Dependencies

[Matthew Smith]

Hi,

I have been using Cardinal on my institutions Linux HPC recently for more memory. It had been working fine but this morning whilst loading Cardinal I got the following error:

Error: package or namespace load failed for ‘Cardinal’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘vctrs’ 0.3.1 is being loaded, but >= 0.3.5 is required

Upon updating 'vctrs' using the command: install.packages("vctrs") I was able to load Cardinal. However now I have noticed commands such as 'summarizePixels', 'pixelApply' and 'process' are not working.

I am confident my commands are correct as they have previously worked and work locally.

I am assuming it is related to dependencies but I am a little confused.  Any help would be greatly appreciated.

Best wishes,

Matt

[Melanie Föll]

Hi Matt,

on Linux you could try installing Cardinal via bioconda, which automatically installs all dependencies: https://anaconda.org/bioconda/bioconductor-cardinal.

Maybe you can specify what you mean by these functions are not working, what is the error message? Maybe try writing Cardinal in front: Cardinal::process etc.

Best,

Melanie

[Matthew Smith]

I will try re-installing via bioconda. Thanks.

There isn't an error message but they don't perform any task. I created my own print function to call within 'process' to see where the error was (as shown below) - but nothing printed so it seems process is not getting to the stage of calling the specified function.

testFunc <- function(x){

  print(x)

}

Cardinal::process(test,  testFunc, label="success")

Best wishes,

Matt

[Matthew Smith]

I fixed this issue - it was more related to the HPC system.