[R-pkg-devel] warning from win_build

Roy Mendelssohn - NOAA Federal roy.mendelssohn at noaa.gov
Thu Dec 29 19:44:34 CET 2016


Thanks,  but as I said,  my next question is how best to proceed with CRAN.  I do not want to waste peoples' time with a submission that I know before hand will be rejected.   Can I submit with this warning?

-Roy


> On Dec 29, 2016, at 10:38 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> 
> 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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>> 
> 
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**********************
"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.



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