[R-pkg-devel] warning from win_build

[Duncan Murdoch]

On 29/12/2016 1:24 PM, Ben Bolker wrote:
>   Sorry, correction/clarification to my last post: it's *not* a bug in
> ggplot2, rather apparently (?) it's something in base R that has broken
> tests in both data.table and ggplot2. (Since your code calls ggplot,
> though, it's presumably in there somewhere, and (?) not your problem.)

The NEWS item is here:

http://developer.r-project.org/blosxom.cgi/R-devel/2016/12/28#n2016-12-28

The issue is discussed in a bit more detail on R-devel (subject "[Rd] 
Unexpected I(NULL) output") and 
<https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17198>.

Overall it seems like a good idea:  some code (perhaps in ggplot2, I 
haven't tried to track it down) appears to be trying to set attributes 
on NULL.  This will silently fail in versions of R prior to R-devel rev 
71841, and will fail with a warning in that version or later.  (Since 
the change to R-devel is very recent, it may change again.)

Duncan Murdoch

>
>   cheers
>     Ben
>
>
>
> On 16-12-29 01:16 PM, Roy Mendelssohn - NOAA Federal wrote:
>> Hi All:
>>
>> I am working on a new submission of my xtractomatic package  (the
>> main change being the use of https).  I develop on a Mac.  When I run
>> on the Mac:
>>
>> devtools::check()
>>
>> I get no errors, notes, or warnings.  However, when I run
>> devtools::build_win(), the response I get back isL
>>
>>
>>> * checking for unstated dependencies in vignettes ... OK * checking
>>> package vignettes in 'inst/doc' ... OK * checking re-building of
>>> vignette outputs ... WARNING Error in re-building vignettes: ...
>>> Quitting from lines 248-261 (Usingxtractomatic.Rmd) Error:
>>> processing vignette 'Usingxtractomatic.Rmd' failed with
>>> diagnostics: (converted from warning) Calling 'structure(NULL, *)'
>>> is deprecated, as NULL cannot have attributes. Consider
>>> 'structure(list(), *)' instead. Execution halted
>>>
>>
>> So this error is from my Vignette.  The offending lines appear to
>> be:
>>
>>> ```{r topotagPlot, fig.align = 'center', fig.width = 6, fig.height
>>> = 4, warning = FALSE} require("ggplot2") alldata <- cbind(tagData,
>>> topo) alldata$lon <- alldata$lon - 360 z <- ggplot(alldata, aes(x =
>>> lon,y = lat)) + geom_point(aes(colour = mean), size = 2.) +
>>> scale_shape_manual(values = c(19, 1)) z + geom_polygon(data = w,
>>> aes(x = long, y = lat, group = group), fill = "grey80") +
>>> theme_bw() + scale_colour_gradient("Depth") + coord_fixed(1.3, xlim
>>> = xlim, ylim = ylim) + ggtitle("Bathymetry at marlin tag
>>> locations")
>>>
>>> ```
>>>
>>
>>
>> Now the vignette builds fine on my machine,  and  I can run it by
>> "hand"  (as an R Notebook, executing each chunk) and it works also.
>> Looking at the offending code chunk,  I can honestly say I have no
>> idea what the error message is referring to.    When I run by hand,
>> I have checked that both tagData and topo are properly defined.  But
>> is that the problem,  is the error message from the  cbind?
>>
>> Thanks for any help.
>>
>> -Roy
>>
>>
>> ********************** "The contents of this message do not reflect
>> any position of the U.S. Government or NOAA." **********************
>> Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS
>> Environmental Research Division Southwest Fisheries Science Center
>> ***Note new street address*** 110 McAllister Way Santa Cruz, CA
>> 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail:
>> Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
>>
>> "Old age and treachery will overcome youth and skill." "From those
>> who have been given much, much will be expected" "the arc of the
>> moral universe is long, but it bends toward justice" -MLK Jr.
>>
>> ______________________________________________
>> R-package-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
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