Q: Cannot Install maftools into BiocManager due to RSQLite I am a relatively new R-user.  I am currently working on trying to read .maf files via the maftools package released by Bioconductor.
I am following the instructions as posted on the Bioconductor website (https://www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html#4_Installation), however, everytime I attempt to run the installation, it gets stuck on RSQLite and I am unsure why. I am running on an M1 Macbook Pro.
Does anyone have any advice on how to work around this?
Thanks!
> if (!require("BiocManager"))
+     install.packages("BiocManager")
> BiocManager::install("maftools")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

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

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23)
Installing package(s) 'maftools'
also installing the dependency 'DNAcopy'

trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/DNAcopy_1.72.0.tgz'
Content type 'application/x-gzip' length 510533 bytes (498 KB)
==================================================
downloaded 498 KB

trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64/contrib/4.2/maftools_2.14.0.tgz'
Content type 'application/x-gzip' length 11533423 bytes (11.0 MB)
==================================================
downloaded 11.0 MB


The downloaded binary packages are in
    /var/folders/29/tbf94jd50wvd083ckp1bk61h979ds4/T//Rtmpalht57/downloaded_packages
Old packages: 'RSQLite'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
        binary source needs_compilation
RSQLite 2.2.18 2.2.19              TRUE

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

trying URL 'https://cran.rstudio.com/src/contrib/RSQLite_2.2.19.tar.gz'
Content type 'application/x-gzip' length 3730412 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

* installing *source* package 'RSQLite' ...
** package 'RSQLite' 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 'RSQLite'
* removing '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RSQLite'
* restoring previous '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RSQLite'

The downloaded source packages are in
    '/private/var/folders/29/tbf94jd50wvd083ckp1bk61h979ds4/T/Rtmpalht57/downloaded_packages'
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package 'RSQLite' had non-zero exit status

I tried entering the installation command:
if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("maftools")

However, it consistently gives me an error that RSQLite had "non-zero exit status".
