giupardeb/epimethex

EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between methylation and gene expression data.

epimethex's Issues

Installation failed

Hi I'm trying to install this, running: R CMD build EpiMethEx. I have R version 4.1, running on mac (x86_64-apple-darwin17.0 ) and BiocManager v 1.30.16. FYI It failed multiple times and requires the following to be installed (and possibly other packages that I already had installed):

BiocManager::install("MultiAssayExperiment")
install.packages("miscTools")
install.packages("RcmdrMisc")
install.packages("psych")

Would recommend adding required installs to your package so users don't have to install them i.e. at the top of the script:

packages <- c("miscTools", "RcmdrMisc", "psych")
install.packages(setdiff(packages, rownames(installed.packages())))

Anyway following installing the required packages I got the error:

* checking for file ‘EpiMethEx/DESCRIPTION’ ... OK
* preparing ‘EpiMethEx’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epimethex_analysis.Rmd’ using rmarkdown
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in `[<-.factor`(`*tmp*`, ri, value = -1.859692469761) :
  invalid factor level, NA generated
Warning in `[<-.factor`(`*tmp*`, ri, value = -0.396742484881) :
  invalid factor level, NA generated
Warning in `[<-.factor`(`*tmp*`, ri, value = 0.225157530238) :
  invalid factor level, NA generated
Quitting from lines 44-80 (epimethex_analysis.Rmd)
Error: processing vignette 'epimethex_analysis.Rmd' failed with diagnostics:
task 1 failed - "undefined columns selected"
--- failed re-building ‘epimethex_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘epimethex_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted

Do you have a pre-built version I can install? Otherwise please let me know if you update the code with the error resolved or if this is no longer under development, cheers!