installation error

[xuebaliang]

hello, recently I failed to install the swne package on the linux server. Thus can you supply it using offline form ".tar.gz"??? In this way I can use "R CMD INSTALL" to install it. Thanks.

[yanwu2014]

Hi! Can you let me know what error you're having? Otherwise I think you can clone the directory locally: git clone git@github.com:yanwu2014/swne.git and install it locally that way

[xuebaliang]

Thanks for your reply. I have tried three ways to install swne, but all of them failed. chenliang@ubuntu:~$ git clone git@github.com:yanwu2014/swne.git Cloning into 'swne'... ssh: connect to host github.com port 22: Connection timed out fatal: Could not read from remote repository.

library("devtools") Loading required package: usethis devtools::install_github("yanwu2014/swne") Error: Failed to install 'unknown package' from GitHub: Timeout was reached: [api.github.com] Connection timed out after 10001 milliseconds devtools::install_local("/data/chenliang/R/offline_R_package/swne-master.zip") Error: Failed to install 'swne-master.zip' from local: Timeout was reached: [api.github.com] Connection timed out after 10000 milliseconds

[xuebaliang]

I suggest that you can pack all codes in .tar.gz and develop it in CRAN or bioconductor. It is very convenient for users.

[yanwu2014]

Ah it seems like some type of connection issue with github then. I'll work on making a tarball ASAP, and yes the eventual plan is to move to CRAN. Thanks for the heads up!

[mr-september]

I, too, cannot install via devtools.

Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE)
devtools::install_github("linxihui/NNLM")
devtools::install_github("yanwu2014/swne")

Error:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'jsonlite'
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package 'swne'
* removing 'C:/Users/username/Documents/R/win-library/4.0/swne
Warning messages:
1: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\username\Documents\R\win-library\4.0\00LOCK\jsonlite\libs\x64\jsonlite.dll to C:\Users\username\Documents\R\win-library\4.0\jsonlite\libs\x64\jsonlite.dll: Permission denied
2: In i.p(...) :
  installation of package ‘C:/Users/username/AppData/Local/Temp/RtmpcvJteA/file498c5ac16713/swne_0.6.16.tar.gz’ had non-zero exit status

Note: I have tried to force (re-?)install jsonlite:

install.packages('jsonlite', dependencies=TRUE, repos='http://cran.rstudio.com/')

This does not solve the above Error

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'jsonlite'

[yanwu2014]

Hmm I can't seem reproduce this error either. Are you installing SWNE from a clean R/RStudio session (with no packages) loaded? Also it might help to try installing the devtools version: devtools::install_github("jeroen/jsonlite")

I also just added jsonlite as an explicit dependency to see if that helps. Let me know if it's still not installing?

[mr-september]

Hmm I can't seem reproduce this error either. Are you installing SWNE from a clean R/RStudio session (with no packages) loaded? Also it might help to try installing the devtools version: devtools::install_github("jeroen/jsonlite")

I also just added jsonlite as an explicit dependency to see if that helps. Let me know if it's still not installing?

I think that did the trick! I attempted again today (no change in my code) and it installed without problems. Thank you!