Genetonic unable to install

[fishmatt]

Hi,

I have used the package before and love it but this was on a different computer. I am struggling to install the package because of this error: Error: object ‘universal’ is not exported by 'namespace:backbone' Backbone package I have is the latest version 2.1.2

Is there a different version of this package i need to use?

Thanks!

[federicomarini]

Can you post the output of sessionInfo? It can be that there is an older version of backbone installed and that is not compatible with the newer GeneTonic. Try reinstalling the latest backbone (even if already present on that machine)?

[fishmatt]

Yes sure. Have attached session info. I have tried reinstalling backbone but no difference. Thanks for the help!

`sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.2 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached): [1] BiocManager_1.30.21 compiler_4.1.2 tools_4.1.2 rstudioapi_0.14 `

[fishmatt]

Update- I tried my mac system to see I got the same problem, which I did I uninstalled backbone and installed the previous version 2.1.0. I loaded the package and gene tonic successfully.

`R version 4.1.3 (2022-03-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.5.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages: [1] GeneTonic_1.6.4 backbone_2.1.0 Biobase_2.54.0 BiocGenerics_0.40.0 `

[federicomarini]

Well, probably the best option is to work with a more recent of R/Bioc/GeneTonic itself. This would make sure you are with the newest features, and the setup works.