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no visible global function definition for ‘median’
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Closed 6 years ago.
When writing a package in R, is it necessary to add base packages (utils, grDevices, stats, etc.) as dependencies in the DESCRIPTION of your package?
Some packages do this, but most seem to not.
I have not found any information in the Writing R Extensions manual regarding this.
You should not set too much dependencies but prefer to use those packages as import :
for instance in the DESCRIPTION you will write
Imports:
graphics,
utils,
stats,
grDevices
In your NAMESPACE you can then use either importFrom, in the case you only have a few functions to use. Then you don't have to point to the function using pkg::fun(), or import pkg which will import the whole package, and again you will not need to use the pkg::fun().
Below an example of what you can write in your NAMESPACE
import(graphics)
importFrom(stats,coef)
importFrom(stats,ftable)
importFrom(stats,na.fail)
importFrom(utils,data)
importFrom(utils,globalVariables)
importFrom(utils,read.csv)
importFrom(utils,select.list)
importFrom(utils,stack)
importFrom(utils,write.table)
If you try to use those functions without importing them or use depends, the R-CMD check will fail.
Related
I often use utility type functions from other packages that are un-exported:
pkg:::fun(). I am wondering if I can use such a function within new functionality/scope in my own R package. What is the correct approach here? Is including the package in my description file enough?
Another trick is using getFromNamespace():
fun <- utils::getFromNamespace("fun", "pkg")
The only advantage over ::: is that you don't get any NOTEs and it's allowed on CRAN. Of course, this is not good practice as a hidden change in pkg can break your package.
Note: With roxygen2 you have to add the utils package to the Imports field of your DESCRIPTION file to fulfill CRAN's requirements. Alternatively, you can put it in your NAMESPACE manually.
Summarising comments from #baptise, and etc...:
::: not allowed on CRAN, so options:
ask author to export it so you can use it in your package via standard imports or suggests.
copy / lift a version of it and clearly cite within your package.
I often use utility type functions from other packages that are un-exported:
pkg:::fun(). I am wondering if I can use such a function within new functionality/scope in my own R package. What is the correct approach here? Is including the package in my description file enough?
Another trick is using getFromNamespace():
fun <- utils::getFromNamespace("fun", "pkg")
The only advantage over ::: is that you don't get any NOTEs and it's allowed on CRAN. Of course, this is not good practice as a hidden change in pkg can break your package.
Note: With roxygen2 you have to add the utils package to the Imports field of your DESCRIPTION file to fulfill CRAN's requirements. Alternatively, you can put it in your NAMESPACE manually.
Summarising comments from #baptise, and etc...:
::: not allowed on CRAN, so options:
ask author to export it so you can use it in your package via standard imports or suggests.
copy / lift a version of it and clearly cite within your package.
This question already has an answer here:
How to declare a dependency on an R package from which you only use S3/S4 methods, but no exports?
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Closed 10 days ago.
I'm writing my first package with roxygen2. The package implements a faster version of pcdtest() from plm package. Thus I call within my package:
merr <- resid(mod)
Package plm implements a S3 method for resid. It exports it in plm's NAMESPACE this way:
S3method("residuals", "panelmodel")
S3method("residuals", "plm")
To be able to use resid(), I import whole plm package via
#' #import plm
Is there any way to access the proper method directly via ::? Or to import just the method? Or other nicer workaround?
Many thanks,
Michal
Late, but... Packages don't need to be attached for their registered S3 methods to be available, they just need to be loaded. Therefore, you don't need necessarily to import(plm) (which loads and attaches the package), but just to importFrom(plm, somefunction) (which loads the package, but attaches just this function), any function or symbol declared as export(somefunction) in plm's NAMESPACE.
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Regular expression to match a line that doesn't contain a word
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Better explanation of when to use Imports/Depends
(4 answers)
Closed 4 years ago.
I am developing an R package that uses third party functions
available in the Bioconductor package "methyilumi"
In the code for my R package at the very beginning I import methylumi
with library(methylumi).
During the development (I use roxygen2 and devtools) everything works fine.
However, when I install the package and run my functions, I get the error:
could not find function "methylumIDAT".
Of course everything is solved if I import the package manually, but how can I make
so that methylumi is available whenever I load my own package?
Since you are using devtools, you can add
devtools::use_package("methyilumi")
in the console, and call methyilumi::methylumIDAT in the body of your function. That way, the package is automatically listed in Imports in the DESCRIPTION file.
This sections gives the instructions for several different cases:
http://r-pkgs.had.co.nz/namespace.html#imports
This is done with the NAMESPACE file and also noted in the DESCRIPTION file. There are a few ways to import a function in NAMESPACE, but the simplest is just importFrom("[PACKAGE_NAME]",[FUNCTION_NAME). Then, in DESCRIPTION, add the package name to imports.
See this very good tutorial from Friedrich Leisch.
http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
If you are a package author, you are hopefully well aware of upcoming changes in package structure when we move to 2.14 in about a week. One of the changes is that all packages will require a NAMESPACE, and one will be generated for you in the event you do not make one (the R equivalent of your Miranda rights in the US). So being good citizen I was trying to figure this out. Here is the section from R-exts:
1.6.5 Summary – converting an existing package
To summarize, converting an existing package to use a namespace
involves several simple steps:
Identify the public definitions and place them in export directives.
Identify S3-style method definitions and write corresponding S3method
declarations. Identify dependencies and replace any require calls by
import directives (and make appropriate changes in the Depends and
Imports fields of the DESCRIPTION file). Replace .First.lib functions
with .onLoad functions or useDynLib directives.
To ensure I do the right thing here, can someone give a short clear definition/answer (am I breaking a rule by having several small but related questions together?). All answers should take 2.14 into account, please:
A definition of NAMESPACE as used by R
Is there a way to generate a NAMESPACE prior to build and check, or do we b/c once and then edit the NAMESPACE created automatically?
The difference between "Depends:" and "Imports:" in the DESCRIPTION file. In particular, why would a I put a package in "Depends:" instead of the "Imports:" or vice versa?
It sounds like "require" is no longer to be used, though it doesn't say that. Is this the correct interpretation?
Thanks!
I've written a little on this topic at https://github.com/hadley/devtools/wiki/Namespaces.
To answer your questions:
See Dirk's answer.
Use roxygen2
Now that every package has a namespace there is little reason to use Depends.
require should only be used to load suggested packages
CRAN packages have had NAMESPACEs since almost time immortal. Just pick a few of your favorite CRAN packages and look at their NAMESPACE files.
It can be as easy as this one-liner (plus comment) taken from snow:
# Export all names unless they start with a dot
exportPattern("^[^.]")
The run R CMD check as usual, and you should be fine in most circumstances.
I'm going to answer my own question with a few details I've learned after switching several packages over to R 2.14.
The description above from the manual sort of gives the impression that whatever you had in Depends: for R 2.13 should be moved over to Imports: in R 2.14. You should do that, but they are not 1-for-1 functionally the same, as I hope will be clear from the notes below.
Here we go:
Depends: should probably be used only for restrictions on versions, like 'R >= 2.10' or 'MASS > 0.1' and nothing else under R 2.14.
Having a namespace is partly a mechanism of notifying users that there may be name conflicts and "replacements" -- in other words overwriting of names in use. The NAMESPACE file must match in items and in order the Imports: field in DESCRIPTION. Function names etc imported will be listed under "loaded via namespace (and not attached)" in sessionInfo(). Those packages are installed but not loaded (i.e. no library(some imported package)).
The other role of a namespace is to make functions available to your package "internally". By that, I mean that if your package uses a function in an imported package, it will be found.
However, when you have an example in an .Rd file to be run during checking, packages that you used to have under Depends: in R 2.13 but are now in Imports: under R 2.14 are not available. This is because the checking environment is pretty much like sourcing a script in a clean environment (assuming you are using R --vanilla so .Rprofiles etc have not been run). Unless you put a library(needed package) statement in your example, it won't work under R 2.14 even if it did under R 2.13. So the old examples do not necessarily run even though your package Imports: the needed packages, because again Imports: is not quite the same as Depends: (strictly, they are attached but not loaded).
Please do correct me if any of this is wrong. Many thanks to Hadley Wickham and others who helped me along!
I recently worked on this for one of my packages. Here are my new Depends, Imports, and Suggests lines
Depends: R (>= 2.15.0)
Imports: nlme, mvtnorm, KFAS (>= 0.9.11), stats, utils, graphics
Suggests: Hmisc, maps, xtable, stringr
stats, utils and graphics are part of base R, but the user could detach them and then my package wouldn't work. If you use R from the command line, you might think 'why would anyone detach those?'. But if a user is using RStudio, say, I could see them going through and 'unclicking' all the packages. Strange thing to do, nonetheless, I don't want my package to stop working if they do that. Or they might redefine, say, the plot function (or some other function) , and then my package would fail.
My NAMESPACE then has the following lines
import(KFAS)
import(stats)
import(utils)
import(graphics)
I don't want to go through and keep track of which stats, utils and graphics functions I use, so I import their whole namespaces. For KFAS, I only need 2 functions, but the exported function names changed between versions so I import the whole namespace and then in my code test which version the user has.
For mvtnorm and nlme, I only use one function so I import just those. I could import the whole namespace, but try to only import what I really use.
importFrom(mvtnorm, rmvnorm)
importFrom(nlme, fdHess)
The vignettes where the Suggests packages appear have
require(package)
lines in them.
For the exported functions in my NAMESPACE, I'm a little torn. CRAN has become strict in not allowing ::: in your package code. That means that if I don't export a function, I am restricting creative re-use. On the other hand, I understand the need to only export functions that you intend to maintain with a stable arg list and output otherwise we break each other's packages by changing the function interface.