[Rd] Question about selective importing of package functions...
I'm working on an update for my CRAN package spatial.tools and I noticed a new warning when running R CMD CHECK --as-cran: * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jonathan Asher Greenberg spatial-to...@estarcion.net' Depends: includes the non-default packages: 'sp' 'raster' 'rgdal' 'mmap' 'abind' 'parallel' 'foreach' 'doParallel' 'rgeos' Adding so many packages to the search path is excessive and importing selectively is preferable. Is this a warning that would need to be fixed pre-CRAN (not really sure how, since I need functions from all of those packages)? Is there a way to import only a single function from a package, if that function is a dependency? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
On 13-10-20 4:43 PM, Jonathan Greenberg wrote: I'm working on an update for my CRAN package spatial.tools and I noticed a new warning when running R CMD CHECK --as-cran: * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jonathan Asher Greenberg spatial-to...@estarcion.net' Depends: includes the non-default packages: 'sp' 'raster' 'rgdal' 'mmap' 'abind' 'parallel' 'foreach' 'doParallel' 'rgeos' Adding so many packages to the search path is excessive and importing selectively is preferable. Is this a warning that would need to be fixed pre-CRAN (not really sure how, since I need functions from all of those packages)? Is there a way to import only a single function from a package, if that function is a dependency? You really want to use imports. Those are defined in the NAMESPACE file; you can import everything from a package if you want, but the best style is in fact to just import exactly what you need. This is more robust than using Depends, and it doesn't add so much to the user's search path, so it's less likely to break something else (e.g. by putting a package on the path that masks some function the user already had there.) Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
Duncan: Thanks -- learning something new today -- quick follow-up, will using the import statements in the NAMESPACE, when a user goes to install.packages(), auto-install the dependent packages the same way Depends forces? --j On Sun, Oct 20, 2013 at 3:49 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 13-10-20 4:43 PM, Jonathan Greenberg wrote: I'm working on an update for my CRAN package spatial.tools and I noticed a new warning when running R CMD CHECK --as-cran: * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jonathan Asher Greenberg spatial-to...@estarcion.net' Depends: includes the non-default packages: 'sp' 'raster' 'rgdal' 'mmap' 'abind' 'parallel' 'foreach' 'doParallel' 'rgeos' Adding so many packages to the search path is excessive and importing selectively is preferable. Is this a warning that would need to be fixed pre-CRAN (not really sure how, since I need functions from all of those packages)? Is there a way to import only a single function from a package, if that function is a dependency? You really want to use imports. Those are defined in the NAMESPACE file; you can import everything from a package if you want, but the best style is in fact to just import exactly what you need. This is more robust than using Depends, and it doesn't add so much to the user's search path, so it's less likely to break something else (e.g. by putting a package on the path that masks some function the user already had there.) Duncan Murdoch -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-10-20 4:43 PM, Jonathan Greenberg wrote: I'm working on an update for my CRAN package spatial.tools and I noticed a new warning when running R CMD CHECK --as-cran: * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jonathan Asher Greenberg spatial-to...@estarcion.net' Depends: includes the non-default packages: 'sp' 'raster' 'rgdal' 'mmap' 'abind' 'parallel' 'foreach' 'doParallel' 'rgeos' Adding so many packages to the search path is excessive and importing selectively is preferable. Is this a warning that would need to be fixed pre-CRAN (not really sure how, since I need functions from all of those packages)? Is there a way to import only a single function from a package, if that function is a dependency? You really want to use imports. Those are defined in the NAMESPACE file; you can import everything from a package if you want, but the best style is in fact to just import exactly what you need. This is more robust than using Depends, and it doesn't add so much to the user's search path, so it's less likely to break something else (e.g. by putting a package on the path that masks some function the user already had there.) That may answer the specific case of the poster but how does one handle the case where one wants the user to be able to access the functions in the dependent package. For example, sqldf depends on gsubfn which provides fn which is used with sqldf to perform substitutions in the SQL string. library(sqldf) tt - 3 fn$sqldf(select * from BOD where Time $tt) I don't want to ask the user to tediously issue a library(gsubfn) too since fn is frequently needed and for literally years this has not been necessary. Also I don't want to duplicate fn's code in sqldf since that makes the whole thing less modular -- it would imply having to change fn in two places if anything in fn changed. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
One more follow-up -- will I now need to include a library() statement in each function? --j On Sun, Oct 20, 2013 at 3:58 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-10-20 4:43 PM, Jonathan Greenberg wrote: I'm working on an update for my CRAN package spatial.tools and I noticed a new warning when running R CMD CHECK --as-cran: * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jonathan Asher Greenberg spatial-to...@estarcion.net' Depends: includes the non-default packages: 'sp' 'raster' 'rgdal' 'mmap' 'abind' 'parallel' 'foreach' 'doParallel' 'rgeos' Adding so many packages to the search path is excessive and importing selectively is preferable. Is this a warning that would need to be fixed pre-CRAN (not really sure how, since I need functions from all of those packages)? Is there a way to import only a single function from a package, if that function is a dependency? You really want to use imports. Those are defined in the NAMESPACE file; you can import everything from a package if you want, but the best style is in fact to just import exactly what you need. This is more robust than using Depends, and it doesn't add so much to the user's search path, so it's less likely to break something else (e.g. by putting a package on the path that masks some function the user already had there.) That may answer the specific case of the poster but how does one handle the case where one wants the user to be able to access the functions in the dependent package. For example, sqldf depends on gsubfn which provides fn which is used with sqldf to perform substitutions in the SQL string. library(sqldf) tt - 3 fn$sqldf(select * from BOD where Time $tt) I don't want to ask the user to tediously issue a library(gsubfn) too since fn is frequently needed and for literally years this has not been necessary. Also I don't want to duplicate fn's code in sqldf since that makes the whole thing less modular -- it would imply having to change fn in two places if anything in fn changed. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
On 20 October 2013 at 16:20, Jonathan Greenberg wrote: | One more follow-up -- will I now need to include a library() statement in | each function? No. NAMESPACE entry, coupled with Imports: in DESCRIPTION. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
To be clear, if I used Depends: somepackage before, and switched over to using Imports: somepackage, I'll need to mod my code that used to have a call to, say, somefunction to now have somepackage::somefunction, correct? --j On Sun, Oct 20, 2013 at 5:34 PM, Dirk Eddelbuettel e...@debian.org wrote: On 20 October 2013 at 16:20, Jonathan Greenberg wrote: | One more follow-up -- will I now need to include a library() statement in | each function? No. NAMESPACE entry, coupled with Imports: in DESCRIPTION. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
On 13-10-20 4:54 PM, Jonathan Greenberg wrote: Duncan: Thanks -- learning something new today -- quick follow-up, will using the import statements in the NAMESPACE, when a user goes to install.packages(), auto-install the dependent packages the same way Depends forces? You need to list the other packages in Imports instead of Depends; then the answer is yes. Duncan Murdoch --j On Sun, Oct 20, 2013 at 3:49 PM, Duncan Murdoch murdoch.dun...@gmail.com mailto:murdoch.dun...@gmail.com wrote: On 13-10-20 4:43 PM, Jonathan Greenberg wrote: I'm working on an update for my CRAN package spatial.tools and I noticed a new warning when running R CMD CHECK --as-cran: * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jonathan Asher Greenberg spatial-to...@estarcion.net mailto:spatial-to...@estarcion.net' Depends: includes the non-default packages: 'sp' 'raster' 'rgdal' 'mmap' 'abind' 'parallel' 'foreach' 'doParallel' 'rgeos' Adding so many packages to the search path is excessive and importing selectively is preferable. Is this a warning that would need to be fixed pre-CRAN (not really sure how, since I need functions from all of those packages)? Is there a way to import only a single function from a package, if that function is a dependency? You really want to use imports. Those are defined in the NAMESPACE file; you can import everything from a package if you want, but the best style is in fact to just import exactly what you need. This is more robust than using Depends, and it doesn't add so much to the user's search path, so it's less likely to break something else (e.g. by putting a package on the path that masks some function the user already had there.) Duncan Murdoch -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ http://www.geog.illinois.edu/%7Ejgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com mailto:jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
Jonathan, import/importFrom directives within the NAMESPACE places the symbol(s) within your package's namespace. They are treated exactly the same as (non-exported) symbols your code defines. ~G On Sun, Oct 20, 2013 at 3:41 PM, Jonathan Greenberg j...@illinois.eduwrote: To be clear, if I used Depends: somepackage before, and switched over to using Imports: somepackage, I'll need to mod my code that used to have a call to, say, somefunction to now have somepackage::somefunction, correct? --j On Sun, Oct 20, 2013 at 5:34 PM, Dirk Eddelbuettel e...@debian.org wrote: On 20 October 2013 at 16:20, Jonathan Greenberg wrote: | One more follow-up -- will I now need to include a library() statement in | each function? No. NAMESPACE entry, coupled with Imports: in DESCRIPTION. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Gabriel Becker Graduate Student Statistics Department University of California, Davis [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
On 13-10-20 6:41 PM, Jonathan Greenberg wrote: To be clear, if I used Depends: somepackage before, and switched over to using Imports: somepackage, I'll need to mod my code that used to have a call to, say, somefunction to now have somepackage::somefunction, correct? No. You need to modify both the DESCRIPTION file as you say above, and the NAMESPACE file to say what to import. Once you do that, those functions will appear to your own package functions without any prefix needed. Duncan Murdoch --j On Sun, Oct 20, 2013 at 5:34 PM, Dirk Eddelbuettel e...@debian.org wrote: On 20 October 2013 at 16:20, Jonathan Greenberg wrote: | One more follow-up -- will I now need to include a library() statement in | each function? No. NAMESPACE entry, coupled with Imports: in DESCRIPTION. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question about selective importing of package functions...
On 13-10-20 04:58 PM, Gabor Grothendieck wrote: On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-10-20 4:43 PM, Jonathan Greenberg wrote: I'm working on an update for my CRAN package spatial.tools and I noticed a new warning when running R CMD CHECK --as-cran: * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jonathan Asher Greenberg spatial-to...@estarcion.net' Depends: includes the non-default packages: 'sp' 'raster' 'rgdal' 'mmap' 'abind' 'parallel' 'foreach' 'doParallel' 'rgeos' Adding so many packages to the search path is excessive and importing selectively is preferable. Is this a warning that would need to be fixed pre-CRAN (not really sure how, since I need functions from all of those packages)? Is there a way to import only a single function from a package, if that function is a dependency? You really want to use imports. Those are defined in the NAMESPACE file; you can import everything from a package if you want, but the best style is in fact to just import exactly what you need. This is more robust than using Depends, and it doesn't add so much to the user's search path, so it's less likely to break something else (e.g. by putting a package on the path that masks some function the user already had there.) That may answer the specific case of the poster but how does one handle the case where one wants the user to be able to access the functions in the dependent package. There are two answers to this, depending on how much of the dependent package you want to make available to the user. If you want most of that package to be available then this is the (only?) exception to the rule. From Writing R Extensions: Field ‘Depends’ should nowadays be used rarely, only for packages which are intended to be put on the search path to make their facilities available to the end user (and not to the package itself): for example it makes sense that a user of package latticeExtra would want the functions of package lattice made available. If you really only want to make a couple of functions available then you can import and export the functions. Currently this has the unfortunate side effect that you need to document the functions, you cannot just re-direct to the documentation in the imported package, at least, I have not figured out how to do that. Paul For example, sqldf depends on gsubfn which provides fn which is used with sqldf to perform substitutions in the SQL string. library(sqldf) tt - 3 fn$sqldf(select * from BOD where Time $tt) I don't want to ask the user to tediously issue a library(gsubfn) too since fn is frequently needed and for literally years this has not been necessary. Also I don't want to duplicate fn's code in sqldf since that makes the whole thing less modular -- it would imply having to change fn in two places if anything in fn changed. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
