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 

[Rd] structure(NULL, *) is deprecated [was: Unexpected I(NULL) output]

[Martin Maechler]

> Martin Maechler 
> on Thu, 22 Dec 2016 10:24:43 +0100 writes:

> Florent Angly 
> on Tue, 20 Dec 2016 13:42:37 +0100 writes:

>> Hi all,
>> I believe there is an issue with passing NULL to the function I().

>> class(NULL)  # "NULL"  (as expected)
>> print(NULL)   # NULL  (as expected)
>> is.null(NULL) # TRUE  (as expected)

>> According to the documentation I() should return a copy of its input
>> with class "AsIs" preprended:

>> class(I(NULL))  # "AsIs"  (as expected)
>> print(I(NULL))   # list()  (not expected! should be NULL)
>> is.null(I(NULL)) # FALSE  (not expected! should be TRUE)

>> So, I() does not behave according to its documentation. 

> yes.

>> In R, it is
>> not possible to give NULL attributes, but I(NULL) attempts to do that
>> nonetheless, using the structure() function. Probably:
>> 1/ structure() should not accept NULL as input since the goal of
>> structure() is to set some attributes, something cannot be done on
>> NULL.

> I tend to agree.  However if we gave an error now, I notice that
> even our own code, e.g., in stats:::formula.default()  would fail.

> Still, I think we should consider *deprecating*  structure(NULL, *),
> so it would give a *warning* (and continue working otherwise)
> (for a while before giving an error a year later).

 [..]

> Martin Maechler
> ETH Zurich

Since svn rev 71841,   structure(NULL, *) now __is__ deprecated
in R-devel, i.e.,

  > structure(NULL, foo = 2)
  list()
  attr(,"foo")
  [1] 2
  Warning message:
  In structure(NULL, foo = 2) :
Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
  > 

A dozen or so CRAN packages now not only give warnings but
partially also  ERRORS in their checks,  which I find strange,
but it may be because of too stringent checks (e.g. checks were
all warnings are turned into errors).

The most prominent packages now giving errors are
data.table and ggplot2,  then also GGally.

Of course, we (the R core team) could make the deprecation even
milder by not giving a warning() but only a message(.) aka
"NOTE";  however, that renders the deprecation process longer and more
complicated (notably for us),  and there is still a few months' time
before this version of R will be released...
and really, as I said,... a new warning should rarely cause
*errors* but rather warnings.

OTOH, some of us have now seen / read on the  R-package-devel  mailing list
that it seems ggplot2 has stopped working correctly (under
R-devel only!) in building packages because of this warning.. 

The current plan is it will eventually, i.e., after the
deprecation period, become an error, so ideally packages are
patched and re-released ASAP.  It's bedtime here now and we will
see tomorrow how to continue.

My current plan is to an e-mail to the package maintainers of CRAN
packages that are affected, at least for those packages that are "easy to find".

Martin Maechler,
ETH Zurich

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

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 

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 

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: 

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.

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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
>> 
> 
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> 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.

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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
>

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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
>

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Re: [Rd] colnames for data.frame could be greatly improved

[Martin Maechler]

> Hi there,
> Any update on this?
> Should I create bugzilla ticket and submit patch?

> Regards
> Jan Gorecki

Hi Jan,

Why should we care that the  do.NULL = FALSE case is slower?
After all do.NULL = TRUE is the default.

In other words, where are use cases where it is problematic that
do.NULL = FALSE is relatively slow?

Shorter code  *is* nicer than longer code,  so I need a bit more
conviction why we should add more code for that special case ..

Martin Maechler, ETH Zurich

> On 20 December 2016 at 01:27, Jan Gorecki  wrote:
> > Hello,
> >
> > colnames seems to be not optimized well for data.frame. It escapes
> > processing for data.frame in
> >
> >   if (is.data.frame(x) && do.NULL)
> > return(names(x))
> >
> > but only when do.NULL true. This makes huge difference when do.NULL
> > false. Minimal edit to `colnames`:
> >
> > if (is.data.frame(x)) {
> > nm <- names(x)
> > if (do.NULL || !is.null(nm))
> > return(nm)
> > else
> > return(paste0(prefix, seq_along(x)))
> > }
> >
> > Script and timings:
> >
> > N=1e7; K=100
> > set.seed(1)
> > DF <- data.frame(
> > id1 = sample(sprintf("id%03d",1:K), N, TRUE),  # large groups (char)
> > id2 = sample(sprintf("id%03d",1:K), N, TRUE),  # large groups (char)
> > id3 = sample(sprintf("id%010d",1:(N/K)), N, TRUE), # small groups (char)
> > id4 = sample(K, N, TRUE),  # large groups (int)
> > id5 = sample(K, N, TRUE),  # large groups (int)
> > id6 = sample(N/K, N, TRUE),# small groups (int)
> > v1 =  sample(5, N, TRUE),  # int in range [1,5]
> > v2 =  sample(5, N, TRUE),  # int in range [1,5]
> > v3 =  sample(round(runif(100,max=100),4), N, TRUE) # numeric e.g. 
> > 23.5749
> > )
> > cat("GB =", round(sum(gc()[,2])/1024, 3), "\n")
> > #GB = 0.397
> > colnames(DF) = NULL
> > system.time(nm1<-colnames(DF, FALSE))
> > #   user  system elapsed
> > # 22.158   0.299  22.498
> > print(nm1)
> > #[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
> >
> > ### restart R
> >
> > colnames <- function (x, do.NULL = TRUE, prefix = "col")
> > {
> > if (is.data.frame(x)) {
> > nm <- names(x)
> > if (do.NULL || !is.null(nm))
> > return(nm)
> > else
> > return(paste0(prefix, seq_along(x)))
> > }
> > dn <- dimnames(x)
> > if (!is.null(dn[[2L]]))
> > dn[[2L]]
> > else {
> > nc <- NCOL(x)
> > if (do.NULL)
> > NULL
> > else if (nc > 0L)
> > paste0(prefix, seq_len(nc))
> > else character()
> > }
> > }
> > N=1e7; K=100
> > set.seed(1)
> > DF <- data.frame(
> > id1 = sample(sprintf("id%03d",1:K), N, TRUE),  # large groups (char)
> > id2 = sample(sprintf("id%03d",1:K), N, TRUE),  # large groups (char)
> > id3 = sample(sprintf("id%010d",1:(N/K)), N, TRUE), # small groups (char)
> > id4 = sample(K, N, TRUE),  # large groups (int)
> > id5 = sample(K, N, TRUE),  # large groups (int)
> > id6 = sample(N/K, N, TRUE),# small groups (int)
> > v1 =  sample(5, N, TRUE),  # int in range [1,5]
> > v2 =  sample(5, N, TRUE),  # int in range [1,5]
> > v3 =  sample(round(runif(100,max=100),4), N, TRUE) # numeric e.g. 
> > 23.5749
> > )
> > cat("GB =", round(sum(gc()[,2])/1024, 3), "\n")
> > #GB = 0.397
> > colnames(DF) = NULL
> > system.time(nm1<-colnames(DF, FALSE))
> > #   user  system elapsed
> > #  0.001   0.000   0.000
> > print(nm1)
> > #[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
> >
> > sessionInfo()
> > #R Under development (unstable) (2016-12-19 r71815)
> > #Platform: x86_64-pc-linux-gnu (64-bit)
> > #Running under: Debian GNU/Linux stretch/sid
> > #
> > #locale:
> > # [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> > # [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> > # [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> > # [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> > # [9] LC_ADDRESS=C   LC_TELEPHONE=C
> > #[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > #
> > #attached base packages:
> > #[1] stats graphics  grDevices utils datasets  methods   base  #
> > #
> > #loaded via a namespace (and not attached):
> > #[1] compiler_3.4.0
> 
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Re: [Rd] Definition of uintptr_t in Rinterface.h

[Laurent Gautier]

Thanks for looking at it. Having  HAVE_UINTPTR_T defined in Rconfig.h
should fix the issue. Will the fix make it to R-3.3.3 (if that point
release is planned, or R-3.3.2-patched), or will it only be with R-3.4 ?


L.

PS: I am forwarding a thank you note to the reporter of the problem on the
rpy2 issue tracker.


2016-12-29 10:55 GMT-05:00 Simon Urbanek :

> The problem is elsewhere - Rinterface.h guards the ultima-ratio fallback
> with HAVE_UINTPTR_T but that config flag is not exported in Rconfig.h.
> Should be now fixed in R-devel - please check if that works for you.
>
> Thanks,
> Simon
>
>
>
> > On Dec 26, 2016, at 11:25 PM, Laurent Gautier 
> wrote:
> >
> > Hi,
> >
> > I was recently pointed out that a definition in Rinterface.h can be
> conflicting
> > with a definition in stdint.h:
> >
> > /usr/include/R/Rinterface.h has:
> > typedef unsigned long uintptr_t;
> >
> > /usr/include/stdint.h has:
> > typedef unsigned int uintptr_t;
> > (when 32bit platform complete definition is:
> >
> > #if __WORDSIZE == 64
> > # ifndef __intptr_t_defined
> > typedef long intintptr_t;
> > #  define __intptr_t_defined
> > # endif
> > typedef unsigned long int   uintptr_t;
> > #else
> > # ifndef __intptr_t_defined
> > typedef int intptr_t;
> > #  define __intptr_t_defined
> > # endif
> > typedef unsigned intuintptr_t;
> > #endif
> >
> > )
> >
> > Is this expected ? Shouldn't R rely on the definition in stdint.h
> > rather than define its own ?
> >
> >
> > (report for the issue:
> > https://bitbucket.org/rpy2/rpy2/issues/389/failed-to-
> compile-with-python-360-on-32
> > )
> >
> >
> > Laurent
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
>

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Re: [Bioc-devel] TabixFileList() constructor broken in devel

[Robert Castelo]

hi Lori,

thanks for the clarification. if this is an intended change then i'd say 
the documentation needs to be updated since, as i showed in my email 
below, it currently says that for functions such as 'TabixFileList()' 
the input 'file' argument should be a 'TabixFile' instance and not a 
character vector.

this change also means the input is switching from a 'TabixFile' 
instance to a 'character' vector, so pipelines or packages doing calls 
to 'TabixFileList()' that have been passing 'TabixFile' instances as 
arguments will have to update those calls to pass a character vector.

  i'd suggest that if there's no good reason to switch, it would be 
safer to add the character vector as an additional possibility in the 
input argument 'file', just as with 'countTabix()', and minimize 
possible breaks of pipelines/packages using 'TabixFileList()'. i've 
encountered this problem because my own package VariantFiltering calls 
'TabixFileList()' although is not a big deal to fix it.

cheers,

robert.

On 28/12/2016 19:44, Shepherd, Lori wrote:
>
> Thank you for bringing this to our attention. There were some updates 
> made a few weeks ago to the behavior and input of 'TabixFileList()' . 
>  Its current implementation will work with a character vector as 
> input.  I will investigate further into why this change was made and 
> if it needs to be addressed.
>
>
> In the meantime:
>
> TabixFileList(tbx)
> will throw an ERROR, but you can still use the same file that was used 
> to create the TabixFile
> tbx <- open(TabixFile(fl, yieldSize=100))
> TabixFileList(fl)
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> *From:* Bioc-devel  on behalf of 
> Robert Castelo 
> *Sent:* Wednesday, December 28, 2016 11:50:58 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] TabixFileList() constructor broken in devel
> hi,
>
> the 'TabixFileList()' constructor in Rsamtools seems to be broken in 
> devel:
>
> library(Rsamtools)
> example(TabixFileList) ## which actually does not construct any
> 'TabixFileList'
> TabixFileList(tbx)
> Error in as.vector(x, "character") :
>cannot coerce type 'environment' to vector of type 'character'
>
> while in release this works fine:
>
> library(Rsamtools)
> example(TabixFileList) ## which actually does not construct any
> 'TabixFileList'
> TabixFileList(tbx)
> TabixFileList of length 1
> names(1): example.gtf.gz
>
> the man page has not changed between devel and release and the current
> description of the argument 'file' supports the use of a 'TabixFile'
> instance as input:
>
>  file: For TabixFile(), A character(1) vector to the tabix file
>path; can be remote (http://, ftp://). For �countTabix�, a
>character(1) or �TabixFile� instance. For others, a
>�TabixFile� instance.
>
> please find below my session information for the devel run.
>
> thanks!
>
> robert.
>
> sessionInfo()
> R Under development (unstable) (2016-11-17 r71661)
> Platform: x86_64-apple-darwin16.1.0 (64-bit)
> Running under: macOS Sierra 10.12.2
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats4parallel  stats graphics  grDevices utils datasets
> [8] methods   base
>
> other attached packages:
>   [1] Rsamtools_1.27.9  Biostrings_2.43.1 XVector_0.15.0
>   [4] GenomicRanges_1.27.17 GenomeInfoDb_1.11.6 IRanges_2.9.14
>   [7] S4Vectors_0.13.5  BiocGenerics_0.21.1 setwidth_1.0-4
> [10] colorout_1.1-0
>
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.21.0compiler_3.4.0 tools_3.4.0 BiocParallel_1.9.3
> [5] bitops_1.0-6
>
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Re: [Rd] Definition of uintptr_t in Rinterface.h

[Simon Urbanek]

The problem is elsewhere - Rinterface.h guards the ultima-ratio fallback with 
HAVE_UINTPTR_T but that config flag is not exported in Rconfig.h. Should be now 
fixed in R-devel - please check if that works for you.

Thanks,
Simon



> On Dec 26, 2016, at 11:25 PM, Laurent Gautier  wrote:
> 
> Hi,
> 
> I was recently pointed out that a definition in Rinterface.h can be 
> conflicting
> with a definition in stdint.h:
> 
> /usr/include/R/Rinterface.h has:
> typedef unsigned long uintptr_t;
> 
> /usr/include/stdint.h has:
> typedef unsigned int uintptr_t;
> (when 32bit platform complete definition is:
> 
> #if __WORDSIZE == 64
> # ifndef __intptr_t_defined
> typedef long intintptr_t;
> #  define __intptr_t_defined
> # endif
> typedef unsigned long int   uintptr_t;
> #else
> # ifndef __intptr_t_defined
> typedef int intptr_t;
> #  define __intptr_t_defined
> # endif
> typedef unsigned intuintptr_t;
> #endif
> 
> )
> 
> Is this expected ? Shouldn't R rely on the definition in stdint.h
> rather than define its own ?
> 
> 
> (report for the issue:
> https://bitbucket.org/rpy2/rpy2/issues/389/failed-to-compile-with-python-360-on-32
> )
> 
> 
> Laurent
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] IRanges findOverlaps and queryHits

[Hervé Pagès]

A couple more things about this: The Hits class is defined in the
S4Vectors package. The changes to the internals of the class happened
in BioC 3.3, almost 1 year ago. The NEWS file in S4Vectors has an entry
under "CHANGES IN VERSION 0.10.0" that describes these changes:

o Many changes to the Hits class:
  - Replace the old Hits class (where the hits had to be sorted by 
query)

with the SortedByQueryHits class.
  - A new Hits class where the hits can be in any order is 
re-introduced as

the parent of the SortedByQueryHits class.
  - The Hits() constructor gets the new 'sort.by.query' argument 
that is
FALSE by default. When 'sort.by.query' is set to TRUE, the 
constructor

returns a SortedByQueryHits instance instead of a Hits instance.
  - Bidirectional coercion is supported between Hits and 
SortedByQueryHits.
When going from Hits to SortedByQueryHits, the hits are sorted 
by query.

  - Add "c" method for Hits objects.
  - Rename Hits slots:
  queryHits -> from
  subjectHits -> to
  queryLength -> nLnode (nb of left nodes)
  subjectLength -> nRnode (nb of right nodes)
  - Add updateObject() method to update serialized Hits objects 
from old

(queryHits/subjectHits) to new (from/to) internal representation.
  - The "show" method for Hits objects now labels columns with 
from/to by

default and switches to queryHits/subjectHits labels only when the
object is a SortedByQueryHits object.
  - New accessors are provided that match the new slot names: 
from(), to(),

nLnode(), nRnode(). The old accessors (queryHits(), subjectHits(),
queryLength(), and subjectLength()) are just aliases for the new
accessors. Also countQueryHits() and countSubjectHits() are now 
aliases

for new countLnodeHits() and countRnodeHits().

Hope this helps,

H.


On 12/20/2016 12:43 PM, Michael Lawrence wrote:

Hi Nathan,

Direct slot access is strongly discouraged, for this very reason. Please
stick to using the accessor.

And yes, Hits was redefined in terms of a graph model last devel cycle.

Michael

On Tue, Dec 20, 2016 at 12:16 PM, Nathan Sheffield 
wrote:


Did the findOverlaps return object get a @queryHits slot removed recently?

I recently got this error running some of my code:

Error: no slot of name "queryHits" for this object of class
"SortedByQueryHits"

My workflow is basically,

fo = findOverlaps(...)
fo@queryHits

Using queryHits(fo) works, and using fo@queryHits to access it via slot
has always worked for me as well -- until this time. I couldn't find
anything in a changelog describing any changes into IRanges slots. Thought
someone here might be able to shed some light on that for me... does anyone
know what happened to the ability to access with @queryHits? Some relevant
sessionInfo():


sessionInfo()

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C LC_TIME=en_US.UTF-8
LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets
methods   base

other attached packages:
 [1] RGenomeUtils_0.01 BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99
BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [4] BSgenome_1.42.0 rtracklayer_1.34.1 Biostrings_2.42.0
 [7] XVector_0.14.0 LOLA_1.4.0 GenomicRanges_1.26.1
[10] GenomeInfoDb_1.10.1 IRanges_2.8.1 S4Vectors_0.12.0
[13] BiocGenerics_0.20.0 ggplot2_2.1.0 simpleCache_0.0.1
[16] extrafont_0.17 data.table_1.9.6 devtools_1.12.0
[19] project.init_0.0.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7plyr_1.8.4 bitops_1.0-6
 tools_3.3.0
 [5] zlibbioc_1.20.0testthat_1.0.2 digest_0.6.10
lattice_0.20-33
 [9] memoise_1.0.0  gtable_0.2.0 Matrix_1.2-6
 yaml_2.1.13
[13] Rttf2pt1_1.3.4 withr_1.0.2 stringr_1.1.0
roxygen2_5.0.1
[17] grid_3.3.0 Biobase_2.34.0 R6_2.2.0
 BiocParallel_1.8.1
[21] XML_3.98-1.4   reshape2_1.4.2 extrafontdb_1.0
magrittr_1.5
[25] GenomicAlignments_1.10.0   Rsamtools_1.26.1 scales_0.4.1
 SummarizedExperiment_1.4.0
[29] colorspace_1.3-0   stringi_1.1.2 RCurl_1.95-4.8
 munsell_0.4.3
[33] chron_2.3-47   crayon_1.3.2





-Nathan

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred