On 5 Dec 2024, at 11:41, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
On 2024-12-05 3:06 a.m., Adelchi Azzalini wrote:
Thanks, Duncan, for the kind advice.
In my understanding, this is what I have done (or I tried to do). My code is as follows:
opt.methods <- c("Nelder-Mead", "BFGS", "nlminb")
if(requireNamespace("nloptr", quietly = TRUE)) {
nloptr.methods <- c("newuoa", "bobyqa", "cobyla")
if(opt.method %in% nloptr.methods) require(nloptr, quietly=TRUE)
You shouldn't use `require(nloptr, quietly=TRUE)`. That puts it on the search list, and packages should generally not modify the search list.
Just before this in your code, you know that nloptr is loaded. You don't know if it's on the search list or not, and that shouldn't matter.
opt.methods <- c(opt.methods, nloptr.methods)
}
<skip>
if(opt.method %in% nloptr.methods) {
pos <- match("package:nloptr", search())
nloptr.method <- get(paste("nloptr", opt.method, sep="::"), pos=pos)
opt <- nloptr.method(<args>)
}
The code above relies on having nloptr on the search list, and you don't know that, so you'll need a different way to set nloptr.method. Another problem is that at this point you don't know if nloptr is loaded or not, because the requireNamespace() call above might have returned FALSE.
What I would do is to set nloptr.method in the code block above, i.e. change the first block to
opt.methods <- c("Nelder-Mead", "BFGS", "nlminb")
if(requireNamespace("nloptr", quietly = TRUE)) {
nloptr.methods <- c("newuoa", "bobyqa", "cobyla")
if(opt.method %in% nloptr.methods)
nloptr.method <- get(opt.method,
envir = loadNamespace("nloptr"))
} else
nloptr.method <- function(...) stop("this optimization needs the nloptr package.")
The second block could then be simplified to
if(opt.method %in% nloptr.methods)
opt <- nloptr.method(<args>)
In the DESCRIPTION file there is
Suggests: ggplot2, survival, nloptr
However, when I run ?R CMD check <etc>?, I get the following message
* checking package dependencies ... ERROR
Namespace dependency missing from DESCRIPTION Imports/Depends entries: ?nloptr?
See section ?The DESCRIPTION file? in the ?Writing R Extensions?
manual.
* DONE
And - admittedly - I have no idea about how to insert appropriate import statements in NAMESPACE.
You shouldn't need to do that.
Duncan Murdoch
On 4 Dec 2024, at 20:56, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
On 2024-12-04 1:25 p.m., Adelchi Azzalini wrote:
Hi. I am working on the development of an existing package (smof, on CRAN). My current aim is widen the list of possible optimizers from which the user can select one method for optimizing a certain task. Well-known possibilities within the base package are optim (with various options) and nlminb. Besides these, I am thinking of including also those of package nloptr, but without forcing users to install this package which perhaps they don't need for other purposes. Hence, I would like to import nloptr only if it is available on the user system; it not, I can just confine the list of optimizers to optim and nlminb.
This idea implies a sort of ?conditional import? of nloptr. Is this possible? Section 1.1.3.1 "Suggested packages" of
https://translation.r-project.org/man/R-exts/R-exts-ko.html#Suggested-packages
seems to hint at such a possibility. See the use of requireNamespace in the second paragraph.
After elaborating along this line, I packaged my code, with nloptr listed on the line Suggests of DESCRIPTION. However this attempt failed a the ?R CMD check ? stage with message
Namespace dependency missing from DESCRIPTION Imports/Depends entries: ?nloptr?
In addition, I have no idea of how to declare a "conditional import? in NAMESPACE.
Is this idea of ?conditional import? totally unfeasible, then?
The usual way to do this is to list the package in Suggests, and then wrap any use of it in `if (requireNamespace("pkg")) { ... }` blocks. This doesn't quite import the functions, you would need to use the `pkg::fn` syntax to access the functions.
If you really want to simulate importing so that you don't need the `pkg::` prefix, you could do it this way: In the `.onLoad` function of your package, you would have code like
if (requireNamespace("pkg")) {
foo <- pkg::foo
bar <- pkg::bar
} else {
foo <- stub
bar <- stub
}
where `stub` is a function that says "you need `pkg` to use this function".
Duncan Murdoch