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Question about selective importing of package functions...
11 messages · Jonathan Greenberg, Gabor Grothendieck, Dirk Eddelbuettel +3 more
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-tools at 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
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On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch
<murdoch.duncan at 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-tools at 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
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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 | edd at debian.org | http://dirk.eddelbuettel.com
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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.duncan at gmail.com <mailto:murdoch.duncan at 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-tools at estarcion.net <mailto:spatial-tools at 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: jgrn307 at hotmail.com <mailto:jgrn307 at hotmail.com>,
Gchat: jgrn307, Skype: jgrn3007
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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 <edd at 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 | edd at debian.org | http://dirk.eddelbuettel.com
On 13-10-20 04:58 PM, Gabor Grothendieck wrote:
On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch <murdoch.duncan at 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-tools at 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.