PureCN.R: no such file or directory

[lbeltrame]

Note, this is probably an issue in the PureCN bioconda package rather than bcbio itself.

PureCN is invoked with

export R_LIBS_USER=/opt/bcbio/anaconda/lib/R/library && unset R_HOME && unset R_LIBS && export PATH=/opt/bcbio/anaconda/bin:"$PATH" && PureCN.R

Except there is no such command in the PATH. It looks like it's not even symlinked in the package (it's in ./library/PureCN/extdata/PureCN.R) , and lacks a shebang.

[roryk]

Thanks Luca-- huh, I'm confused how this ever worked.

[chapmanb]

Luca and Rory;
Thanks much for the heads up. It looks like the automated bioconda updates removed the script changes we had in place to install these files. This is the latest build script:

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/bioconductor-purecn/build.sh

and the steps we need to stick back in to prepare and symlink the right files into the bin path:

https://github.com/bioconda/bioconda-recipes/blob/8ad5f8a743dce362a3229eb753f7aac7149aadc2/recipes/bioconductor-purecn/build.sh

[roryk]

Thanks Brad! I'll fix the bioconda package to restore those steps.

[roryk]

Looks like purecn is on the blacklist because some of the dependencies need R 3.6 which isn't supported by bioconda yet, so we might need to work around this in bcbio for the time being.

[lbeltrame]

In addition, the script is called with the non-existent segmentation function Hclust, I guess that got removed?

No, it's part of the latest version, but not the one that can be installed through bioconda (or the one I have installed)

[roryk]

Hi Luca,

I opened a pull request for the PureCN recipe here: bioconda/bioconda-recipes#16045 where I restored the linking of the scripts. I had to unpin some of the dependencies, and don't have test data to check if it is working right, so if/when that gets merged in it would be sweet if you could test it out.

[roryk]

Sorry, it looks like we're going to be stuck on this until R3.6 is available: bioconda/bioconda-recipes#16045

[roryk]

I updated PureCN this week but we're still waiting on full R 3.6 support in bioconda.

[lbeltrame]

Is there a tracking issue for R 3.6 support in bioconda? Might be useful to keep watch of that one.

[roryk]

Thanks, there isn't AFAICT, but there is a bulk branch here: https://github.com/bioconda/bioconda-recipes/tree/bulk which is where all the recipes are getting updated and periodically gets merged back into master.

[roryk]

Sorry about the long delay, we finally were able to fix this, so we should be all good now.