YosefLab/scone

packages httpuv and digest not installed with dependencies

Opened this issue · 19 comments

allonw commented
packages httpuv and digest not installed with dependencies
drisso commented

Maybe I'm missing something, where are we using the package httpuv?

@mbcole do you know?

allonw commented

This is the error I got while installing:

* installing *source* package 'scone' ...
** R
** data
** inst
** tests
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called 'httpuv'
ERROR: lazy loading failed for package 'scone'
drisso commented

It's not our dependency. Are you using the dependencies=TRUE option?

drisso commented

It may be a dependency of our dependency. Have you tried to manually install it?

allonw commented

Yes, I was using dependencies=TRUE because that's what the front page recommends :)

https://github.com/YosefLab/scone

drisso commented

Yes! And I stand behind that! You should use it :)

allonw commented

PS. I'm sorry if it wasn't clear from the title of the issue: yes, I installed httpuv manually and then everything worked fine.

mbcole commented

Would recursive = TRUE have worked automatically?

drisso commented

can I close this one? Or should we change the README to include the recursive=TRUE?

allonw commented

Whatever you think is right.

My case was that I used recursive=TRUE as appears in the readme and yet of the required packages needed manual installation. Once I installed it, scone's installation went smoothly

drisso commented

In the README there is dependencies=TRUE, but not recursive=TRUE. Did you use recursive?

allonw commented

Sorry, my error. I meant to write that I used dependencies=TRUE as in the readme. I didn't use recusive=TRUE

allonw commented

Updated the issue's name to reflect the problem better (also found it applies to package "digest")

WadeDavis commented

I also have run into a failed installation when using biocLite("YosefLab/scone", dependencies=TRUE).
This occurs for the following packages: mclust, prabclus, curl, flexmix, robustbase, DEoptimR, trimcluster, kernlab, Rcpp

Below is an example of what happens.
``* installing source package 'scone' ...
** R
** data
** inst
** tests
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called 'prabclus'
ERROR: lazy loading failed for package 'scone'

  • removing 'C:/R/R-3.3.1/library/scone' ``
drisso commented

@allonw @WadeDavis are you both on Windows?

allonw commented

When I reported this issue I encountered in Windows. I think I've since saw it in Linux, but it's been a while ago so I'm not sure if I recall correctly by now.

drisso commented

I believe this is an issue with devtools. There are many open issues there that could be related, e.g.,
r-lib/devtools#1298

I would try the following:

  1. Run devtools directly (biocLite uses devtools internally) devtools::install_github("YosefLab/scone", force = TRUE) and/or
  2. Update to the most recent version of devtools and try again
AnneGeijsen commented

Hi!

Were you able to solve the problem? I have the same problem and I tried all suggestions in this post and several others but I am not able to solve the problem.

library("devtools")
devtools::install_github("rwehrens/BatchCorrMetabolomics", force = TRUE)

and

library("devtools")
install_github("rwehrens/BatchCorrMetabolomics")

I also tried to change .libPaths() but nothing seems to work.. I am working in Windows 10.

Thanks a lot!

drisso commented

Hi @AnneGeijsen ,

this is the issue tracker of the scone package, I believe that you have a problem with devtools not scone. If so, you should post it here:
https://github.com/hadley/devtools/issues