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MikeJSeo / SAM

SAM (Significance Analysis of Microarrays) shiny app
https://cran.r-project.org/web/packages/samr/index.html
37 stars 20 forks source link

new user, issues with running SAM #29

Open spinjdoc opened 6 years ago

spinjdoc commented 6 years ago

Hi Mike. Been running SAM for years as an Excel addin, but with minimal-to-no expertise in R or the new SAM. (Just loaded it to make SAM work). On a new Windows 10 PC I newly loaded R 3.4.3 and tried to run the code as noted in the README. It seemed to successfully install the packages, and when I ran the next bit: library(shiny) runGitHub("SAM", "MikeJSeo")

It opened a Chrome window with the app, although everything is rather dark grey.(... supposed to be)? I browsed for the xlsx spreadsheet (one I've used in SAM before) and picked the proper response type and hit Run. Nothing appeared on the screen or changed to suggest that it was running now. After 5-10 min still nothing had changed on the Chrome page screen.

After a short bit, this appeared in the R console window: Listening on http://127.0.0.1:6779 Warning: Error in : package ‘impute’ required by ‘samr’ could not be found Stack trace (innermost first): 43: .getRequiredPackages2 42: library 3: runApp 2: runUrl 1: runGitHub Error : package ‘impute’ required by ‘samr’ could not be found

I was unable to close R console or make anything happen using the menus. Finally had to shut it down using Task Manager. Any idea what's going on? Thanks much!

MikeJSeo commented 6 years ago

It looks like impute package hasn't been installed properly. Also, if it is dark grey color, it means there has been some error. Can you check the impute package has been installed correctly? What does running the code below show you?

source("http://bioconductor.org/biocLite.R") biocLite("impute")

spinjdoc commented 6 years ago

You were correct Mike. It turned out that I needed to run R as admin to get the package installations to stick. Also, I needed to employ the same fix mentioned in previous threads of installing Rtools to get the results to save, but that did the trick. Thanks much!