i have a piece of code where i'm using JuMPand Mambaand both of them export Model.
When i run the code first i get a warning : both Mamba and JuMP export "Model"; uses of it in module QuantumRelay must be qualified, therefore en Error is raised which is :
ERROR: UndefVarError: Model not defined
i need both of the packages Mamba for the MCMC simulation for simulationg draws from a probability distribution and the other for Linear programming.
you can find the package or the code on this link:
https://github.com/marouanehanhasse/Quantum_Relay
check the QuantumRelay module .
Apologizes in advance, because i couldn't post the code here since i'm still new on this community.
In Julia, the using and import keywords are used to bring bindings from another module into the current scope.
using M brings all exported bindings from M directly into scope. If M defines and exports a function my_function, you can use my_function directly in your code after the using statement.
import M imports only the binding M, so you will use M.my_function.
If you want to avoid name clashes as you have with Mamba and JuMP, import at least one of them, and then specify the qualified name, Mamba.Model, JuMP.Model. Subjectively, this also makes your code clearer to read for someone not familiar with both packages and what they export.
Details and other ways to use using and import can be found in the Julia documentation.
Related
Say I have a package that has 5 packages in Depends of the DESCRIPTION file and I have just realised it is not a good practice to have this many packages in Depends due to inevitable import clashes that are starting to pop up as the number of function imports are increasing. I'd like to move, say only package pkg to Imports but I have no clue which functions of pkg are being used in my package. Ideally, I should have unit tests with full coverage of the package source code and by simply removing pkg from the dependencies, I will identify the pkg-specific imports from the test errors of could not find function "foo". But unfortunately, I do not have that breadth of test coverage. I was wondering if there is a more efficient way than going through all the package code to identify these imports.
That is very straightforward. Change
Depends: pkgA, pkgB, pgC
to
Imports: pkgA, pkgB, pgC
and also add this to the NAMESPACE file:
import("pkgA")
import("pkgB")
import("pkgC")
which will globally import all exported symbols so you can continue as before.
You can also selectively import via
importFrom("pkgA", "func1", "func2", "func3")
and if you run R CMD check it will actually (very helpfully) tell you which functions need this. The second method is somewhat more precise but a little more work to set up.
And I don't think we have a tool to remove 'spurious imports'. Finding which imports may be unused may be something you have to check manually (but trying to remove one and seeing if it still builds + checks fine).
I know what a namespace is from other languages but in R I just cannot find a difference between the environment and namespace. Could anyone explain this since in the tutorials I have read (as The Art of R Programming and others) I just cannot find a distinction?
A namespace is something specific to a package. It is defined as a list of directive that allow you to import functions from other packages to be used locally or to export your functions and classes to be used in R.
So if you have created in your package a function called foo you will add to your namespace something like export(foo) to make your function usable.
If you want to import function from a specific package to use them in yours, you will add import(thePackage)
The environment is simply the space where you associate names to values. You can see it as a context in which you can evaluate functions and expressions.
I'm developing an R package which needs to use parallelisation as made available by the snowfall package. snowfall doesn't seem to import the same was as other packages like ggplot2, data.table, etc. I've included snowfall, rlecuyer, and snow in the description file, name space file, and as an import argument in the function itself. When I try to access this function, I get the following error:
Error in sfInit() : could not find function "setDefaultClusterOptions"
The sfInit function seems to have a nostart / nostop argument which it says is related to nested usage of sfInit but that doesn't seem to do the trick for me either.
The actual code itself uses an sfInit (which is where I get the error), some sfExports and sfLibrarys, and an sfLapply.
Possible solution:
It seems to work if I move snow from the import section to the depends section in the Desciption file. I don't know why though.
When you include a package in 'Depends' when one attaches your package they also attach the package on which your package Depends to their namespace.
This and other differences between Depends and Imports is explained well in other questions on this site.
If you look at {snowfall}'s DESCRIPTION you'll see that it Depends on {snow}. It is plausible that the authors of snowfall know something we don't and that {snow} has to be attached to the global search path in order to work. In fact that is the top caveat in the top answer to the question I linked above...
... if your package relies on a package A which itself "Depends" on
another package B, your package will likely need to attach A with a
"Depends directive.
This is because the functions in package A were written with the
expectation that package B and its functions would be attached to the
search() path.
So, in your case, it just so happens that all {snowfall} wants is {snow} and you happened to provide it. However, it appears the more correct behavior may be for you to Depend on {snowfall} directly.
setDefaultClusterOptions is a function from the snow package. You need to import that too.
I am working on a family of R packages, all of which share substantial common code which is housed in an internal package, lets call it myPackageUtilities. So I have several packages
myPackage1, myPackage2, etc...
All of these packages depend on every method in myPackageUtilities. For a real-world example, please see statnet on CRAN. Each dependent package, of course, has
Depends: myPackageUtilities
in its DESCRIPTION file.
My question is: In the R code for myPackage1, which of the following two techniques for accessing methods from myPackageUtilities is preferable:
Use ::: to access the methods in myPackageUtilities, or
Export everything from myPackageUtilities (e.g. by including exportPattern("^[^\\.]") in the NAMESPACE)?
Option 2 clutters the end-user's search path, but the R gurus recommend against using :::.
Follow-up question: If (2) is the better choice, is there a way to export everything using roxygen2?
Suppose we have a package called randomUtils and this package has a function called sd that calculates the Slytherin Defiance Quotient.
Now I write a package called spellbound. If spellbound Depends on randomUtils, then randomUtils::sd will be found in the search path and can conflict with calculating standard deviation.
If spellbound Imports randomUtils, however, then R will install randomUtils but will not load it when spellbound is loaded. Thus, the new version of sd can't be found on the search path, but can still be accessed by randomUtils::sd
With an ever growing body of contributed work on CRAN, it is becoming very important that we use Imports as much as possible so that we don't introduce unexpected behaviors by having conflicting function definitions.
An example of when I have used Depends: when writing the HydeNet package, I wanted the end user to be able to use the rjags package in concert with HydeNet. So I put rjags in Depends so that library (HydeNet) would loaf both packages. (In other words, put rjags on the search path.
Moral of the story, if you don't intend for the user to directly access the functions, it should go in Imports.
I am currently developing a plug-in for the R-Commander GUI. In this package I am using a great deal of other packages which I simply attached by using the Depends option in the description file.
I am however now switching them over to the Imports option and am experiencing some problems with it.
Because I want to use some functions not only internally in my own code, but also be able to print and use them in the script window of R Commander, I will also have to export them in the namespace.
Let's take for example the biclust package. This package has the following exports in its namespace:
# First a bunch of functions are exported (Note that the biclust function is not in here!)
export(drawHeatmap,drawHeatmap2,bubbleplot,...,heatmapBC)
# The classes are exported
exportClasses(BiclustMethod,Biclust,BCBimax,BCCC,BCXmotifs,BCSpectral,BCPlaid)
# Methods are exported
exportMethods(biclust,show,summary)
So when I library(biclust) in an R session, it works as intended, meaning I can use the biclust method/function in the R console.
Now this how my namespace file looks like (or at least the part of it relevant to this discussion)
# I select those functions I need and import them.
importFrom(biclust, drawHeatmap,...,biclustbarchart)
# I import all the classes
importClassesFrom(biclust,BiclustMethod,Biclust,BCBimax,BCCC,BCXmotifs,BCSpectral,BCPlaid)
# I import all the methods
importMethodsFrom(biclust,show,summary,biclust)
# I now export all of the previous again so I can use the doItAndPrint functionality in R Commander
export( drawHeatmap,...,biclustbarchart)
exportClasses(BiclustMethod,Biclust,BCBimax,BCCC,BCXmotifs,BCSpectral,BCPlaid)
exportMethods(biclust,show,summary)
However when I load in my own package now, it is not working as intended. While functions such as drawHeatmap are working, the biclust method/function can not be found.(Though I have clearly imported and exported the method.)
Seemingly the only way to get this working, is to put the biclust method also in the normal export() command.
export(biclust,drawHeatmap,...,biclustbarchart)
Could someone clarify what I am doing wrong or what is going on here? Why are the same exports working for the biclust package, but not for my own package?
The only description of your error is that "it is not working as intended", so the following is a little stab in the dark.
It's useful to distinguish between methods and the generics that they are associated with. Biclust makes available both, and they are tightly associated. importFrom(biclust, biclust) imports the generic and associated methods, importMethodsFrom(biclust, biclust) imports the biclust methods defined in the biclust package, and implicitly the generic(s) on which the methods are defined. These are functionally equivalent so far; I think the original intention of importMethodsFrom() was when pkgA defines a generic, pkgB defines methods on the generic, and pkgD wants to use the generic from pkgA and the methods on that generic defined in pkgA and pkgB -- import(pkgA, foo), importMethodsFrom(pkgB, foo).
On the other end, when you say exportMethods(foo), it instructs R to make foo methods defined in your package available for others to use. But there are no foo methods defined in your package, so nothing is exported (maybe this should generate an error, or the methods that you import should be exported again). On the other hand, export(foo) tells R to export the foo generic, which is available for export -- it's the symbol that you'd imported earlier. (You mention that you "put the biclust method also in the normal export()", but actually it is the generic (and any methods associated with it) available for export.) So exporting biclust, rather than methods defined on it, seems to be what you want to do.
Normally, I would say that importing and then re-exporting functions or generics defined in other packages is not the right thing to do -- biclust, not your package, provides and documents the generic, and biclust would probably belong in Depends: -- presumably, many other functions from biclust are typically used in conjunction with the generic. Perhaps your Rcommander GUI is an exception.
Even though Imports: implies additional work (in the NAMESPACE file), it is usually the case that packages belong as Imports: rather than Depends: -- it makes the code in your package much more robust (imported functions are found in the package name space, rather than on the search path that the user can easily modify) and reduces the likelihood that the user experiences name clashes between identical symbols defined in different packages.