Unable to install on MacOSX Monterey

[Bunmi0616]

HI,

I have not been able to install cytofkit2. I have tried R versions 4.1.0 and 4.1.1 and the final message says:
Downloading GitHub repo JinmiaoChenLab/cytofkit2@HEAD
Error: Failed to install 'cytofkit2' from GitHub:
Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

IT has listed issues with repos, rrcov

BiocManager::install("destiny")
'getOption("repos")' replaces Bioconductor standard repositories,
see '?repositories' for details

replacement repositories:
CRAN: https://cran.case.edu

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0
(2021-05-18)
Installing package(s) 'destiny'
Old packages: 'rrcov'
Update all/some/none? [a/s/n]:
a

There is a binary version available but the source version
is later:
binary source needs_compilation
rrcov 1.6-1 1.6-2 TRUE

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

trying URL 'https://cran.case.edu/src/contrib/rrcov_1.6-2.tar.gz'
Content type 'application/x-gzip' length 1794698 bytes (1.7 MB)

downloaded 1.7 MB

• installing source package ‘rrcov’ ...
  ** package ‘rrcov’ 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 ‘rrcov’
• removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rrcov’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rrcov’

The downloaded source packages are in
‘/private/var/folders/sh/9yjvg83100x4w36m2hnvqtnh0000gn/T/RtmpOA2Ley/downloaded_packages’
Warning messages:
1: In .inet_warning(msg) :
package ‘destiny’ is not available for Bioconductor version '3.13'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘rrcov’ had non-zero exit status

any thoughts?

Thanks,
Bunmi

[raman91]

Hi @Bunmi0616 , you may have to manually install destiny (3.6.0) and all its dependencies since the destiny package is no longer supported by bioconductor. Please install using the following commands :

install.packages("remotes")
remotes::install_github("theislab/destiny")

Thank you