[R-pkg-devel] warning from win_build

On 29/12/2016 2:58 PM, Roy Mendelssohn - NOAA Federal wrote:

HI All:

If any cares,  the offending line is in the  ggplot2  file utilities.r where it has:

#' A waiver object.
#'
#' A waiver is a "flag" object, similar to \code{NULL}, that indicates the
#' calling function should just use the default value.  It is used in certain
#' functions to distinguish between displaying nothing (\code{NULL}) and
#' displaying a default value calculated elsewhere (\code{waiver()})
#'
#' @export
#' @keywords internal
waiver <- function() structure(NULL, class = "waiver")

is.waive <- function(x) inherits(x, "waiver")

If you then do a multi-file search on "waive" you find that it is used all throughout the code base, so anytime waiver() is called, so is the NULL structure.

That usage will work:  though waiver() tries to put a class on NULL,
structure() puts it on a length-zero list instead.  R-devel's complaint
is unnecessary here, but could be avoided with the code change

waiver <- function() structure(list(), class = "waiver")

I've cc'd Hadley to let him know.

Duncan Murdoch

-Roy

On Dec 29, 2016, at 11:44 AM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote:

Thanks.  I can wait.  I will also see if I can figure out a work around in the meantime.  Is the submission to winbuild automated?  That is really the only way I have to check, but I don't want to keep on checking if someone's time is being wasted by that.  If automated,  the I don't mind making repeated submissions.

Thanks again,

-Roy

On Dec 29, 2016, at 11:40 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

On 29/12/2016 1:44 PM, Roy Mendelssohn - NOAA Federal wrote:

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?

I'd recommend waiting a few days.  If you really want to submit soon, you can figure out which is the offending command, and wrap it in something that suppresses the warning (e.g. suppressWarnings(), assuming the conversion to an error happens later).

I don't think your package would be accepted if the vignette won't build on R-devel.

Duncan Murdoch

-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.

**********************
"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.

**********************
"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.

**********************
"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.