Help installing clusterProfiler
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Entering edit mode
masaver • 0
@masaver-23601
Last seen 10 days ago
Germany

Hi everyone,

I'm running Rstudio/R on a Windows 10 machine and I'm trying to install the clusterProfiler package by running this: BiocManager::install("clusterProfiler")

However, I keep getting the following error:

* installing * source * package 'DO.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Bug: Package 'S4Vectors' was created for x86_64-pc-linux-gnu
Additionally: Warning messages:
1: Package 'AnnotationDbi' was created under R version 3.6.1
2: Package 'BiocGenerics' was created under R version 3.6.3
3: Package 'Biobase' was created under R version 3.6.1
4: Package 'IRanges' was created under R version 3.6.2
5: Package 'S4Vectors' was created under R version 3.6.3
Execution stopped
ERROR: lazy loading failed for package 'DO.db'
* removing 'C: /SOME/PATH/R/x86_64-pc-linux-gnu-library/3.6/DO.db'
* installing * source * package 'GO.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Bug: Package 'S4Vectors' was created for x86_64-pc-linux-gnu
Additionally: Warning messages:
1: Package 'AnnotationDbi' was created under R version 3.6.1
2: Package 'BiocGenerics' was created under R version 3.6.3
3: Package 'Biobase' was created under R version 3.6.1
4: Package 'IRanges' was created under R version 3.6.2
5: Package 'S4Vectors' was created under R version 3.6.3
Execution stopped
ERROR: lazy loading failed for package 'GO.db'
* removing 'C: /SOME/PATH/R/x86_64-pc-linux-gnu-library/3.6/GO.db

If it helps, here is my sessionInfo():

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

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

other attached packages:
[1] Biobase_2.46.0      BiocGenerics_0.32.0

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.0      tools_3.6.0

Can anybody tell me what the problem is here ? Thanks in advance for the help !

Best,

-Mathias

clusterProfiler DO.db GO.db lazy load fail • 290 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 18 minutes ago
United States

This doesn't look right:

C: /SOME/PATH/R/x86_64-pc-linux-gnu-library/3.6/DO.db

That looks like some random combination of a Windows file path, a Linux file path and some fake directory code used as an example (the /SOME/PATH part). Usually that's not a thing. So you should check to ensure that that is actually a library path, and if not (shouldn't be), fix it.

Or better yet, just burn that whole install down and install R-4.0.0 and the current 3.11 Bioconductor release. With reasonable library dir like

> .libPaths()
[1] "C:/Users/jmacdon/AppData/Roaming/R/win-library/4.0"
[2] "C:/Program Files/R/R-4.0.0/library"    
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0
Entering edit mode

Thanks James. I did something similar to what you suggested. I re-installed my R libraries in a different folder, and used that one to install clusterProfiler, and ti worked ! So now my .libPaths look like this:

>.libPaths()
"C:/Users/saver.mathias/Desktop/R/3.6"
"C:/Program Files/R/R-3.6.0/library"
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