[R-pkg-devel] warning from win_build

[Roy Mendelssohn - NOAA Federal]

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.mendelss...@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@r-project.org mailing list
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Re: [R-pkg-devel] warning from win_build

[Ben Bolker]

  I think this is a ggplot2-related issue.  Matt Dowle posted about it:

http://blog.h2o.ai/2016/12/behind-the-scenes-of-cran/


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.mendelss...@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@r-project.org mailing list 
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] warning from win_build

[Ben Bolker]

  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.)

  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.mendelss...@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@r-project.org mailing list 
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] warning from win_build

[Roy Mendelssohn - NOAA Federal]

Thanks, that is a big help because I had no idea what the error was referring 
to,.  Can I put this in my comments to cran and that will be sufficient?  
Normally any warning is sufficient for rejection?

I just want to make certain the updated submission goes a cleanly as possible.

-Roy



> On Dec 29, 2016, at 10:24 AM, 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.)
> 
>  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.mendelss...@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@r-project.org mailing list 
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> 
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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.mendelss...@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [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 
.


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.mendelss...@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



__
R-package-devel@r-project.org mailing list
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__
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Re: [R-pkg-devel] warning from win_build

[Roy Mendelssohn - NOAA Federal]

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  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 
> .
> 
> 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.mendelss...@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@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>> 
>> 
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> 
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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.mendelss...@noaa.gov www: http:/

Re: [R-pkg-devel] warning from win_build

[Duncan Murdoch]

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  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 .

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.mendelss...@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@r-project.org mailing list
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https://stat.ethz.ch/mailman/listinfo/r-package-devel


**
"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) 4

Re: [R-pkg-devel] warning from win_build

[Roy Mendelssohn - NOAA Federal]

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  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  
>>> 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 
>>> .
>>> 
>>> 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.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
> 
> "Old age and treachery will overcome youth and skill." "Fro

Re: [R-pkg-devel] warning from win_build

[Roy Mendelssohn - NOAA Federal]

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.

-Roy




> 
> On Dec 29, 2016, at 11:44 AM, Roy Mendelssohn - NOAA Federal 
>  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  
>> 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  
 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 
 .
 
 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, executin

Re: [R-pkg-devel] warning from win_build

[Duncan Murdoch]

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 
 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  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  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 .

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 top