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kdkorthauer / dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
MIT License
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One suggestion regarding the prerequisite packages #4

Closed xinkai-zhou closed 6 years ago

xinkai-zhou commented 6 years ago

Hi Keegan, the paper introduced a very interesting idea and I'm curious to try it out.

Just one simple suggestion regarding the prerequisite packages: since I'm new to WGBS methylation data, I don't have all the common annotation packages installed, and this prevents the dmrseq package from being properly installed. For example, I would get an error message like Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'TxDb.Rnorvegicus.UCSC.rn5.refGene'.

I tried to install the required package and install dmrseq again, but then received a similar error message asking me to install another annotation package.

Since this process seems rather inefficient, would it be possible to somehow give a list of prerequisite packages for the user to install before installing dmrseq?

Here are the annotation packages that I have installed manually so far:

biocLite("TxDb.Dmelanogaster.UCSC.dm3.ensGene")
biocLite("TxDb.Dmelanogaster.UCSC.dm6.ensGene")
biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene")
biocLite("TxDb.Mmusculus.UCSC.mm10.knownGene")
biocLite("TxDb.Mmusculus.UCSC.mm9.knownGene")
biocLite("TxDb.Rnorvegicus.UCSC.rn4.ensGene")
xinkai-zhou commented 6 years ago

seems related: https://github.com/hadley/devtools/issues/700

kdkorthauer commented 6 years ago

Hi @xinkai01,

Apologies for the late reply; it seems my email alerts were temporarily shut off.

I have revised the package to have fewer annotation dependencies, and these dependencies are all listed in the DESCRIPTION file. In addition, I have biocViews: in my DESCRIPTION file, so install_github should know to go and search Bioconductor for any missing dependencies. Please let me know if you continue to have trouble with installation and I'll troubleshoot further.

Best, Keegan