Importing packages in Depend
On Thu, Sep 12, 2013 at 6:49 AM, Benjamin Hofner <benjamin.hofner at fau.de> wrote:
Hi, I am currently preparing a new version of my package papeR. When I run R CMD check using the development version of R I get the following note: Package in Depends field not imported from: ?nlme?, ?lme4?, ?survival? These packages needs to imported from for the case when this namespace is loaded but not attached. I now have problems to fix this issue. It is easy to get rid of two of the three package warnings by using import(lme4) import(survival) in my NAMESPACE. Yet, I cannot import nlme as I then get the following warnings: Warning: replacing previous import ?VarCorr? when loading ?lme4? Warning: replacing previous import ?lmList? when loading ?lme4?
This happens because 'lme4' re-exports the generic function VarCorr() that 'nlme' already exports. R considers this to be a conflict and generates a warnings, which is detected by 'R CMD check'. I've been trying to argue that this warning is unnecessary/not correct because in these cases, the two objects in conflict are actually the same identical object. You can see this by:
nlme::VarCorr
function (x, sigma = 1, rdig = 3)
UseMethod("VarCorr")
<bytecode: 0x00000000111eb728>
<environment: namespace:nlme>
lme4::VarCorr
function (x, sigma = 1, rdig = 3)
UseMethod("VarCorr")
<bytecode: 0x00000000111eb728>
<environment: namespace:nlme>
Note how they are both in the same namespace, i.e.
identical(lme4::VarCorr, nlme::VarCorr)
[1] TRUE I've submitted a patch for this 'Bug 15451 - PATCH: namespaceImportFrom() not to warn when the identical object is imported twice' on 2013-09-10 [https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15451]. The tricky part is to convince R-core. Otherwise, the only solution I know of is either to use importFrom():s or to convince the author of 'lme4' to remove that re-export, which may not be possible. /Henrik
I know that nlme is imported in lme4 but I cannot import both at the same time. Can anyone help me here? I do *not* want or can use importFrom as I rely on multiple functions and also rely on non-exported methods such as summary.lme(). Thanks and all the best, Benjamin -- View this message in context: http://r.789695.n4.nabble.com/Importing-packages-in-Depend-tp4675947.html Sent from the R devel mailing list archive at Nabble.com.
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