Can't install GO.db
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Entering edit mode
Chruut • 0
@b1c69721
Last seen 2.1 years ago
Switzerland

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..

GOexpress GO.db GOSemSim • 2.3k views
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Entering edit mode
shepherl 4.1k
@lshep
Last seen 4 minutes ago
United States

Have you tried installing the missing package and then trying again? It says you are missing bit so try BiocManager::install('bit')

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Entering edit mode

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.

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