Correct use of Depends, Imports and ::

Dear R developers,

Taking advantage of the yesterday discussion about the use of Depends/Import/Suggests/Enhances, I would like to add a related question.

Let's assume, in the DESCRIPTION file of my package foo0, I have:

Depends: foo1
Imports: foo2

while in the NAMESPACE file of my package I have

importFrom("foo2", f2)


and within my package I use the following two external functions:

f1, from package foo1
f2, from package foo2


If I want to use the two previous functions within a function of my package foo0, is it correct to call them as follow ( assuming 'x' is the only argument of 'f1' and 'f2'):

f1(x)
foo2::f2(x)

OR should I use

foo1::f1(x)
f2(x)

OR

f1(x)
f2(x)

OR

something else (the correct way of doing it in R) ?



Finally, can I use the following call in the body of a function of my package foo0:

foo3::f3(x)

without declaring the package 'foo3' in the Imports section of my DESCRIPTION file ?

Thanks in advance for your help,


Mauricio Zambrano-Bigiarini

-- 
=================================================
Water Resources Unit
Institute for Environment and Sustainability (IES)
Joint Research Centre (JRC), European Commission
TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), IT
webinfo    : http://floods.jrc.ec.europa.eu/
=================================================
DISCLAIMER:\ "The views expressed are purely those of th...{{dropped:11}}

On Nov 7, 2012, at 4:04 AM, Mauricio Zambrano-Bigiarini wrote:

Dear R developers,

Taking advantage of the yesterday discussion about the use of Depends/Import/Suggests/Enhances, I would like to add a related question.

Let's assume, in the DESCRIPTION file of my package foo0, I have:

Depends: foo1
Imports: foo2

while in the NAMESPACE file of my package I have

importFrom("foo2", f2)


and within my package I use the following two external functions:

f1, from package foo1
f2, from package foo2


If I want to use the two previous functions within a function of my package foo0, is it correct to call them as follow ( assuming 'x' is the only argument of 'f1' and 'f2'):

f1(x)
foo2::f2(x)

OR should I use

foo1::f1(x)
f2(x)

OR

f1(x)
f2(x)

Yes, this one. You have imported f2 so the whole point of that is that it will be inserted as "f2" into your imports environment, so you want to use it that way. When you use foo2:: you are skipping over imports and addressing the namespace of foo2 directly which sort of defeats the purpose (and is slower).

As for f1, you have attached the package so it is available. I would not use foo1:: for the same reason as above, but there is a risk that it may get clobbered since the call will go through the search path so you may not get f1 from foo1 necessarily - this may or may not be a good thing depending on your intentions. You could import it via import(foo1) to make sure you don't need to go through the search path - that's what I would do if I don't intend overrides. (Whether you want to use Depends or Imports in that case is related to what you intend for the user to see as I was saying in my last comment - if I expect users to use foo1 as well, I would use Depends, otherwise Imports is good enough.)

OR

something else (the correct way of doing it in R) ?



Finally, can I use the following call in the body of a function of my package foo0:

foo3::f3(x)

without declaring the package 'foo3' in the Imports section of my DESCRIPTION file ?

No, it has to be at least in Enhances or Suggests (see R-exts 1.1.1).

Cheers,
Simon

Thanks in advance for your help,


Mauricio Zambrano-Bigiarini

-- 
=================================================
Water Resources Unit
Institute for Environment and Sustainability (IES)
Joint Research Centre (JRC), European Commission
TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), IT
webinfo    : http://floods.jrc.ec.europa.eu/
=================================================
DISCLAIMER:\ "The views expressed are purely those of th...{{dropped:11}}

On Nov 7, 2012, at 9:25 AM, Simon Urbanek wrote:

On Nov 7, 2012, at 4:04 AM, Mauricio Zambrano-Bigiarini wrote:

Dear R developers,

Taking advantage of the yesterday discussion about the use of Depends/Import/Suggests/Enhances, I would like to add a related question.

Let's assume, in the DESCRIPTION file of my package foo0, I have:

Depends: foo1
Imports: foo2

while in the NAMESPACE file of my package I have

importFrom("foo2", f2)


and within my package I use the following two external functions:

f1, from package foo1
f2, from package foo2


If I want to use the two previous functions within a function of my package foo0, is it correct to call them as follow ( assuming 'x' is the only argument of 'f1' and 'f2'):

f1(x)
foo2::f2(x)

OR should I use

foo1::f1(x)
f2(x)

OR

f1(x)
f2(x)

Yes, this one. You have imported f2 so the whole point of that is that it will be inserted as "f2" into your imports environment, so you want to use it that way. When you use foo2:: you are skipping over imports and addressing the namespace of foo2 directly which sort of defeats the purpose (and is slower).

As for f1, you have attached the package so it is available. I would not use foo1:: for the same reason as above, but there is a risk that it may get clobbered since the call will go through the search path so you may not get f1 from foo1 necessarily - this may or may not be a good thing depending on your intentions. You could import it via import(foo1) to make sure you don't need to go through the search path - that's what I would do if I don't intend overrides. (Whether you want to use Depends or Imports in that case is related to what you intend for the user to see as I was saying in my last comment - if I expect users to use foo1 as well, I would use Depends, otherwise Imports is good enough.)

OR

something else (the correct way of doing it in R) ?



Finally, can I use the following call in the body of a function of my package foo0:

foo3::f3(x)

without declaring the package 'foo3' in the Imports section of my DESCRIPTION file ?

No, it has to be at least in Enhances or Suggests (see R-exts 1.1.1).

This should have been "Yes, but it has ..."

On 11/07/12, Simon Urbanek  <simon.urbanek at r-project.org> wrote:

On Nov 7, 2012, at 9:25 AM, Simon Urbanek wrote:

On Nov 7, 2012, at 4:04 AM, Mauricio Zambrano-Bigiarini wrote:

Dear R developers,

Taking advantage of the yesterday discussion about the use of
Depends/Import/Suggests/Enhances, I would like to add a related
question.

Let's assume, in the DESCRIPTION file of my package foo0, I
have:

Depends: foo1 Imports: foo2

while in the NAMESPACE file of my package I have

importFrom("foo2", f2)


and within my package I use the following two external
functions:

f1, from package foo1 f2, from package foo2


If I want to use the two previous functions within a function
of my package foo0, is it correct to call them as follow (
assuming 'x' is the only argument of 'f1' and 'f2'):

f1(x) foo2::f2(x)

OR should I use

foo1::f1(x) f2(x)

OR

f1(x) f2(x)

Yes, this one. You have imported f2 so the whole point of that is
that it will be inserted as "f2" into your imports environment,
so you want to use it that way. When you use foo2:: you are
skipping over imports and addressing the namespace of foo2
directly which sort of defeats the purpose (and is slower).

Thanks Simon for making the point related to f2 clearer for me.

As for f1, you have attached the package so it is available. I
would not use foo1:: for the same reason as above, but there is a
risk that it may get clobbered since the call will go through the
search path so you may not get f1 from foo1 necessarily - this
may or may not be a good thing depending on your intentions. You
could import it via import(foo1) to make sure you don't need to
go through the search path - that's what I would do if I don't
intend overrides. (Whether you want to use Depends or Imports in
that case is related to what you intend for the user to see as I
was saying in my last comment - if I expect users to use foo1 as
well, I would use Depends, otherwise Imports is good enough.)

So, if I'm only using a few functions of foo1, I shouldn't declare
them in Depends, but only in Imports, which also will allow me to be
sure that the functions come from foo1 and not from another package
that have functions with the same, right ?

Hi all,

In a package I maintain, I use the "dqrls" from the base package to fit
regression models. However, I was informed that directly calling
functions from the base package is no longer allowed:

"CRAN packages should use only the public API. Hence they should not use
entry points not declared as API in installed headers nor .Internal()
nor .Call() etc calls to base packages. Such usages can cause packages
to break at any time, even in patched versions of R."

Prof. Ripley suggested that one can replace such calls with lm.wfit,
which will work.

However, in my package, the call will need to be implemented hundreds of
thousands times. Using lm.wfit is much slower. I am wondering whether
there is alternative ways that are more efficient. I can program in C if
needed.

Many thanks.

Best regards,
Yanming

On 07/11/2012 17:52, mauricio zambrano wrote:

On 11/07/12, Simon Urbanek  <simon.urbanek at r-project.org> wrote:

On Nov 7, 2012, at 9:25 AM, Simon Urbanek wrote:

On Nov 7, 2012, at 4:04 AM, Mauricio Zambrano-Bigiarini wrote:

Dear R developers,

Taking advantage of the yesterday discussion about the use of
Depends/Import/Suggests/Enhances, I would like to add a related
question.

Let's assume, in the DESCRIPTION file of my package foo0, I
have:

Depends: foo1 Imports: foo2

while in the NAMESPACE file of my package I have

importFrom("foo2", f2)


and within my package I use the following two external
functions:

f1, from package foo1 f2, from package foo2


If I want to use the two previous functions within a function
of my package foo0, is it correct to call them as follow (
assuming 'x' is the only argument of 'f1' and 'f2'):

f1(x) foo2::f2(x)

OR should I use

foo1::f1(x) f2(x)

OR

f1(x) f2(x)

Yes, this one. You have imported f2 so the whole point of that is
that it will be inserted as "f2" into your imports environment,
so you want to use it that way. When you use foo2:: you are
skipping over imports and addressing the namespace of foo2
directly which sort of defeats the purpose (and is slower).

Thanks Simon for making the point related to f2 clearer for me.

As for f1, you have attached the package so it is available. I
would not use foo1:: for the same reason as above, but there is a
risk that it may get clobbered since the call will go through the
search path so you may not get f1 from foo1 necessarily - this
may or may not be a good thing depending on your intentions. You
could import it via import(foo1) to make sure you don't need to
go through the search path - that's what I would do if I don't
intend overrides. (Whether you want to use Depends or Imports in
that case is related to what you intend for the user to see as I
was saying in my last comment - if I expect users to use foo1 as
well, I would use Depends, otherwise Imports is good enough.)

Or declare in Depends but also import in the NAMESPACE.

So, if I'm only using a few functions of foo1, I shouldn't declare
them in Depends, but only in Imports, which also will allow me to be
sure that the functions come from foo1 and not from another package
that have functions with the same, right ?

Yes, but it would be better to use importsFrom() with just the functions
you need (the list of exported functions from foo1 could change over time).

I've just been through this advising an author of a package who needs to
use intersect() from rgeos, not intersect() from base.

On 07/11/2012 17:52, mauricio zambrano wrote:

On 11/07/12, Simon Urbanek  <simon.urbanek at r-project.org> wrote:

On Nov 7, 2012, at 9:25 AM, Simon Urbanek wrote:

On Nov 7, 2012, at 4:04 AM, Mauricio Zambrano-Bigiarini wrote:

Dear R developers,

Taking advantage of the yesterday discussion about the use of
Depends/Import/Suggests/Enhances, I would like to add a related
question.

Let's assume, in the DESCRIPTION file of my package foo0, I
have:

Depends: foo1 Imports: foo2

while in the NAMESPACE file of my package I have

importFrom("foo2", f2)


and within my package I use the following two external
functions:

f1, from package foo1 f2, from package foo2


If I want to use the two previous functions within a function
of my package foo0, is it correct to call them as follow (
assuming 'x' is the only argument of 'f1' and 'f2'):

f1(x) foo2::f2(x)

OR should I use

foo1::f1(x) f2(x)

OR

f1(x) f2(x)

Yes, this one. You have imported f2 so the whole point of that is
that it will be inserted as "f2" into your imports environment,
so you want to use it that way. When you use foo2:: you are
skipping over imports and addressing the namespace of foo2
directly which sort of defeats the purpose (and is slower).

Thanks Simon for making the point related to f2 clearer for me.

As for f1, you have attached the package so it is available. I
would not use foo1:: for the same reason as above, but there is a
risk that it may get clobbered since the call will go through the
search path so you may not get f1 from foo1 necessarily - this
may or may not be a good thing depending on your intentions. You
could import it via import(foo1) to make sure you don't need to
go through the search path - that's what I would do if I don't
intend overrides. (Whether you want to use Depends or Imports in
that case is related to what you intend for the user to see as I
was saying in my last comment - if I expect users to use foo1 as
well, I would use Depends, otherwise Imports is good enough.)

Or declare in Depends but also import in the NAMESPACE.

So, if I'm only using a few functions of foo1, I shouldn't declare
them in Depends, but only in Imports, which also will allow me to be
sure that the functions come from foo1 and not from another package
that have functions with the same, right ?

Yes, but it would be better to use importsFrom() with just the functions you
need (the list of exported functions from foo1 could change over time).

On 11/7/12 12:00 PM, Prof Brian Ripley wrote:

On 07/11/2012 17:52, mauricio zambrano wrote:

On 11/07/12, Simon Urbanek  <simon.urbanek at r-project.org> wrote:

On Nov 7, 2012, at 9:25 AM, Simon Urbanek wrote:

On Nov 7, 2012, at 4:04 AM, Mauricio Zambrano-Bigiarini wrote:

Dear R developers,

Taking advantage of the yesterday discussion about the use of
Depends/Import/Suggests/Enhances, I would like to add a related
question.

Let's assume, in the DESCRIPTION file of my package foo0, I
have:

Depends: foo1 Imports: foo2

while in the NAMESPACE file of my package I have

importFrom("foo2", f2)


and within my package I use the following two external
functions:

f1, from package foo1 f2, from package foo2


If I want to use the two previous functions within a function
of my package foo0, is it correct to call them as follow (
assuming 'x' is the only argument of 'f1' and 'f2'):

f1(x) foo2::f2(x)

OR should I use

foo1::f1(x) f2(x)

OR

f1(x) f2(x)

Yes, this one. You have imported f2 so the whole point of that is
that it will be inserted as "f2" into your imports environment,
so you want to use it that way. When you use foo2:: you are
skipping over imports and addressing the namespace of foo2
directly which sort of defeats the purpose (and is slower).

Thanks Simon for making the point related to f2 clearer for me.

As for f1, you have attached the package so it is available. I
would not use foo1:: for the same reason as above, but there is a
risk that it may get clobbered since the call will go through the
search path so you may not get f1 from foo1 necessarily - this
may or may not be a good thing depending on your intentions. You
could import it via import(foo1) to make sure you don't need to
go through the search path - that's what I would do if I don't
intend overrides. (Whether you want to use Depends or Imports in
that case is related to what you intend for the user to see as I
was saying in my last comment - if I expect users to use foo1 as
well, I would use Depends, otherwise Imports is good enough.)

Or declare in Depends but also import in the NAMESPACE.

This is especially a good idea if there is any chance that anyone else will
ever want to import your package.  If a package is in Depends but the
functions you use are not explicitly imported in the NAMESPACE (with imports
or importsFrom), it can cause problems as described in this thread:

https://stat.ethz.ch/pipermail/r-devel/2011-September/062043.html