until now I’ve played around with the online version of MetaboAnalyst and it works well. But since I’d like to dive a bit deeper into the data, an installation of the R program would be of great use. Unfortunately, I’m new to this language and thus even the installation seems to be problematic. I’ve installed Rtools and Rbase (4.2.0). Option 1 is using the metanr_packages. This I assume I run in RStudio and once the function is run and metanr_packages() is run as well the following message pops up:
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: http://cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22 ucrt) Installing package(s) 'SSPA' Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.2: cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.2/PACKAGES' Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.2.0/library packages: MASS, nlme  "SSPA" " packages added..." Warning message: package ‘SSPA’ is not available for Bioconductor version '3.15' A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages here
I have simply no idea what to exactly do at this point, so I tried Option 2, which is using the pacman package, which leads to the following message:
Installing package into ‘C:/Users/dymph/AppData/Local/R/win-library/4.2’ (as ‘lib’ is unspecified) trying URL 'http://cran.rstudio.com/bin/windows/contrib/4.2/pacman_0.5.1.zip' Content type 'application/zip' length 389104 bytes (379 KB) downloaded 379 KB package ‘pacman’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\dymph\AppData\Local\Temp\Rtmpqg2SpF\downloaded_packages > > library(pacman) > > pacman::p_load(c("impute", "pcaMethods", "globaltest", "GlobalAncova", "Rgraphviz", "preprocessCore", "genefilter", "SSPA", "sva", "limma", "KEGGgraph", "siggenes","BiocParallel", "MSnbase", "multtest","RBGL","edgeR","fgsea","httr","qs")) Installing package into ‘C:/Users/dymph/AppData/Local/R/win-library/4.2’ (as ‘lib’ is unspecified) Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.2: cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.2/PACKAGES'
This all seems pretty frustrating and any advice on how to get this to run would be greatly appreciated.
Thanks so much,