Files in Collate field missing from package when installing from Github

Question

Note: I cross-posted this question here: https://github.com/hadley/devtools/issues/245

Update: @hadley just closed the issue since he can install now. I have tested it just now and install_github works on Windows too. Apparently I need wait for some time for Github archive to include the new committed changes. For people encounter the same problem, @hadley pointed out that I have .R and .r files in R/ and all the files in DESCRIPTION collate have .r extensions.

I am writing an R package and put it on Github. I can build and load on my own computer. However, after running install_github("KineticEval",username="zhenglei-gao"), I got the following error:

* installing *source* package 'KineticEval' ...
** R
Error in .install_package_code_files(".", instdir) : 
files in 'Collate' field missing from 'C:/Users/z.gao/AppData/Local/Temp/RtmpUzWWYn    /R.INSTALLd3c17515a0/KineticEval/R':
  kingraph.r
  kinplot.r
  FOCUS2006A.r
  FOCUS2006B.r
  FOCUS2006C.r
  FOCUS2006D.r
  modFit1.r
  IRLSkinfit.full.r
  mkinfit.full.r
ERROR: unable to collate and parse R files for package 'KineticEval'
* removing 'C:/Users/z.gao/R-dev/KineticEval'

A related question is here: Files in Collate field missing from package after build from incorrect .Rbuildignore file

But I can't figure out whether the error is also related to my .Rbuildignore file.

Seward

Are you using rstudio and roxygen2? – Yann

@wush978, yes, I use roxygen2 to generate the Collate field. – Seward

Then you should check if roxygenize is executed before R CMD INSTALL – Yann

@wush978, I don't know how to check that. I have locally run roxygenize and push it to Github, then try to use install_github() which automatically runs R CMD INSTALL. I can run R CMD INSTALL and install() without using the Github repository but my own repository. – Seward

I suggest you to check your repository as follow. Run git clone a clean repository first. Run roxygenize on the cloned repository. Run git status to check if any files are modified. – Yann

It installs fine for me. I'm on Linux though. And Hadley runs a Mac I believe so this might be a Windows only issue at the moment. – Lateen

@wush978, I will do that when I have access to my other computer. – Seward

@Dason, good to know that. I will test again on my computer and update. – Seward

Answer 1

For people encounter the same problem, Hadley(from Github) pointed out that I have .R and .r files in R/ and all the files in DESCRIPTION collate have .r extensions. I use roxygenize to generate the collate field in DESCRIPTION.

What I did is deleting all files in R/ in the local repository and copy back, push it to Github. Only renaming .R as .r under Windows does not change the remote repository. Then the error occured again afterwards so I asked here to see if there is something more I should fix. But after a day, the error disappeared.

Seward

So what did you do to fix the problem? – Lateen

@Dason, I just deleted all files in R/ in the local repository and copy back. Only renaming them as .r does not change the remote repository .R as .r. Then the error occured again. After a day, the error disappeared. – Seward

Answer 2

I had the exact same problem. I had a silly mistake in my .Rbuildignore. The file I was missing was named something like OutputPlotGenerator.R, and my .Rbuildignore file included the line output, thus removing / ignoring my R file.

Modestamodeste

Answer 3

For some reason I had the same name twice in my description. One with a .r extension, one with .R as an extension. Removing the wrong one solved the issue.

Bluegreen

Answer 4

For me, I had a new .R file which I had not added to the collate field in the DESCRIPTION file.

Simply adding it to that field solved the problem.

Hadley talks about it in a few places here.

Disfeature

Answer 5

Ran into the same problem:

Error in .install_package_code_files(".", instdir) : 
files in 'Collate' field missing from 'C:/Users/hyche/AppData/Local/Temp/RtmpsxI2G7/R.INSTALLadc4a3f4024/SPORM/R':

  SPORM-package.R

  pmlkh.R

  pwlkh.R

  splkh.R

ERROR: unable to collate and parse R files for package 'SPORM'

It seemed the files in /R could not be found when installing the package from the github repository.

Solution

I moved files in /R to a place outside the package directory in the github desktop, and then pushed the github desktop (without /R) to the github repository. It cleaned /R in the github repository. I then moved files in /R back to the github desktop package. Pushed the package in the github desktop to the github repository again to update /R. Now the problem is gone.

Anguilliform