R devel - Nov 2006 - Formal methods are not loaded from NAMESPACE in reloadedworkspace image

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
>

I haven't had a chance to verify these exact examples, but the likely 
explanation is that loading the workspace does not cache the  saved 
methods.  Assuming this is indeed what's happening, the workaround is to 
cache them "manually" by the call:

  cacheMetaData(.GlobalEnv)

(after attaching the relevant library)

It would be nice to have the same effect occur automatically, but there 
may be issues since the needed class definitions may not be available 
when the saved workspace is reloaded.

A natural question to ask is whether there is some practical motivation 
for this exercise.

Pfaff, Bernhard Dr. wrote:
> 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
>
>   
	[[alternative HTML version deleted]]