I would like to know of some packages that make use of assignInMyNamespace and what it's used for, if it is even advisable to use this function in production code. The help page gives the following information:
assignInMyNamespace is intended to be called from functions within a package, and chooses the namespace as the environment of the function calling it.
However it also gives the following warning about assignInNamespace:
assignInNamespace should not be used in final code, and will in future throw an error if called from a package. Already certain uses are disallowed.
Presumably this is because packages shouldn't ever try to change the namespaces of other packages, which is why the warning doesn't apply to assignInMyNamespace. Is this true?
NB: I am developing a package with an unexported testing function that allows any unexported function in the package to be temporarily replaced with one that saves its inputs and outputs. I am also considering such a technique for switching between memoised / un-memoised versions of functions.
EDIT: In practise, assignInMyNamespace only changes unexported functions - not 'any function in the package' as previously stated. I only realised this recently, and it's actually thrown a spanner in the works with the package I'm developing. Therefore I would also be very interested to know if there is a solution to the problem that works across both exported and unexported functions during package use.
Related
Currently I have in my package DESCRIPTION, a dependency on dbplyr:
Imports:
dbplyr,
dplyr
dbplyr is useful almost solely because of the S3 methods it defines: https://github.com/tidyverse/dbplyr/blob/main/NAMESPACE. The actual functions you call to use dbplyr are almost entirely from dplyr.
By putting dbplyr in my Imports, it should automatically get loaded, but not attached, which should be enough to register its S3 methods: https://r-pkgs.org/dependencies-mindset-background.html#sec-dependencies-attach-vs-load.
This seems to work fine, but whenever I R CMD check, it tells me:
N checking dependencies in R code (10.8s)
Namespace in Imports field not imported from: ‘dbplyr’
All declared Imports should be used.
Firstly, why does R CMD check even check this, considering that it often makes sense to load packages without importing them. Secondly, how am I supposed to satisfy R CMD check without loading things into my namespace that I don't want or need?
I am pretty sure two of your assumptions are false.
First, putting Imports: dbplyr into your DESCRIPTION file won't load it, so its methods won't be loaded from that alone. Basically the Imports field in the DESCRIPTION file just guarantees that dbplyr is available to be loaded when requested. If you import something via the NAMESPACE file, that will cause it to be loaded. If you evaluate dbplyr::something that will cause it to be loaded. Executing loadNamespace("dbplyr") is another way, and there are a few others. You may also load some other package that loads it.
Second, I think you have misinterpreted the error message. It isn't saying that you loaded it without importing it (though it would complain about that too), it is saying that it can't detect any use of it in your package, so maybe it shouldn't be a requirement for installing your package.
Unfortunately, the code to detect uses is fallible, so it sometimes misses uses. Examples I've heard about are:
if the package is only used in the default value for a function argument. This has been fixed in R-devel.
if the package is only used during the build to construct some object, e.g. code like someclass <- R6::R6Class( ... ) needs R6, but the check code won't see it because it looks at someclass, not at the source code that created it.
if the use of the package is hidden by specifying the name of the package in a character variable.
if the need for the package is indirect, e.g. you need to use ggplot2::geom_hex. That needs the hexbin package, but ggplot2 only declares it as "Suggested".
These examples come from this discussion: https://github.com/hadley/r-pkgs/issues/828#issuecomment-1421353457 .
The recommended workaround there is to create an object that refers to the imported package explicitly, e.g. putting the line
dummy_r6 <- function() R6::R6Class
into your package is enough to suppress the note without actually loading R6. (It will be loaded if you ever call this function.)
However, your requirement is stronger: you do need to make sure dbplyr is loaded if you want its methods to be used. I'd put something in your .onLoad() function that triggers the load. For example,
.onLoad <- function(lib, pkg) {
# Make sure the dbplyr methods are loaded
loadNamespace("dbplyr")
}
EDITED TO ADD: As pointed out in the comments, there's a bug in the check code that means it won't detect this as being a use of dbplyr. You really need to do both things, e.g.
.onLoad <- function(lib, pkg) {
# Make sure the dbplyr methods are loaded
loadNamespace("dbplyr")
# Work around bug in code checking in R 4.2.2 for use of packages
dummy <- function() dbplyr::across_apply_fns
}
The function used in the dummy construction is arbitrary; it probably doesn't even need to exist, but I chose one that does.
I created a local package with personal functions to be easily used within R. One of these is aimed to be used in the lidR package within a wrapper function (i.e. grid_metrics). For this reason I took the scheme of this script as a reference, exporting both the long name (e.g. my_metrics(param1, param2,...)) and the lazy one (e.g. .my_metrics), because I really like its ease of use.
Nevertheless, if I load my package and then call the lazy function
library(mypackage)
test = grid_metrics(las, .my_metrics, 20)
it does not work, so I have to load in memory the function by running its code from the file. At this stage, I can use it in both forms.
Within the NAMESPACE file I can see that both forms are exported so my last guess is that this might be related somehow to lazyeval but I don't get how.
It seems that the problem is related to the DESCRIPTION section in which the lidR package was included. Since when I moved from Imports to Depends the issue is solved.
In R, I'm getting an error "could not find function...". The function is present inside the package. Still when I run the package, getting the error.
I am getting this error in the ChainLadder package while running MackChainLadderFunctions.R. For example, the function checktriangle is present inside the package in Chainladder.R. Still, R is not able to recognize the function or call the function.
Two problems here.
function names are case-sensitive (checkTriangle, not checktriangle)
checkTriangle is not exported from the package (i.e., it's a private function intended for use within the package only), so you need ::: to access it ... try ChainLadder:::checkTriangle.
Using private functions is "at your own risk/programmer beware"; private functions are undocumented, may change in future versions, etc.. If you can find a way to do what you need to do with public functions, that is generally preferred.
AFAICT you're running into this problem because you're trying to source() (or cut-and-paste) package code in your R session. This shouldn't happen if you load the package with library("ChainLadder") and use the public functions (if it does, please edit your question to give a little more context about how you're using the package ...)
I created a package with some functions which are helpful at my company. Recently, I restructered the package such that there are helper functions which need not to be accessible for everyone, but are called internally from other (exported) functions of the package. These helper functions are not exported to the namespace (no #' #export in the respective .R files).
Now, when I call one of the "major" (exported) functions, I get the error message (no real function names):
Error in major_function() : could not find function "helper_function"
Im fairly new in building packages, but from what I understood so far (from https://cran.r-project.org/web/packages/roxygen2/vignettes/namespace.html), it should neither be necessary to export the helper functions, nor to add #' importFrom my_package helper_function to the .R file of the major function.
When I tried this, it actually produced errors when checking the package. I also tried to call the helper functions with my_package:::helper_function, but this lead to the note that it should almost never be necessary to call functions from the same package like this.
Maybe useful information:
The error occurs only when I call a major_function_1 which internally calls major_function_2 which calls a helper_function.
I think there is more to your problem than what you state. As long as all your functions are defined in the same namespace (this also means that all your functions need to live in .R files in the same folder), the calling function should find the helper-functions accordingly.
I suspect you have your helper functions nested in some way, and that is causing the problem.
I recommend to recheck your namespace structure, or post a simplistic outline of your package here.
Another reason that could come to mind, is that you do not export your 'mayor_function2' in your NAMESPACE-file in your package root (maybe you have not recompiled the Roxygen documentation generating this file), and additionally have a local shadow of the the calling function 'mayor_function1'. Try to check this and rerun from a clean compile.
I would like to add an idiosyncratically modified function to package written by someone else, with an R Script, i.e. just for the session, not permanently. The specific example is, let's say, bls_map_county2() added to the blscrapeR package. bls_map_county2 is just a copy of the bls_map_county() function with an added ... argument, for purposes of changing a few of the map drawing parameters. I have not yet inserted the additional parameters. Running the function as-is, I get the error:
Error in BLS_map_county(map_data = df, fill_rate = "unemployed_rate", :
could not find function "geom_map"
I assume this is because my function does not point to the blscrapeR namespace. How do I assign my function to the (installed, loaded) blscrapeR namespace, and is there anything else I need to do to let it access whatever machinery from the package it requires?
When I am hacking on a function in a particular package that in turn calls other functions I often use this form after the definition:
mod_func <- function( args) {body hacked}
environment(mod_func) <- environment(old_func)
But I think the function you might really want is assignInNamespace. These methods will allow the access to non-exported functions in loaded packages. They will not however succeed if the package is not loaded. So you may want to have a stopifnot() check surrounding require(pkgname).
There are two parts to this answer - first a generic answer to your question, and 2nd a specific answer for the particular function that you reference, in which the problem is something slightly different.
1) generic solution to accessing internal functions when you edit a package function
You should already have access to the package namespace, since you loaded it, so it is only the unexported functions that will give you issues.
I usually just prepend the package name with the ::: operator to the non exported functions. I.e., find every instance of a call to some_internal_function(), and replace it with PackageName:::some_internal_function(). If there are several different internal functions called within the function you are editing, you may need to do this a few times for each of the offending function calls.
The help page for ::: does contain these warnings
Beware -- use ':::' at your own risk!
and
It is typically a design mistake to use ::: in your code since the
corresponding object has probably been kept internal for a good
reason. Consider contacting the package maintainer if you feel the
need to access the object for anything but mere inspection.
But for what you are doing, in terms of temporarily hacking another function from the same package for your own use, these warnings should be safe to ignore (at you own risk, of course - as it says in the manual)
2) In the case of blscrapeR ::bls_map_county()
The offending line in this case is
ggplot2::ggplot() + geom_map(...
in which the package writers have specified the ggplot2 namespace for ggplot(), but forgotten to do so for geom_map() which is also part of ggplot2 (and not an internal function in blscrapeR ).
In this case, just load ggplot2, and you should be good to go.
You may also consider contacting the package maintainer to inform them of this error.