I've now rerun R CMD check SparseM on today's R-devel and I'm happy to report that things look much better after the changes made last night.
I now get: * checking for missing documentation entries ... WARNING Undocumented code objects: %x% as.matrix diag diag<- diff t Undocumented S4 methods: \S4method{coerce}{vector,matrix.diag.csr} \S4method{diff}{matrix.csr} All user-level objects in a package (including S4 classes and methods) Obviously the S4methods are items I should deal with...I'm still uncertain what to do about the Undocumented code objects. url: www.econ.uiuc.edu/~roger/my.html Roger Koenker email [EMAIL PROTECTED] Department of Economics vox: 217-333-4558 University of Illinois fax: 217-244-6678 Champaign, IL 61820 On Mon, 25 Aug 2003, John Chambers wrote: > Seems that methods are being attributed a bit strangely in undoc(). > Here's what I get with, I think, current r-devel and SparseM. > > R> library(tools) > R> undoc("methods") > R> library(SparseM) > [1] "SparseM library loaded" > R> undoc("SparseM") > Undocumented code objects: > %x% as.matrix diag diag<- diff t > Undocumented S4 methods: > \S4method{initialize}{traceable} \S4method{initialize}{signature} > \S4method{initialize}{environment} > R> undoc("methods") > Undocumented S4 methods: > \S4method{initialize}{matrix.csr} \S4method{initialize}{matrix.coo} > Warning message: > package:methods is required by package:SparseM (still attached) in: > detach(pos = pos) > > Notice that methods for initialize() seem to be cross-attributed to > "methods" and "SparseM". (And despite the message, there IS > documentation for both method?initialize("traceable") and > method?initialize("matrix.csr"), but of course in the other package.) > > If it's relevant, after the undoc("methods"), the order of the search > list has been altered, with methods in position 2 (maybe related to the > warning message when it was detached from its previous position?). > > The "Undocumented code objects" messages are "real", but not your > fault--we'll have to figure what to do about them. You created methods > for "diag" (I assume), which is a non-generic in base. The result is to > create a generic version of diag(), which is assigned in your package. > (In general, with namespaces, I don't think it's possible to assign the > generic back into the original package, even just into the exported > environment.) > > R> find("diag") > [1] "package:SparseM" "package:base" > > This creates a formal "conflict" but in my understanding not one that > should be reported, nor should you be expected to document the function > diag(), as opposed to methods created for it. > > [Just got back to e-mail after 3 days away. Will look at this and your > other mail, probably not until tomorrow.] > > Thanks, > John > > Roger Koenker wrote: > > > > I have another S4 methods query -- this time about undocumented objects: > > I'm now getting the following warning from R CMD check SparseM: > > > > * checking for missing documentation entries ... WARNING > > Undocumented code objects: > > %x% as.matrix diag diag<- diff t > > Undocumented S4 methods: > > \S4method{coerce}{ANY,array} \S4method{coerce}{ANY,call} > > \S4method{coerce}{ANY,character} \S4method{coerce}{ANY,complex} > > \S4method{coerce}{ANY,environment} \S4method{coerce}{ANY,expression} > > \S4method{coerce}{ANY,function} \S4method{coerce}{ANY,integer} > > \S4method{coerce}{ANY,list} \S4method{coerce}{ANY,logical} > > \S4method{coerce}{ANY,matrix} \S4method{coerce}{ANY,name} > > \S4method{coerce}{ANY,numeric} \S4method{coerce}{ANY,single} > > \S4method{coerce}{ANY,ts} \S4method{coerce}{ANY,vector} > > \S4method{coerce}{ANY,NULL} > > \S4method{coerce}{vector,matrix.diag.csr} > > \S4method{diff}{matrix.csr} \S4method{initialize}{traceable} > > \S4method{initialize}{signature} \S4method{initialize}{environment} > > > > A couple of these are directly related to the package, but the rest > > seem to be items that I wouldn't have thought that I should be responsible > > for documenting. I'm wondering whether the coerce items are related to > > my earlier query. Even supposing that they were due to some blunder > > of mine, I'm still puzzled by the initialize items which were present > > even before I began to mess with my new setClass strategy. Again, > > many thanks for any suggestions. > > > > url: www.econ.uiuc.edu/~roger/my.html Roger Koenker > > email [EMAIL PROTECTED] Department of Economics > > vox: 217-333-4558 University of Illinois > > fax: 217-244-6678 Champaign, IL 61820 > > > > ______________________________________________ > > [EMAIL PROTECTED] mailing list > > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel > > -- > John M. Chambers [EMAIL PROTECTED] > Bell Labs, Lucent Technologies office: (908)582-2681 > 700 Mountain Avenue, Room 2C-282 fax: (908)582-3340 > Murray Hill, NJ 07974 web: http://www.cs.bell-labs.com/~jmc > ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel