Failed to install 'sake' from github: Not found

[raquelgarza]

Hello,

I followed the instructions to install sake in a macOS Mojave 10.14.5 with R 3.5.1, but I am getting this "not found" error:

source("http://bioconductor.org/biocLite.R")
biocLite(c("annotate", "AnnotationHub", "biomaRt", "DESeq2", "gage", "gageData", "GO.db", "pathview", "plotly", "DT", "install_github"))

install.packages("devtools")
devtools::install_github("renozao/pkgmaker", ref="develop")
devtools::install_github("naikai/sake")

> Downloading GitHub repo naikai/sake@master
Error: Failed to install 'sake' from GitHub:
  HTTP error 404.
  Not Found

  Did you spell the repo owner (`Bioconductor-mirror`) and repo name (`biomaRt`) correctly?
  - If spelling is correct, check that you have the required permissions to access the repo.

It is pretty weird since I don't even get the correct repo owner / name in the error message. It's not a network problem (I have tried several ones), neither I'm using a vpn, so I'm not sure why can't I reach it.

Any suggestions would be greatly appreciated.

[molikd]

> devtools::install_github("naikai/sake@master")
Downloading GitHub repo naikai/sake@master
Error: Failed to install 'sake' from GitHub:
  HTTP error 404.
  Not Found

  Did you spell the repo owner (`Bioconductor-mirror`) and repo name (`biomaRt`) correctly?
  - If spelling is correct, check that you have the required permissions to access the repo.

I get the same issue.

in the meantime, try the following library/install method:

githubinstall::gh_install_packages("naikai/sake")

fromt the githubinstall library

[raquelgarza]

Thank you molikd, but I got a similar error:

Downloading GitHub repo naikai/sake@master
Error: Failed to install 'sake' from GitHub:
  HTTP error 404.
  Not Found

  Did you spell the repo owner (`Bioconductor-mirror`) and repo name (`biomaRt`) correctly?
  - If spelling is correct, check that you have the required permissions to access the repo.
In addition: Warning message:
In fread(download_url, sep = "\t", header = FALSE, stringsAsFactors = FALSE,  :
  Found and resolved improper quoting out-of-sample. First healed line 4848: <<Puriney  honfleuR    "Evening, honfleuR" by Seurat>>. If the fields are not quoted (e.g. field separator does not appear within any field), try quote="" to avoid this warning.

[molikd]

ra7555ga-s,

Looks like something with the build process.

Could you please try a binary package install:

pkgurl <- "https://github.com/naikai/sake/releases/download/0.4.0/sake_0.4.0.tgz" 

install.packages(pkgurl, repos=NULL, type="source")

[raquelgarza]

This worked! Thank you 😁

[ColeWunderlich]

I think this is because biomaRt is incorrectly specified in the Remotes: field of the DESCRIPTION file.
https://github.com/naikai/sake/blob/9bb22b24861d7f8a07e8a09c0baa88911bd1ba26/DESCRIPTION#L16-L18 The following change seems to fix it (now downloads from Bioconductor directly):

bioc::release/biomaRt,

This error is linkey occurring because the github repository Bioconductor-mirror no longer exists.

[naikai]

Thanks @ColeWunderlich for the help. Seems like it's now working again.