Hi

I am on Debian 12 (stable) and just installed R-4.3.2 and Bioconductor v3.18 successfully and then installed alot of my favourite Bioconductor packages.

However with ChAMP, the DNA methylation package, it said it couldn't be found. Nevertheless "ChAMPdata", which is an accompanying package, could be found. So that's puzzling.

I visited the links on this packages's Bioconductor page, and for v3.18 all seemed to be fairly OK, so I guess this problem had not been detected. So what was up? I changed my repositories but no resolution to problem.

Thanks.

Try a manual install of the package. Go to ChAMP's Bioconductor webpage.

Do a "git clone" of the bioconductor git repo and run devtools::install() inside ChAMP's root repo folder.

Then it will say that "DMRcate" was not available for Bioc V3.18.

Clearly it's a dependency of ChAMP. Do the same git clone and devtools::install() for DMRcate.

Then it will say that "DSS" is not available.

Clearly it's a dependency of DMRcate. Do the same git clone and devtools::install() for DSS. This time, it will install properly. Go back to DMRcate, you'll find it will install properly this time. And so onto to ChAMP, again with all its dependencies sorted, it will install. So that's your problem solved.

Extensive testing has not been done, but it does install ChAMP ... either properly or improperly.