R devel - Mar 2015 - Submit a package which use doParallel

Hi,

I'm trying to submit my first package which depends on doParallel:

Depends: R (>= 3.0), igraph, doParallel

Running hadley devtools: devtools::check() and devtools::release() result
in no problem (no ERROR nor NOTE on Linux, Mac and Windows).

However, when in use the devtools::build_win() command, it results in the
following note:

* checking R code for possible problems ... NOTE

complete_network: no visible global function definition for '%dopar%'
complete_network: no visible global function definition for '%:%'
complete_network: no visible global function definition for 'foreach'
sample_network: no visible global function definition for '%dopar%'
sample_network: no visible global function definition for 'foreach'

Googling for " no visible global function definition for '%dopar%'
" result
in a few CRAN packages with
similar note e.g.
http://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/penDvine-00check.html

1) Is there a special way to include the doParallel package so that this
error do not occur?

2) Installing the doParallel package "before" running any test on
windows
seems to remove this note. Is there any way to specify it in the
DESCRIPTION?

Best regards,

Have a nice day.

-- 
Etienne Lord, Ph.D.
Post-Doc Bioinformatics.
Universit? du Qu?bec ? Montr?al
Universit? de Montr?al

	[[alternative HTML version deleted]]

On Thu, 2015-03-05 at 18:03 -0500, Etienne Lord wrote:
> Hi,
> 
> I'm trying to submit my first package which depends on doParallel:
> 
> Depends: R (>= 3.0), igraph, doParallel
add foreach to your Depends.  That should resolve the error you're
seeing.

> Running hadley devtools: devtools::check() and devtools::release() result
> in no problem (no ERROR nor NOTE on Linux, Mac and Windows).
> 
> However, when in use the devtools::build_win() command, it results in the
> following note:
> 
> * checking R code for possible problems ... NOTE
> 
> complete_network: no visible global function definition for
'%dopar%'
> complete_network: no visible global function definition for '%:%'
> complete_network: no visible global function definition for
'foreach'
<...>
> 2) Installing the doParallel package "before" running any test on
windows
> seems to remove this note. Is there any way to specify it in the
> DESCRIPTION?
-- 
Brian G. Peterson
http://braverock.com/brian/
Ph: 773-459-4973
IM: bgpbraverock

On 05/03/2015 6:03 PM, Etienne Lord wrote:
> Hi,
> 
> I'm trying to submit my first package which depends on doParallel:
> 
> Depends: R (>= 3.0), igraph, doParallel
It's much better to import what you need.  If someone calls one of your
functions using :: notation, it will fail, because it won't know where
to find the doParallel objects.
> 
> Running hadley devtools: devtools::check() and devtools::release() result
> in no problem (no ERROR nor NOTE on Linux, Mac and Windows).
> 
> However, when in use the devtools::build_win() command, it results in the
> following note:
> 
> * checking R code for possible problems ... NOTE
> 
> complete_network: no visible global function definition for
'%dopar%'
> complete_network: no visible global function definition for '%:%'
> complete_network: no visible global function definition for
'foreach'
> sample_network: no visible global function definition for '%dopar%'
> sample_network: no visible global function definition for 'foreach'
> 
> Googling for " no visible global function definition for
'%dopar%' " result
> in a few CRAN packages with
> similar note e.g.
>
http://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/penDvine-00check.html
> 
> 1) Is there a special way to include the doParallel package so that this
> error do not occur?
List it in the DESCRIPTION as "Imports:  doParallel" and in your
NAMESPACE file import the functions you need.
> 
> 2) Installing the doParallel package "before" running any test on
windows
> seems to remove this note. Is there any way to specify it in the
> DESCRIPTION?
That's a problem with testing within a session.  It's best to run checks
on a vanilla system, using R CMD check.

Duncan Murdoch

On 05/03/2015 6:16 PM, Brian G. Peterson wrote:
> On Thu, 2015-03-05 at 18:03 -0500, Etienne Lord wrote:
>> Hi,
>>
>> I'm trying to submit my first package which depends on doParallel:
>>
>> Depends: R (>= 3.0), igraph, doParallel
> 
> add foreach to your Depends.  That should resolve the error you're
> seeing.
Please don't do that.  Use Imports.

Duncan Murdoch
> 
> 
>> Running hadley devtools: devtools::check() and devtools::release()
result
>> in no problem (no ERROR nor NOTE on Linux, Mac and Windows).
>>
>> However, when in use the devtools::build_win() command, it results in
the
>> following note:
>>
>> * checking R code for possible problems ... NOTE
>>
>> complete_network: no visible global function definition for
'%dopar%'
>> complete_network: no visible global function definition for
'%:%'
>> complete_network: no visible global function definition for
'foreach'
> 
> <...>
> 
>> 2) Installing the doParallel package "before" running any
test on windows
>> seems to remove this note. Is there any way to specify it in the
>> DESCRIPTION?
>