Kushal K Dey

@ron-geller Thanks for contacting. Unfortunately, I have moved away from software development role to more of an epidemiologist, and currently don't have much bandwidth to work on software update issues....

@JRodrigoF ashr will soon be re-instated on CRAN, but in the meantime, since you are using the Github version of Logolas I presume, you can install ashr from Github [https://github.com/stephens999/ashr],...

Hi @BelenJM, Did you install the maptpx from Github as specified in README? devtools::install_github("TaddyLab/maptpx") If not, can you please check if that fixes the issue? This error seems to be...

Yes, aRchaic requires R version >=3.5. We did mention it in the vignette but perhaps it was not very clear...we have updated the installation information in the vignette and the...

Thanks @rsh249 for that heads up. We are actually having an issue with fixing the old version (R>=3.4) of Logolas on Bioconductor and we hope to be able to fix...

@rsh249 Can you please elaborate on the directory structure you have? Are all the folders you are calling in aRchaic_prepare have CSV files in them? Since it works when you...

yes that indeed looks like a bug in the code, thanks for pointing it out. I have updated the script. Sorry for the inconvenience caused.

Yes, that is in our long-term pipeline. We are working on having the dependencies on Bioc first. Also, since the package is in a bit of a flux, with users...

So, the latest updated version of Logolas is in Bioconductor 3.7, which needs the latest R version - R 3.5.0. It worked for me on R 3.5.0. I will try...

Thanks @benjin44 for checking it out. We are looking into how best to fix the broken old version. So, I will keep this issue open.