[Rd] Question about selective importing of package functions...

2013-10-20 Thread Jonathan Greenberg 
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 '
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

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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Duncan Murdoch 

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 '
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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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Jonathan Greenberg 
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 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 '
>> 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

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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Gabor Grothendieck 
On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch
 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 '
>> 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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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Jonathan Greenberg 
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  wrote:

> On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch
>  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 '
> >> 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

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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Dirk Eddelbuettel 

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

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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Jonathan Greenberg 
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  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

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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Duncan Murdoch 

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
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
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/ 
AIM: jgrn307, MSN: jgrn...@hotmail.com ,
Gchat: jgrn307, Skype: jgrn3007


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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Gabriel Becker 
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 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?
>
> --j
>
>
> On Sun, Oct 20, 2013 at 5:34 PM, Dirk Eddelbuettel  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
>
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>
> __
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>



-- 
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis

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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Duncan Murdoch 

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  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







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Re: [Rd] Question about selective importing of package functions...

2013-10-20 Thread Paul Gilbert 



On 13-10-20 04:58 PM, Gabor Grothendieck wrote:

On Sun, Oct 20, 2013 at 4:49 PM, Duncan Murdoch
 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 '
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.



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