transition from depends to imports

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transition from depends to imports

Andreas Leha
Hi all,

I am having trouble to do a particular transition from depends to
imports in one of my packages.

This packages uses 'wilcoxsign_test' from the 'coin' package.  And this
is the only function from the coin package that it uses (directly).

(Everything works fine, as long as my package depends on the coin
package.)

My guess was, that I would need to only import that function from the
coin package. (I.e. to move the coin package from Depends
to Imports in the DESCRIPTION and in the NAMESPACE do
'importFrom(coin,wilcoxsign_test)'.)

But then, calling wilcoxsign_test leads to this error:
,----
| Error in formula2data(formula, data, subset, frame = parent.frame(), ...) :
|   could not find function "ModelEnvFormula"
`----

Now, formula2data is an unexported function in the coin package and
ModelEnvFormula is a (exported) function in modeltools.

So, I tried to import ModelEnvFormula from modeltools -- no avail.
And I tried to import formula2data from coin -- not possible
And I tried to import the whole coin package -- no avail.

So, here is the question:  How do I import 'wilcoxsign_test' from the
coin package in a way, that it is usable?

Many thanks in advance.

Regards,
Andreas

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Re: transition from depends to imports

Duncan Murdoch-2
On 09/05/2014, 5:08 PM, Andreas Leha wrote:

> Hi all,
>
> I am having trouble to do a particular transition from depends to
> imports in one of my packages.
>
> This packages uses 'wilcoxsign_test' from the 'coin' package.  And this
> is the only function from the coin package that it uses (directly).
>
> (Everything works fine, as long as my package depends on the coin
> package.)
>
> My guess was, that I would need to only import that function from the
> coin package. (I.e. to move the coin package from Depends
> to Imports in the DESCRIPTION and in the NAMESPACE do
> 'importFrom(coin,wilcoxsign_test)'.)
>
> But then, calling wilcoxsign_test leads to this error:
> ,----
> | Error in formula2data(formula, data, subset, frame = parent.frame(), ...) :
> |   could not find function "ModelEnvFormula"
> `----
>
> Now, formula2data is an unexported function in the coin package and
> ModelEnvFormula is a (exported) function in modeltools.
>
> So, I tried to import ModelEnvFormula from modeltools -- no avail.
> And I tried to import formula2data from coin -- not possible
> And I tried to import the whole coin package -- no avail.
>
> So, here is the question:  How do I import 'wilcoxsign_test' from the
> coin package in a way, that it is usable?
>

Which version of the packages are you using?  The current version of
coin imports ModelEnvFormula from modeltools, so it should be able to
find that function.

Duncan Murdoch

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Re: transition from depends to imports

Andreas Leha
Hi Duncan,

Thank you for your follow-up and fast response!

Duncan Murdoch <[hidden email]> writes:

> On 09/05/2014, 5:08 PM, Andreas Leha wrote:
>> Hi all,
>>
>> I am having trouble to do a particular transition from depends to
>> imports in one of my packages.
>>
>> This packages uses 'wilcoxsign_test' from the 'coin' package.  And this
>> is the only function from the coin package that it uses (directly).
>>
>> (Everything works fine, as long as my package depends on the coin
>> package.)
>>
>> My guess was, that I would need to only import that function from the
>> coin package. (I.e. to move the coin package from Depends
>> to Imports in the DESCRIPTION and in the NAMESPACE do
>> 'importFrom(coin,wilcoxsign_test)'.)
>>
>> But then, calling wilcoxsign_test leads to this error:
>> ,----
>> | Error in formula2data(formula, data, subset, frame = parent.frame(), ...) :
>> |   could not find function "ModelEnvFormula"
>> `----
>>
>> Now, formula2data is an unexported function in the coin package and
>> ModelEnvFormula is a (exported) function in modeltools.
>>
>> So, I tried to import ModelEnvFormula from modeltools -- no avail.
>> And I tried to import formula2data from coin -- not possible
>> And I tried to import the whole coin package -- no avail.
>>
>> So, here is the question:  How do I import 'wilcoxsign_test' from the
>> coin package in a way, that it is usable?
>>
>
> Which version of the packages are you using?  The current version of
> coin imports ModelEnvFormula from modeltools, so it should be able to
> find that function.
>
> Duncan Murdoch

As it seems, the version I use(d) depends on modeltools.

,----
| > packageDescription("coin")
| Package: coin
| Title: Conditional Inference Procedures in a Permutation Test Framework
| Date: 2013-04-26
| Version: 1.0-22
| Author: Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel and Achim
|         Zeileis
| Maintainer: Torsten Hothorn <[hidden email]>
| Description: Conditional inference procedures for the general
|         independence problem including two-sample, K-sample
|         (non-parametric ANOVA), correlation, censored, ordered and
|         multivariate problems.
| Depends: R (>= 2.2.0), methods, survival, mvtnorm (>= 0.8-0),
|         modeltools (>= 0.2-9)
| Suggests: multcomp, xtable, e1071, vcd
| Enhances: Biobase
| LazyLoad: yes
| LazyData: yes
| License: GPL-2
| Packaged: 2013-04-26 12:33:15 UTC; hothorn
| NeedsCompilation: yes
| Repository: CRAN
| Date/Publication: 2013-04-26 15:27:04
| Built: R 3.0.1; x86_64-pc-linux-gnu; 2013-05-29 16:07:42 UTC; unix
|
| -- File: /usr/lib/R/site-library/coin/Meta/package.rds
`----

I can confirm that updating coin (to version 1.1-0) did resolve my
problem.  Thank you very much!


This leads to the follow-up question:  How would I have correctly dealt
with this situation if my dependency ('coin') had not been updated?

Regards,
Andreas

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Re: transition from depends to imports

Duncan Murdoch-2
On 09/05/2014, 5:39 PM, Andreas Leha wrote:

> Hi Duncan,
>
> Thank you for your follow-up and fast response!
>
> Duncan Murdoch <[hidden email]> writes:
>
>> On 09/05/2014, 5:08 PM, Andreas Leha wrote:
>>> Hi all,
>>>
>>> I am having trouble to do a particular transition from depends to
>>> imports in one of my packages.
>>>
>>> This packages uses 'wilcoxsign_test' from the 'coin' package.  And this
>>> is the only function from the coin package that it uses (directly).
>>>
>>> (Everything works fine, as long as my package depends on the coin
>>> package.)
>>>
>>> My guess was, that I would need to only import that function from the
>>> coin package. (I.e. to move the coin package from Depends
>>> to Imports in the DESCRIPTION and in the NAMESPACE do
>>> 'importFrom(coin,wilcoxsign_test)'.)
>>>
>>> But then, calling wilcoxsign_test leads to this error:
>>> ,----
>>> | Error in formula2data(formula, data, subset, frame = parent.frame(), ...) :
>>> |   could not find function "ModelEnvFormula"
>>> `----
>>>
>>> Now, formula2data is an unexported function in the coin package and
>>> ModelEnvFormula is a (exported) function in modeltools.
>>>
>>> So, I tried to import ModelEnvFormula from modeltools -- no avail.
>>> And I tried to import formula2data from coin -- not possible
>>> And I tried to import the whole coin package -- no avail.
>>>
>>> So, here is the question:  How do I import 'wilcoxsign_test' from the
>>> coin package in a way, that it is usable?
>>>
>>
>> Which version of the packages are you using?  The current version of
>> coin imports ModelEnvFormula from modeltools, so it should be able to
>> find that function.
>>
>> Duncan Murdoch
>
> As it seems, the version I use(d) depends on modeltools.
>
> ,----
> | > packageDescription("coin")
> | Package: coin
> | Title: Conditional Inference Procedures in a Permutation Test Framework
> | Date: 2013-04-26
> | Version: 1.0-22
> | Author: Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel and Achim
> |         Zeileis
> | Maintainer: Torsten Hothorn <[hidden email]>
> | Description: Conditional inference procedures for the general
> |         independence problem including two-sample, K-sample
> |         (non-parametric ANOVA), correlation, censored, ordered and
> |         multivariate problems.
> | Depends: R (>= 2.2.0), methods, survival, mvtnorm (>= 0.8-0),
> |         modeltools (>= 0.2-9)
> | Suggests: multcomp, xtable, e1071, vcd
> | Enhances: Biobase
> | LazyLoad: yes
> | LazyData: yes
> | License: GPL-2
> | Packaged: 2013-04-26 12:33:15 UTC; hothorn
> | NeedsCompilation: yes
> | Repository: CRAN
> | Date/Publication: 2013-04-26 15:27:04
> | Built: R 3.0.1; x86_64-pc-linux-gnu; 2013-05-29 16:07:42 UTC; unix
> |
> | -- File: /usr/lib/R/site-library/coin/Meta/package.rds
> `----
>
> I can confirm that updating coin (to version 1.1-0) did resolve my
> problem.  Thank you very much!
>
>
> This leads to the follow-up question:  How would I have correctly dealt
> with this situation if my dependency ('coin') had not been updated?

I think the only workaround would be for you to say your package Depends
on modeltools.  It's really a coin issue, not yours, and the right
people fixed it.

Duncan Murdoch

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Re: transition from depends to imports

Andreas Leha
Duncan Murdoch <[hidden email]> writes:

> On 09/05/2014, 5:39 PM, Andreas Leha wrote:
>> Hi Duncan,
>>
>> Thank you for your follow-up and fast response!
>>
>> Duncan Murdoch <[hidden email]> writes:
>>
>>> On 09/05/2014, 5:08 PM, Andreas Leha wrote:
>>>> Hi all,
>>>>
>>>> I am having trouble to do a particular transition from depends to
>>>> imports in one of my packages.
>>>>
>>>> This packages uses 'wilcoxsign_test' from the 'coin' package.  And this
>>>> is the only function from the coin package that it uses (directly).
>>>>
>>>> (Everything works fine, as long as my package depends on the coin
>>>> package.)
>>>>
>>>> My guess was, that I would need to only import that function from the
>>>> coin package. (I.e. to move the coin package from Depends
>>>> to Imports in the DESCRIPTION and in the NAMESPACE do
>>>> 'importFrom(coin,wilcoxsign_test)'.)
>>>>
>>>> But then, calling wilcoxsign_test leads to this error:
>>>> ,----
>>>> | Error in formula2data(formula, data, subset, frame = parent.frame(), ...) :
>>>> |   could not find function "ModelEnvFormula"
>>>> `----
>>>>
>>>> Now, formula2data is an unexported function in the coin package and
>>>> ModelEnvFormula is a (exported) function in modeltools.
>>>>
>>>> So, I tried to import ModelEnvFormula from modeltools -- no avail.
>>>> And I tried to import formula2data from coin -- not possible
>>>> And I tried to import the whole coin package -- no avail.
>>>>
>>>> So, here is the question:  How do I import 'wilcoxsign_test' from the
>>>> coin package in a way, that it is usable?
>>>>
>>>
>>> Which version of the packages are you using?  The current version of
>>> coin imports ModelEnvFormula from modeltools, so it should be able to
>>> find that function.
>>>
>>> Duncan Murdoch
>>
>> As it seems, the version I use(d) depends on modeltools.
>>
>> ,----
>> | > packageDescription("coin")
>> | Package: coin
>> | Title: Conditional Inference Procedures in a Permutation Test Framework
>> | Date: 2013-04-26
>> | Version: 1.0-22
>> | Author: Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel and Achim
>> |         Zeileis
>> | Maintainer: Torsten Hothorn <[hidden email]>
>> | Description: Conditional inference procedures for the general
>> |         independence problem including two-sample, K-sample
>> |         (non-parametric ANOVA), correlation, censored, ordered and
>> |         multivariate problems.
>> | Depends: R (>= 2.2.0), methods, survival, mvtnorm (>= 0.8-0),
>> |         modeltools (>= 0.2-9)
>> | Suggests: multcomp, xtable, e1071, vcd
>> | Enhances: Biobase
>> | LazyLoad: yes
>> | LazyData: yes
>> | License: GPL-2
>> | Packaged: 2013-04-26 12:33:15 UTC; hothorn
>> | NeedsCompilation: yes
>> | Repository: CRAN
>> | Date/Publication: 2013-04-26 15:27:04
>> | Built: R 3.0.1; x86_64-pc-linux-gnu; 2013-05-29 16:07:42 UTC; unix
>> |
>> | -- File: /usr/lib/R/site-library/coin/Meta/package.rds
>> `----
>>
>> I can confirm that updating coin (to version 1.1-0) did resolve my
>> problem.  Thank you very much!
>>
>>
>> This leads to the follow-up question:  How would I have correctly dealt
>> with this situation if my dependency ('coin') had not been updated?
>
> I think the only workaround would be for you to say your package
> Depends on modeltools.  It's really a coin issue, not yours, and the
> right people fixed it.
>

They did, indeed.  Thank you for the info and for your quick help on
this!

Regards,
Andreas

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