Possible roxygen2 4.0.0 bug?

[Eduardo Ibanez]

Hello,

I think I found a bug in the latest version of roxygen2 (4.0.0). I'm running R 3.1.0 on Windows.

I'm writing a package that uses figures in the documentation and I do so by following the answer in http://stackoverflow.com/a/7953949. That answer points to http://cran.r-project.org/doc/manuals/R-exts.html#Figures that says "http://cran.r-project.org/doc/manuals/R-exts.html#Figures".

If you create that folder, the new version of roxygen2 tries to access and modify the folder as a file and throws an error. For example,

> upgradeRoxygen()
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") : cannot open file './man/figures': Permission denied

It looks like folders should be excluded from roxygen functions, if this is really a bug.

Alternatively, is there a preferable way to include images?

Thanks in advance,
Eduardo

[Hadley Wickham]

Hi Eduardo,

upgradeRoxygen() has been done away with in the latest dev version, so
this should no longer be a problem. (upgrades now happen automatically
because I figured out a safer way to do it)

Hadley

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[Eduardo Ibanez]

Hadley,

Thanks for the fast response. The problem is not limited to upgradeRoxygen(). I find the same error message when running devtools::document()

To reproduce this error, I downloaded the trunk version of ggplot2 (https://github.com/hadley/ggplot2/archive/master.zip), loaded devtools and run

> document()

Updating ggplot2 documentation

Loading ggplot2

Writing label_wrap_gen.Rd

Writing labeller.Rd

Next, I added the (empty) folder "man/figures" and document() does not work anymore:

> document()

Updating ggplot2 documentation

Loading ggplot2

Error in file(con, "r") : cannot open the connection

In addition: Warning message:

In file(con, "r") :

  cannot open file 'C:\Users\eibanez\Documents\Rdevelop\ggplot2-master/man/figures': Permission denied

Would this be fixed in the dev version of roxygen2?

Thanks,

Eduardo

[Hadley Wickham]

It seems to be - I couldn't recreate the error.

Hadley

[Eduardo Ibanez]

Mmm, it might be a Windows-only error. The development version does not work either.

I found that the error originates in the first line of "first_time" (https://github.com/klutometis/roxygen/blob/master/R/safety.R#L2). The dir() function will return a list of both files and directories (at least in Windows), as shown below in item number 4:

> dir("man", full.names = TRUE)

[1] "man/calculate_elcc.Rd"    "man/calculate_metrics.Rd" "man/capacity_value.Rd"   

[4] "man/figures"              "man/format_timedata.Rd"   "man/outage_table.Rd"     

[7] "man/repra.Rd"             "man/sliding_window.Rd" 

I am sending a pull request with the following lines that takes folders out of generated. An alternative would be to use a filter in dir().

generated <- generated[file.info(generated)$isdir]

Thanks,

Eduardo

[Remko Duursma]

The error still persists (I had posted this to http://stackoverflow.com/questions/23797391/roxygen2-4-0-1-fails-when-man-figures-is-present)

I have tried dev version 4.0.1.99