Tirgit
commented
5 years ago Hi kieroneil,
Could you try two things?
- Not sure which R version you are using, but make sure you use R>3.5.0 (although perhaps you should upgrade to 3.6.0)
- Can you try install pcaMethods from Bioconductor first? Here is how you would do it: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("pcaMethods")
see more info here: https://www.bioconductor.org/packages/release/bioc/html/pcaMethods.html
Please let me know if these worked for you! T
I was going to walk through the complete tutorial and ran into issues immediately.
> library(missCompare)Error: package or namespace load failed for ‘missCompare’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘pcaMethods’ In addition: Warning message: package ‘missCompare’ was built under R version 3.5.3> cleaned <- missCompare::clean(clindata_miss, var_removal_threshold = 0.5, ind_removal_threshold = 0.8, missingness_coding = -9)Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘pcaMethods’> install.packages("pcaMethods")Installing package into ‘C:/Users/koneil/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘pcaMethods’ is not available (for R version 3.5.1)> devtools::install_github("hredestig/pcaMethods")Downloading GitHub repo hredestig/pcaMethods@master Error: Could not find tools necessary to compile a package In addition: Warning messages: 1: In untar2(tarfile, files, list, exdir) : skipping pax global extended headers 2: In untar2(tarfile, files, list, exdir) : skipping pax global extended headersI ended up downloading a lot of build tools and got the same error message and decided to abandon.
It looks like a useful package for missing values. I'll re-try once the pcaMethods issue has been resolved.