Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Library Paths not loading #3

Open
MattBixley opened this issue Aug 1, 2024 · 3 comments
Open

Library Paths not loading #3

MattBixley opened this issue Aug 1, 2024 · 3 comments
Assignees

Comments

@MattBixley
Copy link

MattBixley commented Aug 1, 2024

When selecting the R-Geo Module the incorrect library paths are loaded.

from logs - R-Geo is loaded
56) R-Geo/4.3.2-foss-2023a

from RStudio .libPaths() function

[1] "/home/shared/mattbixley/R/foss-2023a/4.3"                         
[2] "/opt/nesi/CS400_centos7_bdw/R/4.3.2-foss-2023a/lib64/R/library"   

Should look like this

[1] "/scale_wlg_persistent/filesets/home/matt.bixley/R/foss-2023a/4.3"   
[2] "/scale_wlg_persistent/filesets/opt_nesi/CS400_centos7_bdw/R-Geo/4.3.2-foss-2023a"   
[3] "/scale_wlg_persistent/filesets/opt_nesi/CS400_centos7_bdw/R/4.3.2-foss-2023a/lib64/R/library"   

This means that the main packages raster and terra are not available.

This also occurs with Bioconductor 3.17 which should show 4 libraries. App appears to be limited to 2 libraries showing. This was also seen on eRI

@MattBixley
Copy link
Author

Will work on the possible solution of R-Geo libraries being in the same pathway as the base R library.
Will do this on eri as proof of concept.

@DininduSenanayake DininduSenanayake self-assigned this Sep 7, 2024
@MattBixley
Copy link
Author

MattBixley commented Sep 18, 2024

Working Solution:

Using the R-Geo module in the test envionment, as above
`> .libPaths()

[1] "/nesi/home/mattbixley/R/foss-2023a/4.3"
[2] "/opt/nesi/CS400_centos7_bdw/R/4.3.2-foss-2023a/lib64/R/library"
`

Code to add new libraries
`>myPaths <- .libPaths()

myPaths <- c(myPaths, "/opt/nesi/CS400_centos7_bdw/R-Geo/4.3.2-foss-2023a")
myPaths <- c(myPaths[1], myPaths[3], myPaths[2]) # switch them
.libPaths(myPaths)
check>.libPaths()
[1] "/nesi/home/mattbixley/R/foss-2023a/4.3"
[2] "/opt/nesi/CS400_centos7_bdw/R-Geo/4.3.2-foss-2023a"
[3] "/opt/nesi/CS400_centos7_bdw/R/4.3.2-foss-2023a/lib64/R/library"
`

This can be made permanent by placing in the .Rprofile, but should then also include the Bioconductor pathway. Bioconductor actually uses the following libraries
User, System, Bioconductor AND R-Geo

Will add to current user documentation as workarounds.

@MattBixley
Copy link
Author

Also note that selected versions will require different paths eg 4.1, 4.2, 4.3 etc

Bioconductor 3.17 Paths
> .libPaths() [1] "/scale_wlg_persistent/filesets/home/matt.bixley/R/gimkl-2022a/4.3" [2] "/scale_wlg_persistent/filesets/opt_nesi/CS400_centos7_bdw/R-bundle-Bioconductor/3.17-gimkl-2022a-R-4.3.1" [3] "/scale_wlg_persistent/filesets/opt_nesi/CS400_centos7_bdw/R-Geo/4.3.1-gimkl-2022a" [4] "/scale_wlg_persistent/filesets/opt_nesi/CS400_centos7_bdw/R/4.3.1-gimkl-2022a/lib64/R/library"

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants