Entering edit mode
Hello everyone.
I hate to ask questions about installing packages, but I really don't know what to do here. GO.db can't be installed on my device. Apparently R 4.2.2 is too new.
if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
BiocManager::install("GO.db",dependencies=TRUE)
'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 4.2.2 (2022-10-31)
Installing package(s) 'GO.db'
installing the source package ‘GO.db’
trying URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GO.db_3.16.0.tar.gz'
Content type 'application/x-gzip' length 29540685 bytes (28.2 MB)
==================================================
downloaded 28.2 MB
* installing *source* package ‘GO.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘AnnotationDbi’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘bit’
Execution halted
ERROR: lazy loading failed for package ‘GO.db’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/GO.db’
The downloaded source packages are in
‘/private/var/folders/vx/ygy6jxxj4szc6s_80rbpj51c0000gn/T/RtmpsDR1tr/downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘GO.db’ had non-zero exit status
sessionInfo( )
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.5.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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
other attached packages:
[1] BiocManager_1.30.19
loaded via a namespace (and not attached):
[1] colorspace_2.0-3 scales_1.2.1 compiler_4.2.2 R6_2.5.1
[5] cli_3.4.1 tools_4.2.2 lifecycle_1.0.3 munsell_0.5.0
[9] rlang_1.0.6
Does anyone know what I can do? I'm using an M1 Apple device..
Thank you! I somehow missed that.. I needed to install XCode in order to install "bit" and some other packages additionally. After that it worked.