I am writing a report about the version incompatibility between mzR and Rcpp packages. I have tried updating mzR and upgrading my Bioconductor installation, but they did not work for me.

> devtools::install_github("ftwkoopmans/msdap", upgrade = "never")
Downloading GitHub repo ftwkoopmans/msdap@HEAD
✓  checking for file ‘/private/var/folders/l2/7hwhm6494z72nc5249h_yw2m0000gn/T/RtmpuzATY3/remotesc9d424eff8d/ftwkoopmans-msdap-c7b8ca0/DESCRIPTION’ ...
─  preparing ‘msdap’:
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘msdap_1.0.1.tar.gz’

* installing *source* package ‘msdap’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.8.3). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so, 0x0006): Library not loaded: /opt/X11/lib/libXrender.1.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so
  Reason: tried: '/opt/X11/lib/libXrender.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libXrender.1.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/jre/lib/server/libXrender.1.dylib' (no such file)
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘msdap’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/msdap’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/l2/7hwhm6494z72nc5249h_yw2m0000gn/T//RtmpuzATY3/filec9d532f662c/msdap_1.0.1.tar.gz’ had non-zero exit status


> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13   magrittr_2.0.3    usethis_2.1.5     devtools_2.4.3    pkgload_1.2.4    
 [6] R6_2.5.1          rlang_1.0.2       fastmap_1.1.0     tools_4.1.3       pkgbuild_1.3.1   
[11] sessioninfo_1.2.2 cli_3.2.0         withr_2.5.0       ellipsis_0.3.2    remotes_2.4.2    
[16] rprojroot_2.0.3   lifecycle_1.0.1   crayon_1.5.1      brio_1.1.3        processx_3.5.3   
[21] purrr_0.3.4       callr_3.7.0       fs_1.5.2          ps_1.7.0          curl_4.3.2       
[26] testthat_3.1.3    memoise_2.0.1     glue_1.6.2        cachem_1.0.6      compiler_4.1.3   
[31] desc_1.4.1        prettyunits_1.1.1

There is no incompatibility betweem mzR and Rcpp. This message

Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.8.3). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

can be ignored. The version if Rcpp used to compile the package used to matter, but not anymore.

Your error

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so, 0x0006): Library not loaded: /opt/X11/lib/libXrender.1.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so
  Reason: tried: '/opt/X11/lib/libXrender.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libXrender.1.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/jre/lib/server/libXrender.1.dylib' (no such file)
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘msdap’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/msdap’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/l2/7hwhm6494z72nc5249h_yw2m0000gn/T//RtmpuzATY3/filec9d532f662c/msdap_1.0.1.tar.gz’ had non-zero exit status

has to do with the package you try to install. Something with pdftools, apparently.