Problems during installation and running

[Leonardo Caserta]

Hello, 

I had some porblems during installation and running of MixviR but was able to solve and now looks like it is running fine. I thought it could be useful to post here the steps I took to make it work: 

#Uninstall R
#install R
#Install Rtools following the instructions at: https://cran.r-project.org/bin/windows/Rtools/rtools40.html
#Make sure you delete the .Renviron file at your C:\Documents folder

#Install MixviR:
install.packages("MixviR", dependencies = TRUE)

#If you get the following error message, install Biostrings:

Error in `dplyr::summarise()`:
! Problem while computing `translation = translate_fwd(ALT, code = code.num)`.
ℹ The error occurred in group 1: GENE = "E".
Caused by error in `loadNamespace()`:
! there is no package called ‘Biostrings’
Run `rlang::last_error()` to see where the error occurred.

#Install Biostrings:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")

#Reload libraries:

library(MixviR)
library(BiocManager)

[Mike Sovic]

Hi Leonardo,

Interestingly, your post came just shortly after another that had a similar issue. Looks like you've gotten it solved - thanks so much for passing along your solution. I would guess that for most folks, the key parts of your solution are where you installed Biostrings. As I mentioned in that other related post, I think doing the following (as you have as part of your solution) before running the MixviR functions/examples should solve this in most cases...

install.packages("BiocManager")

BiocManager::install("Biostrings")

I'll see if I can get this fixed in the next version so that Biostrings gets included as necessary as part of the CRAN install, but for now, hopefully the above will work for anyone who doesn't already have its (note you'll only need to do this once - not every time you load and run MixviR). I'm hoping the uninstall/reinstall R and Rtools parts of your solution aren't necessary in most cases - I'm not sure why they would be, but would love to hear from any other folks if they turn out to be.

          Mike