R devel - Nov 2006 - WG: Formal methods are not loaded from NAMESPACE inreloadedworkspace image

Sorry, to bother the list one more time: but the following worked at
least for 'urca':

in NAMESPACE I now included explicitly:

import(methods)

a fix of the 'urca'-package will be uploaded to CRAN on the weekend.
Fritz, will this work for ypur package 'flexclust' too? I have in my
DESCRIPTION imports: methods and in flexclust it is in depends: methods.
However, both packages have not import(methods) in their NAMESPACE.
Anyway, I wonder why 'import(methods)' is explicitly needed in
NAMESPACE? Would a smart and bright soul be so kind and enlighten a
flabbergasted one? :-) Many thanks!

Best,
Bernhard
>Dear R-Devel subscriber,
>
>as a follow up to my yesterday's email: I tested an analogous example
>with the S4-package "flexclust" by executing the following code:
>
>library(flexclust)
>example(cclust)
>cl
>
>After saving the work space and starting a new R process with the
>restored work space, the same behaviour (i.e., the methods pertinent to
>"flexclust" are not used, even after executing 
library(flexclust)).
>Yesterday, I executed the code below on a Linux platform with R 2.4.0
>and it showed the same behaviour as R 2.5.0dev on Windows. As it seems
>right now, the behaviour is platform independent and not peculiar to R
>2.5.0dev.
>
>Any pointers and help for solving this problem is much appreciated.
>
>Best,
>Bernhard   
>
>>Dear R-Devel subscriber,
>>
>>I was hinted to the following problem with package 'urca':
>>
>>If one starts R and executes for instance:
>>
>>> library(urca)
>>> example(ur.df)
>>## output as expected, but omitted here
>>> class(lc.df)
>>[1] "ur.df"
>>attr(,"package")
>>[1] "urca"
>>> class(summary(lc.df))
>>[1] "sumurca"
>>attr(,"package")
>>[1] "urca"
>>> 
>>
>>everything works fine. Now, save the workspace image and quit R. After
>>starting R again with the previously restored workspace image one has:
>>
>>> ls()
>>[1] "lc.df"   "Raotbl3"
>>> class(lc.df)
>>[1] "ur.df"
>>attr(,"package")
>>[1] "urca"
>>
>>lc.df
>>## now the 'show'-method for objects of class 'ur.df' is
not utilised,
>>rather the generic 
>>## displaying all slots
>>
>>> library(urca)
>>> lc.df
>>
>>## still the same as compared to the above output.
>>## similarily
>>
>>> class(summary(lc.df))
>>[1] "table"
>>
>>
>>In the NAMESPACE file export directives for methods and classes are
>>included as:
>>
>>## Classes       
>>exportClasses("urca", "ca.jo",
"cajo.test", "ur.kpss", "ca.po",
>>"ur.ers", "ur.pp", "ur.sp",
"ur.df", "ur.za", "sumurca")
>>## Methods
>>exportMethods("show", "plot", "summary")
>>
>>Any help or pointers for solving this problem is much appreciated.
>>
>>Best,
>>Bernhard
>>
>>> sessionInfo()
>>R version 2.5.0 Under development (unstable) (2006-10-10 r39600) 
>>i386-pc-mingw32 
>>
>>locale:
>>LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_
>>MONETARY>>German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>>
>>attached base packages:
>>[1] "methods"   "stats"     "graphics" 
"grDevices"
>"datasets"  "utils"
>>
>>[7] "base"     
>>
>>other attached packages:
>>    urca fortunes 
>> "1.0-0"  "1.3-2" 
>>*****************************************************************
>>Confidentiality Note: The information contained in this 
>>mess...{{dropped}}
>>
>>______________________________________________
>>R-devel at r-project.org mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>______________________________________________
>R-devel at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-devel
>

"Pfaff, Bernhard Dr." <Bernhard_Pfaff at fra.invesco.com>
writes:
> Sorry, to bother the list one more time: but the following worked at
> least for 'urca':
>
> in NAMESPACE I now included explicitly:
>
> import(methods)
>
> a fix of the 'urca'-package will be uploaded to CRAN on the
weekend.
> Fritz, will this work for ypur package 'flexclust' too? I have in
my
> DESCRIPTION imports: methods and in flexclust it is in depends: methods.
> However, both packages have not import(methods) in their NAMESPACE.
> Anyway, I wonder why 'import(methods)' is explicitly needed in
> NAMESPACE? Would a smart and bright soul be so kind and enlighten a
> flabbergasted one? :-) Many thanks!
Because 4 > 1.

I share your flabbergasted state.  As I understand it, if you want to
use methods, you might need to:

1. Say so in .onLoad where you require(methods)

2. Certainly Depends: methods

3. As you found, in the NAMESPACE file it helps to import(methods)

4. But then you also need to Import: methods

+ seth

Well, at the moment I'm a little confused too.  It's not at all as 
simple as my previous mail suggested.

Here's what I know, and unfortunately I won't have too much time to look
further for a while.

Starting from a clean folder (no saved workspace):

 > library(urca)
 > showMethods("summary")
Function: summary (package base)
object="ANY"
object="ca.jo"
object="ca.po"
object="cajo.test"
object="ur.df"
object="ur.ers"
object="ur.kpss"
object="ur.pp"
object="ur.sp"
object="ur.za"

so you do get the methods desired.

But after example(ur.df), quit and save the workspace, then restart R:

 > library(urca)
 > showMethods("summary")

Function "summary":
 <not a generic function>

The effect does depend on something related to the example() 
calculation; just saving an arbitrary object in the workspace won't 
produce the bug.

I'll look into the effect of having an explicit import(methods) when I 
get a chance, but it's not clear why that is connected to running the 
example.

(Now the question is interesting enough that I won't give you a hard 
time about the practical motivation!)


Pfaff, Bernhard Dr. wrote:
> Sorry, to bother the list one more time: but the following worked at
> least for 'urca':
>
> in NAMESPACE I now included explicitly:
>
> import(methods)
>
> a fix of the 'urca'-package will be uploaded to CRAN on the
weekend.
> Fritz, will this work for ypur package 'flexclust' too? I have in
my
> DESCRIPTION imports: methods and in flexclust it is in depends: methods.
> However, both packages have not import(methods) in their NAMESPACE.
> Anyway, I wonder why 'import(methods)' is explicitly needed in
> NAMESPACE? Would a smart and bright soul be so kind and enlighten a
> flabbergasted one? :-) Many thanks!
>
> Best,
> Bernhard
>
>   
>> Dear R-Devel subscriber,
>>
>> as a follow up to my yesterday's email: I tested an analogous
example
>> with the S4-package "flexclust" by executing the following
code:
>>
>> library(flexclust)
>> example(cclust)
>> cl
>>
>> After saving the work space and starting a new R process with the
>> restored work space, the same behaviour (i.e., the methods pertinent to
>> "flexclust" are not used, even after executing 
library(flexclust)).
>> Yesterday, I executed the code below on a Linux platform with R 2.4.0
>> and it showed the same behaviour as R 2.5.0dev on Windows. As it seems
>> right now, the behaviour is platform independent and not peculiar to R
>> 2.5.0dev.
>>
>> Any pointers and help for solving this problem is much appreciated.
>>
>> Best,
>> Bernhard   
>>
>>     
>>> Dear R-Devel subscriber,
>>>
>>> I was hinted to the following problem with package 'urca':
>>>
>>> If one starts R and executes for instance:
>>>
>>>       
>>>> library(urca)
>>>> example(ur.df)
>>>>         
>>> ## output as expected, but omitted here
>>>       
>>>> class(lc.df)
>>>>         
>>> [1] "ur.df"
>>> attr(,"package")
>>> [1] "urca"
>>>       
>>>> class(summary(lc.df))
>>>>         
>>> [1] "sumurca"
>>> attr(,"package")
>>> [1] "urca"
>>>       
>>> everything works fine. Now, save the workspace image and quit R.
After
>>> starting R again with the previously restored workspace image one
has:
>>>
>>>       
>>>> ls()
>>>>         
>>> [1] "lc.df"   "Raotbl3"
>>>       
>>>> class(lc.df)
>>>>         
>>> [1] "ur.df"
>>> attr(,"package")
>>> [1] "urca"
>>>
>>> lc.df
>>> ## now the 'show'-method for objects of class
'ur.df' is not utilised,
>>> rather the generic 
>>> ## displaying all slots
>>>
>>>       
>>>> library(urca)
>>>> lc.df
>>>>         
>>> ## still the same as compared to the above output.
>>> ## similarily
>>>
>>>       
>>>> class(summary(lc.df))
>>>>         
>>> [1] "table"
>>>
>>>
>>> In the NAMESPACE file export directives for methods and classes are
>>> included as:
>>>
>>> ## Classes       
>>> exportClasses("urca", "ca.jo",
"cajo.test", "ur.kpss", "ca.po",
>>> "ur.ers", "ur.pp", "ur.sp",
"ur.df", "ur.za", "sumurca")
>>> ## Methods
>>> exportMethods("show", "plot",
"summary")
>>>
>>> Any help or pointers for solving this problem is much appreciated.
>>>
>>> Best,
>>> Bernhard
>>>
>>>       
>>>> sessionInfo()
>>>>         
>>> R version 2.5.0 Under development (unstable) (2006-10-10 r39600) 
>>> i386-pc-mingw32 
>>>
>>> locale:
>>> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_
>>> MONETARY>>>
German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>>>
>>> attached base packages:
>>> [1] "methods"   "stats"    
"graphics"  "grDevices"
>>>       
>> "datasets"  "utils"
>>     
>>> [7] "base"     
>>>
>>> other attached packages:
>>>    urca fortunes 
>>> "1.0-0"  "1.3-2" 
>>> *****************************************************************
>>> Confidentiality Note: The information contained in this 
>>> mess...{{dropped}}
>>>
>>> ______________________________________________
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>       
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>     
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>   
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