Problems with devtools and install_github "genomicsclass/GSE5859Subset"

General
#1

I have been trying to fix this error since two days. I have R Studio version 3.6.0 and I have downloaded Rtools34 in order to install devtools. I need this for
install_github("genomicsclass/GSE5859Subset") for a homework
So while the install.packages ("devtools") work, I get all these warning and error messages and I cannot proceed

> library(devtools)
Loading required package: usethis
Warning messages:
1: package ‘devtools’ was built under R version 3.6.3 
2: package ‘usethis’ was built under R version 3.6.3 
> install_github("genomicsclass/GSE5859Subset")
Error: Failed to install 'unknown package' from GitHub:
  HTTP error 403.
  API rate limit exceeded for 157.32.239.55. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

  Rate limit remaining: 0/60
  Rate limit reset at: 2020-05-26 15:42:00 UTC

  To increase your GitHub API rate limit
  - Use `usethis::browse_github_pat()` to create a Personal Access Token.
  - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.
> library(GSE5859Subset)
Error in library(GSE5859Subset) : 
  there is no package called ‘GSE5859Subset’

Any help would be greatly appreciated. Thank you.

#2

Have a look at this repo, that doesn't look like an R package to me. It's just a .rda file and a readme.

Ah, I see you cross posted here: https://github.com/genomicsclass/labs/issues/96

https://github.com/genomicsclass/GSE5859Subset.

#3

Hello,
Yes I also cross posted in github. But I really cannot find a solution.

I am taking an online course and I need to answer questions on this dataset to proceed further.
It seems very easy as it is shown in the video for the online course. Just install the "devtools" package and then install the dataset from github.
Ok. 2 questions:

  1. I have R 3.6.0 and are the warning messages with devtools a problem to begin with (you can see my query above)??

2a. How do you then open an .Rda file? 2b. What does this API rate limit exceeded mean? Does creating this Personal Access Token as suggested to increase the Github API rate limit useful?

Thank you.

#4

Hello,
I uninstalled and reinstalled R, Rtools and RStudio.
Then using the same code, I could successfully install package devtools but I am still getting error messages which are preventing me from proceeding any further. Thank you for your help.

library(devtools)
Error: package or namespace load failed for ‘devtools’:
.onLoad failed in loadNamespace() for 'pkgload', details:
call: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
error: there is no package called ‘backports’

install_github("genomicsclass/GSE5859Subset")
Error in install_github("genomicsclass/GSE5859Subset") :
could not find function "install_github"
library(GSE5859Subset)
Error in library(GSE5859Subset) :
there is no package called ‘GSE5859Subset’

#5

Install the missing dependency

install.packages("backports")
#6

Hello,
I already did and the library(devtools) now loads.

But when I type > install_github("genomicsclass/GSE5859Subset")
I get
Downloading GitHub repo genomicsclass/GSE5859Subset@master
Error: Failed to install 'GSE5859Subset' from GitHub:
System command 'Rcmd.exe' failed, exit status: -1, stdout + stderr empty

I guess this is the only concern. If this is resolved then I can type library(GSE5859Subset) and data(GSE5859Subset) and do the analysis with the data.
Any help would be greatly appreciated. Thank you.

#7

That github repo is not a package so you can't install it, it is just an .Rda file that you can download and read into R.

#8

Yes, I did that...finally.
Thank you

#9

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.