-42~1.2/include" -DNDEBUG  -I'C:/R/R-4.2.2/library/S4Vectors/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_DelayedArray.c -o R_init_DelayedArray.o
sh: line 1: gcc: command not found
make: *** [C:/R/R-42~1.2/etc/x64/Makeconf:253: R_init_DelayedArray.o] Error 127
ERROR: compilation failed for package 'DelayedArray'
* removing 'C:/R/R-4.2.2/library/DelayedArray'
* restoring previous 'C:/R/R-4.2.2/library/DelayedArray'
* installing *source* package 'GenomicRanges' ...
** using staged installation
** libs
gcc  -I"C:/R/R-42~1.2/include" -DNDEBUG  -I'C:/R/R-4.2.2/library/S4Vectors/include' -I'C:/R/R-4.2.2/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
sh: line 1: gcc: command not found
make: *** [C:/R/R-42~1.2/etc/x64/Makeconf:253: IRanges_stubs.o] Error 127
ERROR: compilation failed for package 'GenomicRanges'
* removing 'C:/R/R-4.2.2/library/GenomicRanges'
* restoring previous 'C:/R/R-4.2.2/library/GenomicRanges'

The downloaded source packages are in
    ‘C:\Users\10496\AppData\Local\Temp\Rtmpc7SkRr\downloaded_packages’
Error in BiocManager::install(version = "3.16") : 
  non-numeric argument to binary operator
In addition: Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘DelayedArray’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘GenomicRanges’ had non-zero exit status

If you are getting this error

sh: line 1: gcc: command not found

It means your installation of RTools is somehow broken. Or maybe RStudio is dumb and doesn't pick up the PATH variable correctly? I don't know, as I don't use RStudio. I have no problem installing the source version of DelayedArray on my Windows box using Emacs/ESS and RTools 4.2

* installing *source* package 'DelayedArray' ...
** using staged installation
** libs
gcc  -I"c:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG  -I'C:/Users/jmacdon/AppData/Local/R/win-library/4.2/S4Vectors/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_DelayedArray.c -o R_init_DelayedArray.o
gcc  -I"c:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG  -I'C:/Users/jmacdon/AppData/Local/R/win-library/4.2/S4Vectors/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"c:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG  -I'C:/Users/jmacdon/AppData/Local/R/win-library/4.2/S4Vectors/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c abind.c -o abind.o
gcc  -I"c:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG  -I'C:/Users/jmacdon/AppData/Local/R/win-library/4.2/S4Vectors/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c array_selection.c -o array_selection.o
gcc  -I"c:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG  -I'C:/Users/jmacdon/AppData/Local/R/win-library/4.2/S4Vectors/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c compress_atomic_vector.c -o compress_atomic_vector.o
compress_atomic_vector.c: In function 'C_encode_atomic_vector':
compress_atomic_vector.c:66:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
   66 |  return ans;
      |         ^~~
compress_atomic_vector.c: In function 'C_decode_atomic_vector':
compress_atomic_vector.c:73:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
   73 |  return ans;
      |         ^~~
compress_atomic_vector.c: In function 'C_compress_atomic_vector':
compress_atomic_vector.c:85:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
   85 |  return ans;
      |         ^~~
compress_atomic_vector.c: In function 'C_decompress_atomic_vector':
compress_atomic_vector.c:92:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
   92 |  return ans;
      |         ^~~
gcc  -I"c:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG  -I'C:/Users/jmacdon/AppData/Local/R/win-library/4.2/S4Vectors/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -shared -s -static-libgcc -o DelayedArray.dll tmp.def R_init_DelayedArray.o S4Vectors_stubs.o abind.o array_selection.o compress_atomic_vector.o sparseMatrix_utils.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -Lc:/PROGRA~1/R/R-42~1.2/bin/x64 -lR
installing to C:/Users/jmacdon/AppData/Local/R/win-library/4.2/00LOCK-DelayedArray/00new/DelayedArray/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'rowsum' in package 'DelayedArray'
Creating a new generic function for 'apply' in package 'DelayedArray'
Creating a new generic function for 'sweep' in package 'DelayedArray'
Creating a new generic function for 'scale' in package 'DelayedArray'
Creating a generic function for 'dnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'pnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'pbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dpois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'ppois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qpois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dlogis' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'plogis' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qlogis' from package 'stats' in package 'DelayedArray'
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (DelayedArray)

> sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

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

other attached packages:
[1] BiocManager_1.30.19

loaded via a namespace (and not attached):
[1] compiler_4.2.2 tools_4.2.2

Maybe run R using the GUI or on the command line or try re-installing RTools.