[Rd] format: different S4 behavior in a package
R-Devel-ers: I have an S4 method that simply formats an object: setGeneric(formatMe, function(x) standardGeneric(formatMe)) setMethod(formatMe, ANY, function(x) format(x)) If I issue the above in an R session, then define an S4 class with its own format method, I get the desired result: setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv [1] format a-new(A,1968) formatMe(a) [1] Hey Jude However, if I put the two formatMe definitions into a package (Test), I do not get the desired result. start new R session library(Test) setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv [1] format a-new(A,1968) formatMe(a) [1] 1968 The disconnect does not occur, however, if the S4 format method is an S3 incarnation: setClass(B,contains=numeric,S3methods=TRUE) [1] B format.B - function(x, ...) Don't make it bad b-new(B,1968) formatMe(b) [1] Don't make it bad Could the problem be in Test's NAMESPACE file? There is only one line: exportMethods(formatMe) Here is Test's DESCRIPTION file: Package: Test Type: Package Title: Testing format Version: 1.0 Date: 2010-06-22 Author: Dan Murphy Maintainer: Dan Murphy snipped Depends: methods Description: Does format in a package work with S4 format method? License: GPL (= 2) LazyLoad: yes (I would send the Help file, but I don't think that is the problem.) I am using version 2.11.1 on a Windows Vista machine. Any guidance would be appreciated. Thank you Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] format: different S4 behavior in a package
There is not a single definition of formatMe() in your message, therefore nothing works for me, not even the very first version... Best, Uwe Ligges On 23.06.2010 09:16, Daniel Murphy wrote: R-Devel-ers: I have an S4 method that simply formats an object: setGeneric(formatMe, function(x) standardGeneric(formatMe)) setMethod(formatMe, ANY, function(x) format(x)) If I issue the above in an R session, then define an S4 class with its own format method, I get the desired result: setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv [1] format a-new(A,1968) formatMe(a) [1] Hey Jude However, if I put the two formatMe definitions into a package (Test), I do not get the desired result. start new R session library(Test) setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv [1] format a-new(A,1968) formatMe(a) [1] 1968 The disconnect does not occur, however, if the S4 format method is an S3 incarnation: setClass(B,contains=numeric,S3methods=TRUE) [1] B format.B- function(x, ...) Don't make it bad b-new(B,1968) formatMe(b) [1] Don't make it bad Could the problem be in Test's NAMESPACE file? There is only one line: exportMethods(formatMe) Here is Test's DESCRIPTION file: Package: Test Type: Package Title: Testing format Version: 1.0 Date: 2010-06-22 Author: Dan Murphy Maintainer: Dan Murphysnipped Depends: methods Description: Does format in a package work with S4 format method? License: GPL (= 2) LazyLoad: yes (I would send the Help file, but I don't think that is the problem.) I am using version 2.11.1 on a Windows Vista machine. Any guidance would be appreciated. Thank you Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] format: different S4 behavior in a package
On 06/23/2010 12:16 AM, Daniel Murphy wrote: R-Devel-ers: I have an S4 method that simply formats an object: setGeneric(formatMe, function(x) standardGeneric(formatMe)) setMethod(formatMe, ANY, function(x) format(x)) If I issue the above in an R session, then define an S4 class with its own format method, I get the desired result: setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv [1] format a-new(A,1968) formatMe(a) [1] Hey Jude However, if I put the two formatMe definitions into a package (Test), I do not get the desired result. start new R session library(Test) setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv This is the clue -- you're creating a new S4 generic, so there's a base::format, and a .GlobalEnv::format. Test::formatMe respects its name space, and sees base::format. In the S3 case, base::format is already an S3 generic, and you're just adding a method, so there's only base::format for everyone to find. In Test, you could setGeneric(format) and then export(format). It might also be enough to just export(format); I'm not sure. Martin [1] format a-new(A,1968) formatMe(a) [1] 1968 The disconnect does not occur, however, if the S4 format method is an S3 incarnation: setClass(B,contains=numeric,S3methods=TRUE) [1] B format.B - function(x, ...) Don't make it bad b-new(B,1968) formatMe(b) [1] Don't make it bad Could the problem be in Test's NAMESPACE file? There is only one line: exportMethods(formatMe) Here is Test's DESCRIPTION file: Package: Test Type: Package Title: Testing format Version: 1.0 Date: 2010-06-22 Author: Dan Murphy Maintainer: Dan Murphy snipped Depends: methods Description: Does format in a package work with S4 format method? License: GPL (= 2) LazyLoad: yes (I would send the Help file, but I don't think that is the problem.) I am using version 2.11.1 on a Windows Vista machine. Any guidance would be appreciated. Thank you Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] format: different S4 behavior in a package
Thank you, Martin. That worked. And fyi 'export(format)' alone was not sufficient. Best, Dan On Wed, Jun 23, 2010 at 5:15 AM, Martin Morgan mtmor...@fhcrc.org wrote: On 06/23/2010 12:16 AM, Daniel Murphy wrote: R-Devel-ers: I have an S4 method that simply formats an object: setGeneric(formatMe, function(x) standardGeneric(formatMe)) setMethod(formatMe, ANY, function(x) format(x)) If I issue the above in an R session, then define an S4 class with its own format method, I get the desired result: setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv [1] format a-new(A,1968) formatMe(a) [1] Hey Jude However, if I put the two formatMe definitions into a package (Test), I do not get the desired result. start new R session library(Test) setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv This is the clue -- you're creating a new S4 generic, so there's a base::format, and a .GlobalEnv::format. Test::formatMe respects its name space, and sees base::format. In the S3 case, base::format is already an S3 generic, and you're just adding a method, so there's only base::format for everyone to find. In Test, you could setGeneric(format) and then export(format). It might also be enough to just export(format); I'm not sure. Martin [1] format a-new(A,1968) formatMe(a) [1] 1968 The disconnect does not occur, however, if the S4 format method is an S3 incarnation: setClass(B,contains=numeric,S3methods=TRUE) [1] B format.B - function(x, ...) Don't make it bad b-new(B,1968) formatMe(b) [1] Don't make it bad Could the problem be in Test's NAMESPACE file? There is only one line: exportMethods(formatMe) Here is Test's DESCRIPTION file: Package: Test Type: Package Title: Testing format Version: 1.0 Date: 2010-06-22 Author: Dan Murphy Maintainer: Dan Murphy snipped Depends: methods Description: Does format in a package work with S4 format method? License: GPL (= 2) LazyLoad: yes (I would send the Help file, but I don't think that is the problem.) I am using version 2.11.1 on a Windows Vista machine. Any guidance would be appreciated. Thank you Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
