I was unable to load DESeq2 this morning. I have tried to uninstall R and R Studio then reinstall them, but I still got the same warning when running library(DESeq2):

Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘bit’

I have tried install.packages("bit") This is what I got:

> install.packages("bit")


  There is a binary version available but the source version is later:

    binary source needs_compilation

bit 1.1-12 1.1-13              TRUE


Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes

installing the source package ‘bit’


trying URL 'https://cran.rstudio.com/src/contrib/bit_1.1-13.tar.gz'

Content type 'application/x-gzip' length 54723 bytes (53 KB)

==================================================

downloaded 53 KB


* installing *source* package ‘bit’ ...

** package ‘bit’ successfully unpacked and MD5 sums checked

** libs

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

ERROR: compilation failed for package ‘bit’

* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/bit’

Warning in install.packages :

  installation of package ‘bit’ had non-zero exit status


The downloaded source packages are in

‘/private/var/folders/x7/cl6c9fjs0mq8k2lnrw7ls6q40000gn/T/RtmpLbCPrO/downloaded_packages’

Alternatively, I've tried biocLite("bit")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).

Installing package(s) ‘bit’


  There is a binary version available but the source version is later:

    binary source needs_compilation

bit 1.1-12 1.1-13              TRUE


Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes

installing the source package ‘bit’


trying URL 'https://cran.rstudio.com/src/contrib/bit_1.1-13.tar.gz'

Content type 'application/x-gzip' length 54723 bytes (53 KB)

==================================================

downloaded 53 KB


* installing *source* package ‘bit’ ...

** package ‘bit’ successfully unpacked and MD5 sums checked

** libs

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

ERROR: compilation failed for package ‘bit’

* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/bit’


The downloaded source packages are in

‘/private/var/folders/x7/cl6c9fjs0mq8k2lnrw7ls6q40000gn/T/RtmpLbCPrO/downloaded_packages’

Old packages: 'RcppArmadillo'

Update all/some/none? [a/s/n]: 

If answering a, I will be lead to here:

There is a binary version available but the source version is later:
                   binary    source needs_compilation
RcppArmadillo 0.8.400.0.0 0.8.500.0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) 

If answering yes, I would have received the same warning:

Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘bit’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘RcppArmadillo’ had non-zero exit status

Does anyone know how to solve the problem?

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] SummarizedExperiment_1.10.1 DelayedArray_0.6.0         
 [3] BiocParallel_1.14.1         matrixStats_0.53.1         
 [5] Biobase_2.40.0              GenomicRanges_1.32.3       
 [7] GenomeInfoDb_1.16.0         IRanges_2.14.10            
 [9] S4Vectors_0.18.2            BiocGenerics_0.26.0        
[11] BiocInstaller_1.30.0        RcppArmadillo_0.8.400.0.0  
[13] ggplot2_2.2.1              

loaded via a namespace (and not attached):
 [1] splines_3.5.0          lattice_0.20-35        colorspace_1.3-2      
 [4] htmltools_0.3.6        yaml_2.1.19            base64enc_0.1-3       
 [7] XML_3.98-1.11          survival_2.42-3        rlang_0.2.0           
[10] pillar_1.2.2           DBI_1.0.0              foreign_0.8-70        
[13] RColorBrewer_1.1-2     GenomeInfoDbData_1.1.0 plyr_1.8.4            
[16] stringr_1.3.1          zlibbioc_1.26.0        munsell_0.4.3         
[19] gtable_0.2.0           htmlwidgets_1.2        latticeExtra_0.6-28   
[22] knitr_1.20             htmlTable_1.11.2       Rcpp_0.12.17          
[25] acepack_1.4.1          xtable_1.8-2           scales_0.5.0          
[28] backports_1.1.2        checkmate_1.8.5        Hmisc_4.1-1           
[31] XVector_0.20.0         gridExtra_2.3          digest_0.6.15         
[34] stringi_1.2.2          grid_3.5.0             tools_3.5.0           
[37] bitops_1.0-6           magrittr_1.5           lazyeval_0.2.1        
[40] RCurl_1.95-4.10        tibble_1.4.2           Formula_1.2-3         
[43] cluster_2.0.7-1        Matrix_1.2-14          data.table_1.11.2     
[46] rstudioapi_0.7         rpart_4.1-13           nnet_7.3-12           
[49] compiler_3.5.0        

How about at this stage:

"Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes"

Instead try: no