I'm working on update of my package. However I'm struggling with dependencies/imports. I use two conflicted packages - ggplot2 and psych and their functions alpha and of course alpha object of ggplot2 differs from alpha function of psych package.
When building package I get an warning:
Warning: replacing previous import 'ggplot2::alpha' by 'psych::alpha' when loading 'ShinyItemAnalysis'
Hence I wont be able to publish my package on CRAN (untill I solved this warning). Is there any easy way how to avoid this import conflict?
Note that when using roxygen2 package to build NAMESPACE from fellow .R scripts, it is very helpful to delete the NAMESPACE file and run roxygen2 again. Solves many problems.
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.
Title should be pretty clear I hope. I'm writing a package called forecasting, with imports for dplyr among other packages. With the imports written in to the DESCRIPTION file, I am able to force these other packages to be installed along with forecasting - is there an equivalent way to do this for the loading of the package? In other words, is there a way that when I load my package with library(forecasting), it automatically also loads dplyr and the other packages?
Thanks
Yes.
Re-read "Writing R Extensions". The Depends: forces both the initial installation as well as the loading of the depended-upon packages.
But these days you want Imports: along with importFrom() in the NAMESPACE file which is more fine-grained.
But first things first: get it working with Depends.
Edit:
Opps you're correct, the documentation I referenced is not a primary source. Perhaps this is better:
From the R documentation:
The ‘Depends’ field gives a comma-separated list of package names which this package depends on. Those packages will be attached before the current package when library or require is called.
and
The ‘Imports’ field lists packages whose namespaces are imported from (as specified in the NAMESPACE file) but which do not need to be attached. Namespaces accessed by the ‘::’ and ‘:::’ operators must be listed here, or in ‘Suggests’ or ‘Enhances’
Original:
From the R packages documentation:
Adding a package dependency here [the DESCRIPTION file] ensures that it’ll be installed. However, it does not mean that it will be attached along with your package (i.e., library(x)). The best practice is to explicitly refer to external functions using the syntax package::function(). This makes it very easy to identify which functions live outside of your package. This is especially useful when you read your code in the future.
I'm trying to use Imports: instead of Depends: in the DESCRIPTION files of my packages, yet I still feel I've got some more to understand on this ;-)
What I learned from this post (by the way: awesome post!!!) is that everything my package, say mypkg, imports (say imported.pkg) via Imports: lives in environment imports:mypkg instead of being attached to the search path. When trying to find foo that ships with imported.pkg, R looks in imports:mypkg before traversing the search list. So far, so good.
Actual question
If imported.pkg (imported by mypkg) depends on a certain other package (stated in Depends: section of the package's DESCRIPTION file), do I need to make this very package a Depends: dependency of my package in order for R to find functions of that package? So it seems to me at the moment as otherwise R complains.
Evidence
Seems like simply importing such a package is not enough. As an example, take package roxygen2 (CRAN). It depends on digest while importing a bunch of other packages. I imported it (along with digest as mypkg also needs it) and checked environment imports:mypkg which does list the digest function: "digest" %in% parent.env(asNamespace("mypkg")) returns TRUE
Yet when running roxygenize() from within a function that is part of mypkg, R complains that it can't find digest.
You could have a look at my blog : http://r2d2.quartzbio.com/posts/package-depends-dirty-hack-solution.html
Now i have a better and cleaner solution but not published yet.
Hope it helps.
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.