I am a student of SISG Module 17. We learned about the TopmedPipeline functions during the module. This is an extremely useful package but I have only been able to run this through the DataStage and not my own computer. I am simply not able to install TopmedPipeline.
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/winst/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘topmedpipeline’ is not available (for R version 3.6.0)
This support site is for Bioconductor maintained packages. TopmedPipeline is not a Bioconductor maintained package and you might have better luck on StackOverflow or Biostars.
For What Its worth. It does not look like TopmedPipeline is an official CRAN or Bioconductor package. Without it being an official CRAN package it will not install directly from install.packages. The reference I found to TopmedPipeline is a Github repository. If this is what you are looking for, you can install this package through BiocManager or devtools
With BiocManager I got this error message:
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing github package(s) 'remotes UW-GAC/analysis_pipeline/TopmedPipeline/'
Error: Failed to install 'unknown package' from GitHub:
attempt to set an attribute on NULL
With devtools I got his error message:
Error in installgithub("UW-GAC/analysispipeline/TopmedPipeline/") :
could not find function "install_github"
Installing package into ‘C:/Users/winst/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package 'TopmedPipeline' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called 'jomo'
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package 'TopmedPipeline'
* removing 'C:/Users/winst/Documents/R/win-library/3.6/TopmedPipeline'
Error: Failed to install 'TopmedPipeline' from GitHub:
(converted from warning) installation of package ‘C:/Users/winst/AppData/Local/Temp/RtmpGEHmlD/file505815da1f3d/TopmedPipeline_2.5.0.tar.gz’ had non-zero exit status
In summary, the installation code for TopmedPipeline is:
install.packages("devtools")
install.packages("jomo")
devtools::installgithub("UW-GAC/analysispipeline/TopmedPipeline/")
Thank you for you help Shepherl,
With BiocManager I got this error message: Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing github package(s) 'remotes UW-GAC/analysis_pipeline/TopmedPipeline/' Error: Failed to install 'unknown package' from GitHub: attempt to set an attribute on NULL
With devtools I got his error message: Error in installgithub("UW-GAC/analysispipeline/TopmedPipeline/") : could not find function "install_github"
try
devtools::install_github("UW-GAC/analysispipeline/TopmedPipeline/")Thank you again Shepherl,
Got a short run with this error message:
Thank you Shepherl, it worked.
In summary, the installation code for TopmedPipeline is: install.packages("devtools") install.packages("jomo") devtools::installgithub("UW-GAC/analysispipeline/TopmedPipeline/")