Hello, I have encountered an error when installing DEP on my MacBook. I have looked through the forum and tried to re-install "bitops" but no solution. I'm not an expert user of R either. Details on the error and sessionInfo() are below. Any advice/suggestion are greatly appreciated :)

if(!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("DEP")
a
Yes

> install.packages("BiocManager")
Installing package into ‘/Users/00070611/Library/R/4.0/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/BiocManager_1.30.12.tgz'
Content type 'application/x-gzip' length 318571 bytes (311 KB)
==================================================
downloaded 311 KB


The downloaded binary packages are in
    /var/folders/hn/039m87_s3yjbqnbxbw043rhw2m0d6j/T//RtmpQpnvAS/downloaded_packages
> BiocManager::install("DEP")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.5 (2021-03-31)
Installing package(s) 'DEP'
trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/macosx/contrib/4.0/DEP_1.12.0.tgz'
Content type 'application/x-gzip' length 3114328 bytes (3.0 MB)
==================================================
downloaded 3.0 MB


The downloaded binary packages are in
    /var/folders/hn/039m87_s3yjbqnbxbw043rhw2m0d6j/T//RtmpQpnvAS/downloaded_packages
Installation paths not writeable, unable to update packages
  path: /Library/Frameworks/R.framework/Versions/4.0/Resources/library
  packages:
    cluster, mgcv
Old packages: 'bitops'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
       binary source needs_compilation
bitops  1.0-6  1.0-7              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘bitops’

trying URL 'https://cran.rstudio.com/src/contrib/bitops_1.0-7.tar.gz'
Content type 'application/x-gzip' length 10809 bytes (10 KB)
==================================================
downloaded 10 KB

* installing *source* package ‘bitops’ ...
** package ‘bitops’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘bitops’
* removing ‘/Users/00070611/Library/R/4.0/library/bitops’
* restoring previous ‘/Users/00070611/Library/R/4.0/library/bitops’

The downloaded source packages are in
‘/private/var/folders/hn/039m87_s3yjbqnbxbw043rhw2m0d6j/T/RtmpQpnvAS/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘bitops’ had non-zero exit status


> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.12 compiler_4.0.5      tools_4.0.5         yaml_2.2.1

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

It seems you may have updated your OS version and this can be solved by reinstalling the Xcode toolkit. You will have to open Terminal and run :

xcode-select --install

If it doesn't work after this you could try running this code before : xcode-select --reset