When i Am trying to use limma and minfi i get the following error:

sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Biostrings_2.50.2           XVector_0.22.0              SummarizedExperiment_1.12.0
 [4] DelayedArray_0.8.0          BiocParallel_1.16.6         matrixStats_0.54.0         
 [7] Biobase_2.42.0              locfit_1.5-9.1              iterators_1.0.10           
[10] foreach_1.4.4               GenomicRanges_1.34.0        GenomeInfoDb_1.18.2        
[13] BiocManager_1.30.4          IRanges_2.16.0              S4Vectors_0.20.1           
[16] BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'XML' is missing or broken
2: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'RCurl' is missing or broken

 RStudio.version()
Error in RStudio.version() : could not find function "RStudio.version"

library(minfi)
Loading required package: bumphunter
Error: package or namespace load failed for ‘bumphunter’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘rtracklayer’
Error: package ‘bumphunter’ could not be loaded

It is like nothing is working in R, and i do not know why??

Maybe you can try install 'bumphunter' package first, then rety minfi. Then you may get more specific error.

Sometimes this error happens when some of your package failed to be installed, which might be trigger by missing library, env setting.e.g.