[R] How to link two R packages together

Thu Aug 2 16:51:09 CEST 2012

Inline.

On Thu, Aug 2, 2012 at 7:39 AM, Joshua Wiley <jwiley.psych at gmail.com> wrote:
> Hi Xuan,
>
> I would expect ~/R/ to be the R_HOME directory, though perhaps I am
> wrong.  Also, you only need a depends or an imports, not both.  At a
> simplified level, the difference is that importing PKG2 in PKG1 makes
> the (exported) functions in PKG2 available to PKG1. Depends also makes
> the (exported) functions in PKG2 available to PKG1, but it _also_
> makes them available to the user.  This can be good or bad, with the
> recommendation now being not to. The reason it can be good is if you
> want your users to have access to functions in both packages without
> explicitly loading both.
This is false, I believe.  From the manual:

"The R INSTALL facilities check if the version of R used is recent
enough for the package being installed,and the list of packages which
is specified will be attached (after checking version requirements)
before the current package, ..."

So including a package in  Depends leads not only to loading, but attaching.

-- Bert

 However, let's say that function foo() is
> defined in PKG2 and in PKG3. PKG1 does not know about PKG3, and the
> user had PKG3 loaded prior to loading PKG1. Then when PKG1 loads, PKG2
> also loads, and because all the exported functions from PKG2 are
> included, PKG2::foo() masks PKG3::foo(), which can be annoying for
> users if your package adds unnecessary functions to the search path
> potentially masking the versions they wanted to use.
>
> That was a rather convoluted explanation, but hopefully it is somewhat clear.
>
> Sincerely,
>
> Josh
>
> On Thu, Aug 2, 2012 at 7:02 AM, Xuan Zhao <xuan.zhao at sentrana.com> wrote:
>> Hi All,
>> Thank you so much for all the help you have provided, I really appreciate it!
>> The problem is solved, I just added PKG2 to the dependency of PKG1 in the description file, also (I don't know if it's necessary or not), I added "import(PKG2)" to the NAMESPACE file. In addition to that, I install PKG2 under a path R can recognize, namely, belong to ".libPaths()".
>> I have tried other ways besides install it under the path R can recognize, like  adding a file ~/.R/check.Environ, whose contents are: 'R_LIBS_SITE=${R_LIBS_SITE-'directoryunderwhichPKG2isinstalled'}', but it still doesn't work.
>> I looked through the manual, they just say the file 'check.Environ' should be put under '~/.R', but I am not should what the "~/" should be. Is that my home directory or what? Should that be the host? I am not the host of the server, does that matter?
>> Thank you so much for the help!
>> Yours,
>> Xuan
>>
>> -----Original Message-----
>> From: Bert Gunter [mailto:gunter.berton at gene.com]
>> Sent: Thursday, August 02, 2012 9:42 AM
>> To: Joshua Wiley
>> Cc: Michael Weylandt; r-help at r-project.org; Xuan Zhao
>> Subject: Re: [R] How to link two R packages together
>>
>> Josh:
>>
>> You may be right ... but I still do not think so. Note that the post begins with:
>>
>> One of them (PKG1) needs to use the functions
>>> of the other package (PKG2).
>>
>> This is exactly what imports are for. I believe that, because he/she failed to RTFM, he/she is not being accurate in his/her use of the relevant terms. Certainly, to me at least, it is unclear. Moreover, as I understand it (see the manual) imports are preferred over dependencies, as I indicated in my reply.
>>
>> Anyway, in either case, the central advice is that which both Michael and I gave: RTFM. Perhaps it's a generation gap (I am old), but I believe there has been a trend for new R users to post here without making any significant effort to consult the docs. This strikes me as intellectually lazy and, frankly, inconsiderate to those like yourself
>> -- or BDR -- who are willing to give up their time and effort to help those with legitimate questions. You and others may consider this an overreaction of course.
>>
>> Sorry for the rant, but it seems relevant to your close parsing of the thread.
>>
>> -- Cheers,
>> Bert
>>
>> On Wed, Aug 1, 2012 at 10:35 PM, Joshua Wiley <jwiley.psych at gmail.com> wrote:
>>> On Wed, Aug 1, 2012 at 10:28 PM, Bert Gunter <gunter.berton at gene.com> wrote:
>>>> On Wed, Aug 1, 2012 at 6:45 PM, Michael Weylandt
>>>> <michael.weylandt at gmail.com> wrote:
>>>>> Isn't this what package dependencies are for?
>>>>
>>>> No. It's what package imports are for (preferably).
>>>> As always, the OP should RTFM -- in this case the one to which you
>>>> refer on the next line, especially the NAMESPACES section.
>>>
>>> But note that the original question included, "when I load one package
>>> using 'library("PKG1")', PKG2 can be loaded at the same." which
>>> imports does not exactly do. They become available to the package, but
>>> not to the user, so if you really need both packages loaded to the
>>> search path, then you need a dependency, not imports.
>>>
>>> Cheers,
>>>
>>> Josh
>>>
>>>>
>>>> -- Bert
>>>>
>>>>>
>>>>> See the description of the DESCRIPTION file in Writing R Extensions
>>>>>
>>>>> Michael
>>>>>
>>>>> On Aug 1, 2012, at 5:27 PM, xuan zhao <xuan.zhao at sentrana.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>> I have built two R packages. One of them (PKG1) needs to use the
>>>>>> functions of the other package (PKG2).
>>>>>> So I need to link these two packages together, so that the
>>>>>> functions of PKG2 can be available to PKG1. And when I load one
>>>>>> package using 'library("PKG1")', PKG2 can be loaded at the same.
>>>>>> Any ideas welcome.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> View this message in context:
>>>>>> http://r.789695.n4.nabble.com/How-to-link-two-R-packages-together-t
>>>>>> p4638765.html Sent from the R help mailing list archive at
>>>>>> Nabble.com.
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-help at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>> PLEASE do read the posting guide
>>>>>> http://www.R-project.org/posting-guide.html
>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Bert Gunter
>>>> Genentech Nonclinical Biostatistics
>>>>
>>>> Internal Contact Info:
>>>> Phone: 467-7374
>>>> Website:
>>>> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pd
>>>> b-biostatistics/pdb-ncb-home.htm
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>>>
>>> --
>>> Joshua Wiley
>>> Ph.D. Student, Health Psychology
>>> Programmer Analyst II, Statistical Consulting Group University of
>>> California, Los Angeles https://joshuawiley.com/
>>
>>
>>
>> --
>>
>> Bert Gunter
>> Genentech Nonclinical Biostatistics
>>
>> Internal Contact Info:
>> Phone: 467-7374
>> Website:
>> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
>
>
> --
> Joshua Wiley
> Ph.D. Student, Health Psychology
> Programmer Analyst II, Statistical Consulting Group
> University of California, Los Angeles
> https://joshuawiley.com/
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm