I'm looking for help trying to install IRanges from BiocManager on a Mac.
Here's the install log with the error:
BiocManager::install("IRanges")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Installing package(s) 'IRanges'
also installing the dependency ‘S4Vectors’
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2:
cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘S4Vectors’ ‘IRanges’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source packages ‘S4Vectors’, ‘IRanges’
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/S4Vectors_0.34.0.tar.gz'
Content type 'application/x-gzip' length 618611 bytes (604 KB)
==================================================
downloaded 604 KB
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/IRanges_2.30.1.tar.gz'
Content type 'application/x-gzip' length 456213 bytes (445 KB)
==================================================
downloaded 445 KB
* installing *source* package ‘S4Vectors’ ...
** 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 ‘S4Vectors’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges’
The downloaded source packages are in
‘/private/var/folders/y4/qnpttkr96hdcv5b8jhnjvp9w0000gn/T/Rtmp0PjDEd/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘S4Vectors’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘IRanges’ had non-zero exit status
I don't know what to do. It previously installed smoothly on my old Mac but it doesn't on the new one ... Any idea?
