Re: [Rd] Compatibility issues caused by new simplify argument in apply function
> Lukas Lehnert via R-devel
> on Fri, 22 May 2020 12:26:05 +0200 writes:
> Dear R Developers,
> the new simplify argument in apply causes that my package (hsdar) does
not
> pass the
> checks in R-devel.
> The workaround, Kurt Hornik send me, is working for the R-code:
> if("simplify" %in% names(formals(base::apply)))
> do something
> else
> do something else
> Unfortunately, I cannot conditionalize the man pages of the functions.
Why should you do that? In other words: Why change the
argument list of your function(s) ?
That \Sexpr{} does not work as a section is "obvious" (for some),
but I really don't see why you should change the argument list
or defaults of your hdara package functions at all.
Martin Maechler
ETH Zurich and R Core
> I get the message
> that "applySpeclib.Rd:12-14: Section \Sexpr is unrecognized and will be
> dropped" if I try to
> dynamically define the entire usage section. If I try to use \Sexpr
inside the
> \usage section,
> I get the following warning: "applySpeclib.Rd:13-15: Tag \Sexpr is
invalid in
> a \usage block"
> Does anybody have an idea how to proceed. The full code is available
below.
> Thanks
> Lukas
> *1. Code for full usage section:*
> ..
> \description{
> Apply function over all spectra or a subset of spectra in a
\code{Speclib}.
> }
> \Sexpr[echo=TRUE,results=rd,stage=install]{
> hsdar:::.applyInHelp1("Speclib", usage = TRUE)
> }
> \arguments{
> ..
> *Function .applyInHelp1*
> .applyInHelp1 <- function(fun_name, usage)
> {
> if (usage)
> {
> if ("simplify" %in% names(formals(base::apply)))
> {
> return(paste0("\\usage{\n",
> "\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...,
> simplify = TRUE)\n",
> "}"))
> } else {
> return(paste0("\\usage{\n",
> "\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...)
> \n",
> "}"))
> }
> } else {
> if ("simplify" %in% names(formals(base::apply)))
> {
> return("}\n\\item{simplify}{Currently ignored")
> } else {
> return("")
> }
> }
> }
> *2. Using \Sexpr inside the \usage block*
> \usage{
> \S4method{apply}{Speclib}(X, FUN, bySI = NULL, ...
> \Sexpr[echo=TRUE,results=rd,stage=install]{
> hsdar:::.applyInHelp2(usage = TRUE)
> }
> )
> }
> *Function .applyInHelp2*
> .applyInHelp2 <- function(usage)
> {
> if (usage)
> {
> if ("simplify" %in% names(formals(base::apply)))
> {
> return(", simplify = TRUE)")
> }
> } else {
> if ("simplify" %in% names(formals(base::apply)))
> {
> return("}\n\\item{simplify}{Currently ignored")
> } else {
> return("")
> }
> }
> }
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Re: [Rd] Compatibility issues caused by new simplify argument in apply function
I am sorry for being not specific enough. Both of you were right with your
guess how the initial problem looked like.
I followed the suggestion of Henrik and at least on my computer it seems to
work (sometimes solutions are much easier than you think). Let's see what CRAN
tells me...
Thank you for your time and thinking about the problem!
Best
Lukas
Am Freitag, 22. Mai 2020, 17:47:00 CEST schrieb Henrik Bengtsson:
> Interesting problem. I'm very rusty on S4 but would one solution be
> to, already now, add 'simplify = TRUE' to the S4 method and document
> it;
>
> setMethod("apply", signature(X = "Speclib"),
> function(X,
>FUN,
>bySI = NULL,
>...,
>simplify = TRUE) {
>
> ?
>
> Henrik
>
> On Fri, May 22, 2020 at 6:26 AM Duncan Murdoch
wrote:
> > You didn't explained what the error is. This is what it looks like to
> > me, but I'm probably wrong in some details:
> >
> > 1. R-devel added an argument to the apply() function, so the header has
> > changed from
> >
> >function (X, MARGIN, FUN, ...)
> >
> > to
> >
> >function(X, MARGIN, FUN, ..., simplify = TRUE)
> >
> > 2. Your package converted the function apply() to an S4 generic.
> >
> > 3. Now the signatures of your methods for this generic need to have the
> > simplify argument, but if you do that, they won't work in previous
> > versions of R.
> >
> > You'd like to have conditional code and documentation to depend on the
> > version of R.
> >
> > Is that all correct?
> >
> > I don't think it's possible, for the reasons you found. Certainly you
> > can have conditional code, but the docs are going to fail.
> >
> > One thing that might work is in versions of R before this change, export
> > your own version of apply, with the change in place, i.e.
> >
> > if(!("simplify" %in% names(formals(base::apply
> >
> >apply <- function(X, MARGIN, FUN, ..., simplify = TRUE) {
> >
> > base::apply(X, MARGIN, FUN, ...)
> >
> >}
> >
> > and then conditionally export "apply" in these old versions. Then your
> > docs could match the new version everywhere.
> >
> > Another thing is to maintain two versions of your package, one for R
> > versions before the change, another for versions after the change. Add
> > appropriate entries in the DESCRIPTION file, e.g.
> >
> > Depends: R (> 4.0)
> >
> > Another is to argue with R Core that this change to a really old
> > function is too hard to accommodate, and they should back it out, maybe
> > by making a new function with the new signature.
> >
> > Or you could make a new function with the old signature, and use that
> > instead of apply().
> >
> > Duncan Murdoch
> >
> > On 22/05/2020 6:26 a.m., Lukas Lehnert via R-devel wrote:
> > > Dear R Developers,
> > >
> > > the new simplify argument in apply causes that my package (hsdar) does
> > > not
> > > pass the
> > > checks in R-devel.
> > >
> > > The workaround, Kurt Hornik send me, is working for the R-code:
> > > if("simplify" %in% names(formals(base::apply)))
> > >
> > > do something
> > >
> > > else
> > >
> > > do something else
> > >
> > > Unfortunately, I cannot conditionalize the man pages of the functions. I
> > > get the message
> > > that "applySpeclib.Rd:12-14: Section \Sexpr is unrecognized and will be
> > > dropped" if I try to
> > > dynamically define the entire usage section. If I try to use \Sexpr
> > > inside the \usage section,
> > > I get the following warning: "applySpeclib.Rd:13-15: Tag \Sexpr is
> > > invalid in a \usage block"
> > >
> > > Does anybody have an idea how to proceed. The full code is available
> > > below.
> > >
> > > Thanks
> > >
> > > Lukas
> > >
> > >
> > > *1. Code for full usage section:*
> > > ..
> > > \description{
> > > Apply function over all spectra or a subset of spectra in a
> > > \code{Speclib}.
> > > }
> > >
> > > \Sexpr[echo=TRUE,results=rd,stage=install]{
> > >
> > >hsdar:::.applyInHelp1("Speclib", usage = TRUE)
> > >
> > > }
> > >
> > > \arguments{
> > > ..
> > >
> > > *Function .applyInHelp1*
> > > .applyInHelp1 <- function(fun_name, usage)
> > > {
> > >
> > >if (usage)
> > >{
> > >
> > > if ("simplify" %in% names(formals(base::apply)))
> > > {
> > >
> > >return(paste0("\\usage{\n",
> > >
> > > "\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN,
> > > ...,
> > >
> > > simplify = TRUE)\n",
> > >
> > > "}"))
> > >
> > > } else {
> > >
> > >return(paste0("\\usage{\n",
> > >
> > > "\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN,
> > > ...)
> > >
> > > \n",
> > >
> > > "}"))
> > >
> > > }
> > >
> > >} else {
> > >
> > > if ("simplify" %in% names(formals(base::apply)))
> > > {
> > >
> > >
Re: [Rd] Compatibility issues caused by new simplify argument in apply function
On 22/05/2020 11:47 a.m., Henrik Bengtsson wrote:
Interesting problem. I'm very rusty on S4 but would one solution be
to, already now, add 'simplify = TRUE' to the S4 method and document
it;
setMethod("apply", signature(X = "Speclib"),
function(X,
FUN,
bySI = NULL,
...,
simplify = TRUE) {
?
Yes, that sounds like an ideal solution. The docs can say it is ignored
in old versions and passed on in new ones.
Duncan Murdoch
Henrik
On Fri, May 22, 2020 at 6:26 AM Duncan Murdoch wrote:
You didn't explained what the error is. This is what it looks like to
me, but I'm probably wrong in some details:
1. R-devel added an argument to the apply() function, so the header has
changed from
function (X, MARGIN, FUN, ...)
to
function(X, MARGIN, FUN, ..., simplify = TRUE)
2. Your package converted the function apply() to an S4 generic.
3. Now the signatures of your methods for this generic need to have the
simplify argument, but if you do that, they won't work in previous
versions of R.
You'd like to have conditional code and documentation to depend on the
version of R.
Is that all correct?
I don't think it's possible, for the reasons you found. Certainly you
can have conditional code, but the docs are going to fail.
One thing that might work is in versions of R before this change, export
your own version of apply, with the change in place, i.e.
if(!("simplify" %in% names(formals(base::apply
apply <- function(X, MARGIN, FUN, ..., simplify = TRUE) {
base::apply(X, MARGIN, FUN, ...)
}
and then conditionally export "apply" in these old versions. Then your
docs could match the new version everywhere.
Another thing is to maintain two versions of your package, one for R
versions before the change, another for versions after the change. Add
appropriate entries in the DESCRIPTION file, e.g.
Depends: R (> 4.0)
Another is to argue with R Core that this change to a really old
function is too hard to accommodate, and they should back it out, maybe
by making a new function with the new signature.
Or you could make a new function with the old signature, and use that
instead of apply().
Duncan Murdoch
On 22/05/2020 6:26 a.m., Lukas Lehnert via R-devel wrote:
Dear R Developers,
the new simplify argument in apply causes that my package (hsdar) does not
pass the
checks in R-devel.
The workaround, Kurt Hornik send me, is working for the R-code:
if("simplify" %in% names(formals(base::apply)))
do something
else
do something else
Unfortunately, I cannot conditionalize the man pages of the functions. I get
the message
that "applySpeclib.Rd:12-14: Section \Sexpr is unrecognized and will be
dropped" if I try to
dynamically define the entire usage section. If I try to use \Sexpr inside the
\usage section,
I get the following warning: "applySpeclib.Rd:13-15: Tag \Sexpr is invalid in
a \usage block"
Does anybody have an idea how to proceed. The full code is available below.
Thanks
Lukas
*1. Code for full usage section:*
..
\description{
Apply function over all spectra or a subset of spectra in a \code{Speclib}.
}
\Sexpr[echo=TRUE,results=rd,stage=install]{
hsdar:::.applyInHelp1("Speclib", usage = TRUE)
}
\arguments{
..
*Function .applyInHelp1*
.applyInHelp1 <- function(fun_name, usage)
{
if (usage)
{
if ("simplify" %in% names(formals(base::apply)))
{
return(paste0("\\usage{\n",
"\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...,
simplify = TRUE)\n",
"}"))
} else {
return(paste0("\\usage{\n",
"\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...)
\n",
"}"))
}
} else {
if ("simplify" %in% names(formals(base::apply)))
{
return("}\n\\item{simplify}{Currently ignored")
} else {
return("")
}
}
}
*2. Using \Sexpr inside the \usage block*
\usage{
\S4method{apply}{Speclib}(X, FUN, bySI = NULL, ...
\Sexpr[echo=TRUE,results=rd,stage=install]{
hsdar:::.applyInHelp2(usage = TRUE)
}
)
}
*Function .applyInHelp2*
.applyInHelp2 <- function(usage)
{
if (usage)
{
if ("simplify" %in% names(formals(base::apply)))
{
return(", simplify = TRUE)")
}
} else {
if ("simplify" %in% names(formals(base::apply)))
{
return("}\n\\item{simplify}{Currently ignored")
} else {
return("")
}
}
}
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Re: [Rd] Compatibility issues caused by new simplify argument in apply function
Interesting problem. I'm very rusty on S4 but would one solution be
to, already now, add 'simplify = TRUE' to the S4 method and document
it;
setMethod("apply", signature(X = "Speclib"),
function(X,
FUN,
bySI = NULL,
...,
simplify = TRUE) {
?
Henrik
On Fri, May 22, 2020 at 6:26 AM Duncan Murdoch wrote:
>
> You didn't explained what the error is. This is what it looks like to
> me, but I'm probably wrong in some details:
>
> 1. R-devel added an argument to the apply() function, so the header has
> changed from
>
>function (X, MARGIN, FUN, ...)
>
> to
>
>function(X, MARGIN, FUN, ..., simplify = TRUE)
>
> 2. Your package converted the function apply() to an S4 generic.
>
> 3. Now the signatures of your methods for this generic need to have the
> simplify argument, but if you do that, they won't work in previous
> versions of R.
>
> You'd like to have conditional code and documentation to depend on the
> version of R.
>
> Is that all correct?
>
> I don't think it's possible, for the reasons you found. Certainly you
> can have conditional code, but the docs are going to fail.
>
> One thing that might work is in versions of R before this change, export
> your own version of apply, with the change in place, i.e.
>
> if(!("simplify" %in% names(formals(base::apply
>apply <- function(X, MARGIN, FUN, ..., simplify = TRUE) {
> base::apply(X, MARGIN, FUN, ...)
>}
>
> and then conditionally export "apply" in these old versions. Then your
> docs could match the new version everywhere.
>
> Another thing is to maintain two versions of your package, one for R
> versions before the change, another for versions after the change. Add
> appropriate entries in the DESCRIPTION file, e.g.
>
> Depends: R (> 4.0)
>
> Another is to argue with R Core that this change to a really old
> function is too hard to accommodate, and they should back it out, maybe
> by making a new function with the new signature.
>
> Or you could make a new function with the old signature, and use that
> instead of apply().
>
> Duncan Murdoch
>
>
>
> On 22/05/2020 6:26 a.m., Lukas Lehnert via R-devel wrote:
> > Dear R Developers,
> >
> > the new simplify argument in apply causes that my package (hsdar) does not
> > pass the
> > checks in R-devel.
> >
> > The workaround, Kurt Hornik send me, is working for the R-code:
> > if("simplify" %in% names(formals(base::apply)))
> > do something
> > else
> > do something else
> >
> > Unfortunately, I cannot conditionalize the man pages of the functions. I get
> > the message
> > that "applySpeclib.Rd:12-14: Section \Sexpr is unrecognized and will be
> > dropped" if I try to
> > dynamically define the entire usage section. If I try to use \Sexpr inside
> > the
> > \usage section,
> > I get the following warning: "applySpeclib.Rd:13-15: Tag \Sexpr is invalid
> > in
> > a \usage block"
> >
> > Does anybody have an idea how to proceed. The full code is available below.
> >
> > Thanks
> >
> > Lukas
> >
> >
> > *1. Code for full usage section:*
> > ..
> > \description{
> > Apply function over all spectra or a subset of spectra in a \code{Speclib}.
> > }
> >
> > \Sexpr[echo=TRUE,results=rd,stage=install]{
> >hsdar:::.applyInHelp1("Speclib", usage = TRUE)
> > }
> >
> > \arguments{
> > ..
> >
> > *Function .applyInHelp1*
> > .applyInHelp1 <- function(fun_name, usage)
> > {
> >if (usage)
> >{
> > if ("simplify" %in% names(formals(base::apply)))
> > {
> >return(paste0("\\usage{\n",
> > "\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...,
> > simplify = TRUE)\n",
> > "}"))
> > } else {
> >return(paste0("\\usage{\n",
> > "\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...)
> > \n",
> > "}"))
> > }
> >} else {
> > if ("simplify" %in% names(formals(base::apply)))
> > {
> >return("}\n\\item{simplify}{Currently ignored")
> > } else {
> >return("")
> > }
> >}
> > }
> >
> >
> > *2. Using \Sexpr inside the \usage block*
> > \usage{
> > \S4method{apply}{Speclib}(X, FUN, bySI = NULL, ...
> > \Sexpr[echo=TRUE,results=rd,stage=install]{
> >hsdar:::.applyInHelp2(usage = TRUE)
> > }
> > )
> > }
> >
> >
> > *Function .applyInHelp2*
> > .applyInHelp2 <- function(usage)
> > {
> >if (usage)
> >{
> > if ("simplify" %in% names(formals(base::apply)))
> > {
> >return(", simplify = TRUE)")
> > }
> >} else {
> > if ("simplify" %in% names(formals(base::apply)))
> > {
> >return("}\n\\item{simplify}{Currently ignored")
> > } else {
> >return("")
> > }
> >}
> > }
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> __
>
Re: [Rd] Compatibility issues caused by new simplify argument in apply function
You didn't explained what the error is. This is what it looks like to
me, but I'm probably wrong in some details:
1. R-devel added an argument to the apply() function, so the header has
changed from
function (X, MARGIN, FUN, ...)
to
function(X, MARGIN, FUN, ..., simplify = TRUE)
2. Your package converted the function apply() to an S4 generic.
3. Now the signatures of your methods for this generic need to have the
simplify argument, but if you do that, they won't work in previous
versions of R.
You'd like to have conditional code and documentation to depend on the
version of R.
Is that all correct?
I don't think it's possible, for the reasons you found. Certainly you
can have conditional code, but the docs are going to fail.
One thing that might work is in versions of R before this change, export
your own version of apply, with the change in place, i.e.
if(!("simplify" %in% names(formals(base::apply
apply <- function(X, MARGIN, FUN, ..., simplify = TRUE) {
base::apply(X, MARGIN, FUN, ...)
}
and then conditionally export "apply" in these old versions. Then your
docs could match the new version everywhere.
Another thing is to maintain two versions of your package, one for R
versions before the change, another for versions after the change. Add
appropriate entries in the DESCRIPTION file, e.g.
Depends: R (> 4.0)
Another is to argue with R Core that this change to a really old
function is too hard to accommodate, and they should back it out, maybe
by making a new function with the new signature.
Or you could make a new function with the old signature, and use that
instead of apply().
Duncan Murdoch
On 22/05/2020 6:26 a.m., Lukas Lehnert via R-devel wrote:
Dear R Developers,
the new simplify argument in apply causes that my package (hsdar) does not
pass the
checks in R-devel.
The workaround, Kurt Hornik send me, is working for the R-code:
if("simplify" %in% names(formals(base::apply)))
do something
else
do something else
Unfortunately, I cannot conditionalize the man pages of the functions. I get
the message
that "applySpeclib.Rd:12-14: Section \Sexpr is unrecognized and will be
dropped" if I try to
dynamically define the entire usage section. If I try to use \Sexpr inside the
\usage section,
I get the following warning: "applySpeclib.Rd:13-15: Tag \Sexpr is invalid in
a \usage block"
Does anybody have an idea how to proceed. The full code is available below.
Thanks
Lukas
*1. Code for full usage section:*
..
\description{
Apply function over all spectra or a subset of spectra in a \code{Speclib}.
}
\Sexpr[echo=TRUE,results=rd,stage=install]{
hsdar:::.applyInHelp1("Speclib", usage = TRUE)
}
\arguments{
..
*Function .applyInHelp1*
.applyInHelp1 <- function(fun_name, usage)
{
if (usage)
{
if ("simplify" %in% names(formals(base::apply)))
{
return(paste0("\\usage{\n",
"\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...,
simplify = TRUE)\n",
"}"))
} else {
return(paste0("\\usage{\n",
"\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...)
\n",
"}"))
}
} else {
if ("simplify" %in% names(formals(base::apply)))
{
return("}\n\\item{simplify}{Currently ignored")
} else {
return("")
}
}
}
*2. Using \Sexpr inside the \usage block*
\usage{
\S4method{apply}{Speclib}(X, FUN, bySI = NULL, ...
\Sexpr[echo=TRUE,results=rd,stage=install]{
hsdar:::.applyInHelp2(usage = TRUE)
}
)
}
*Function .applyInHelp2*
.applyInHelp2 <- function(usage)
{
if (usage)
{
if ("simplify" %in% names(formals(base::apply)))
{
return(", simplify = TRUE)")
}
} else {
if ("simplify" %in% names(formals(base::apply)))
{
return("}\n\\item{simplify}{Currently ignored")
} else {
return("")
}
}
}
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[Rd] Compatibility issues caused by new simplify argument in apply function
Dear R Developers,
the new simplify argument in apply causes that my package (hsdar) does not
pass the
checks in R-devel.
The workaround, Kurt Hornik send me, is working for the R-code:
if("simplify" %in% names(formals(base::apply)))
do something
else
do something else
Unfortunately, I cannot conditionalize the man pages of the functions. I get
the message
that "applySpeclib.Rd:12-14: Section \Sexpr is unrecognized and will be
dropped" if I try to
dynamically define the entire usage section. If I try to use \Sexpr inside the
\usage section,
I get the following warning: "applySpeclib.Rd:13-15: Tag \Sexpr is invalid in
a \usage block"
Does anybody have an idea how to proceed. The full code is available below.
Thanks
Lukas
*1. Code for full usage section:*
..
\description{
Apply function over all spectra or a subset of spectra in a \code{Speclib}.
}
\Sexpr[echo=TRUE,results=rd,stage=install]{
hsdar:::.applyInHelp1("Speclib", usage = TRUE)
}
\arguments{
..
*Function .applyInHelp1*
.applyInHelp1 <- function(fun_name, usage)
{
if (usage)
{
if ("simplify" %in% names(formals(base::apply)))
{
return(paste0("\\usage{\n",
"\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...,
simplify = TRUE)\n",
"}"))
} else {
return(paste0("\\usage{\n",
"\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN, ...)
\n",
"}"))
}
} else {
if ("simplify" %in% names(formals(base::apply)))
{
return("}\n\\item{simplify}{Currently ignored")
} else {
return("")
}
}
}
*2. Using \Sexpr inside the \usage block*
\usage{
\S4method{apply}{Speclib}(X, FUN, bySI = NULL, ...
\Sexpr[echo=TRUE,results=rd,stage=install]{
hsdar:::.applyInHelp2(usage = TRUE)
}
)
}
*Function .applyInHelp2*
.applyInHelp2 <- function(usage)
{
if (usage)
{
if ("simplify" %in% names(formals(base::apply)))
{
return(", simplify = TRUE)")
}
} else {
if ("simplify" %in% names(formals(base::apply)))
{
return("}\n\\item{simplify}{Currently ignored")
} else {
return("")
}
}
}
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