[R-pkg-devel] Unexpected symbol when checking package examples

[Duncan Murdoch]

On 12/11/2018 7:56 AM, Jared Knowles wrote:
> Thank you so much for the help!
> 
> The origin of this mistake was mine - I forgot a ' following a # in my 
> roxygen example code - which meant roxygen ignored the closing parens on 
> the next line. (See example)
> 
> \donttest{
> #' # You can also pass additional arguments to predictInterval through 
> REimpact
> #' g1 <- lmer(y ~ lectage + studage + (1|d) + (1|s), data=InstEval)
> #' zed <- REimpact(g1, newdata = InstEval[9:12, ], groupFctr = "d", 
> n.sims = 50,
> #'                 include.resid.var = TRUE)
> #' zed2 <- REimpact(g1, newdata = InstEval[9:12, ], groupFctr = "s", 
> n.sims = 50,
> #'                  include.resid.var = TRUE)
> #' zed3 <- REimpact(g1, newdata = InstEval[9:12, ], groupFctr = "d", 
> breaks = 5,
> #                 n.sims = 50, include.resid.var = TRUE)
> #' }
> 
> Thanks everyone for the help. I never would have found this mistake 
> without this list.

Perhaps roxygen should try parsing the code it inserts as examples.  It 
can probably give a better error message than R could, since it knows 
which .R file it's looking at when the problem happens.

Duncan Murdoch

> 
>           Jared
> 
> 
> On Sun, Nov 11, 2018 at 6:53 PM Duncan Murdoch <murdoch.duncan using gmail.com 
> <mailto:murdoch.duncan using gmail.com>> wrote:
> 
>     On 11/11/2018 3:39 PM, Jared Knowles wrote:
>      > Hi!
>      >
>      > I have a bit of a weird issue when I'm trying to check my package
>     merTools
>      > (source repo available here: https://github.com/jknowles/merTools
>      >
>      > On Windows and Linux builds for R-release and R-devel, when R CMD
>     CHECK
>      > checks examples, it returns the following error below:
>      >
>      > Warning: parse error in file 'merTools-Ex.R':
>      > 1: unexpected symbol
>      > 117: cleanEx()
>      > 118: nameEx
> 
>     I also get this error on MacOS.
> 
>      >
>      >
>      > Upon inspecting the example file generated by R CMD CHECK
>     (mertools-Ex.R) -
>      > it contains only valid R code. I can run it line by line or
>     source the
>      > whole file in R without any errors. But, during the check
>     process, this
>      > error occurs.
> 
>     The problem is in the REimpact help file.  It contains this:
> 
>     zed3 <- REimpact(g1, newdata = InstEval[9:12, ], groupFctr = "d",
>     breaks
>     = 5,
> 
>     and there's no closing paren.
> 
>     This is in a \donttest section of the examples, so it gets deleted when
>     running the examples, and that's the version of merTools-Ex.R that is
>     left at the end.  But the warning happened in a different test,
> 
>     * checking for unstated dependencies in examples ... WARNING
>     Warning: parse error in file 'merTools-Ex.R':
>     1: unexpected symbol
>     118: cleanEx()
>     119: nameEx
>            ^
> 
>     and it is based on a different version of that file that doesn't omit
>     the \donttest section.
> 
>     This is arguably an R bug:  the line numbers are misleading, since they
>     refer to a version of the file that no longer exists.  Perhaps when you
>     say \donttest, no tests should be done.
> 
>     Duncan Murdoch
> 
> 
> 
>      > The functions cleanEx() and nameEx() appear to be created as part
>     of the
>      > checking process.
>      >
>      > I have not changed the examples in the code since the last time I
>     ran R CMD
>      > CHECK so I am quite confident that the example code for all
>     functions is
>      > valid R code.
>      >
>      > Any ideas on what might be the source of this problem?
>      >
>      >                 Thanks!
>      >                   Jared
>      >
>      >
>      >
>      > Jared Knowles
>      > President, Civilytics Consulting LLC
>      > www.jaredknowles.com <http://www.jaredknowles.com>
>      >
>      >       [[alternative HTML version deleted]]
>      >
>      > ______________________________________________
>      > R-package-devel using r-project.org
>     <mailto:R-package-devel using r-project.org> mailing list
>      > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>      >
>