Cannot install GO.db and org.Hs.eg.db
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Gabriel • 0
@d3c85dbb
Last seen 6 hours ago
United Kingdom

I can install other packages in Bioconductor, but not GO.db and org.Hs.eg.db. It always fails at lazy loading but it doesn't state why. I have tried uninstalling and reinstalling R, Rstudio, Bioconductor, and restarting my computer, R session.

> BiocManager::install('org.Hs.eg.db')

trying URL 'https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Hs.eg.db_3.20.0.tar.gz'
Content type 'application/x-gzip' length 98233708 bytes (93.7 MB)
downloaded 93.7 MB

* installing *source* package 'org.Hs.eg.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
package 'IRanges' was built under R version 4.4.2 
ERROR: lazy loading failed for package 'org.Hs.eg.db'
* removing 'C:/Users/gabri/R/win-library/4.4/org.Hs.eg.db'


> session_info()

R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default


locale:
[1] LC_COLLATE=English_Singapore.utf8  LC_CTYPE=English_Singapore.utf8   
[3] LC_MONETARY=English_Singapore.utf8 LC_NUMERIC=C                      
[5] LC_TIME=English_Singapore.utf8    

time zone: Asia/Singapore
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.25 compiler_4.4.1      tools_4.4.1
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The downloaded source packages are in 'C:Users\gabri\AppData\Local\Temp\RtmpailNer\downloaded_packages' Installation paths not writeable, unable to update packages path: C:/Program Files (x86)/R/R-4.4.1/library packages: boot, cluster, foreign, MASS, Matrix, nlme, survival Warning message: In install.packages(...) : installation of package 'org.Hs.eg.db' had non-zero exit status

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@james-w-macdonald-5106
Last seen 1 hour ago
United States

You might try tracing the namespace loading.

Sys.setenv("_R_TRACE_LOADNAMESPACE_"="2")
install("org.Hs.eg.db")

And see if there is an obvious problem with a required package loading.

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