Re: [Bioc-devel] issue about S4 slot has a dist object.

[Michael Lawrence]

I ended up just changing the methods package to condition on the "verbose"
option, instead of "warn", which was entirely inappropriate, after I read
the documentation. So it should no longer report these issues, which
shouldn't really hurt anything. Defining them in BiocGenerics is merely a
convenience.

On Wed, Apr 1, 2015 at 9:39 PM, Michael Lawrence  wrote:

> I used my unreleased rgtags package to search for references to
> setOldClass in Bioc:
>
> library(rgtags)
> classes <- sub(".*\\.", "", methods(print))
> defs <- do.call(c, lapply(classes, findDefinitions))
> oldClass <- lapply(expr(defs), `[[`, 1L) == quote(setOldClass)
> defs[oldClass]
>
>tagname  path line
> 1 AsIs BiocGenerics/R/S3-classes-as-S4-classes.R   20
> 2  POSIXlt   gmapR/R/GsnapOutput-class.R   10
> 3 dist   MLInterfaces/R/AllClasses.R  105
> 4 dist MLInterfaces/inst/oldFiles/INIT.R   15
> 5 dist  graph/R/AllClasses.R   45
> 6 dist   phyloseq/R/allClasses.R  151
> 7  formula  biovizBase/R/facets-method.R   21
> 8  formula geeni/R/gdManager-class.R8
> 9 function   gQTLstats/R/allS4.R1
> 10  hclust  MLInterfaces/inst/oldFiles/classInterfaces.R   16
> 11  hclust   chroGPS/R/clusGPS.R2
> 12  kmeans  MLInterfaces/inst/oldFiles/classInterfaces.R   17
> 13 numeric_version AnnotationHub/R/AnnotationHubMetadata-class.R3
> 14 numeric_version AnnotationHubData/R/AnnotationHubMetadata-class.R   12
> 15  prcomp MLInterfaces/R/clDesign.R   23
> 16  prcomp  MLInterfaces/inst/oldFiles/classInterfaces.R   18
> 17 sessionInfoGGtools/R/AllClasses.R1
>
> Note that POSIXlt, formula and function are already defined by the methods
> package. I have removed the calls from gmapR and biovizBase, but the
> maintainers of the other packages should be notified. It looks like "dist"
> was a good choice, because it is in three packages. The rest of the classes
> are somewhat specialized. What's the deal with AnnotationHub and
> AnnotationHubData? I will run a similar analysis of CRAN.
>
>
> On Wed, Apr 1, 2015 at 5:18 PM, Hervé Pagès  wrote:
>
>> On 04/01/2015 05:05 PM, Michael Lawrence wrote:
>>
>>> So this explains why I wasn't able to figure out how that package was
>>> importing graph, and, yes, I also thought it was strange that graph did
>>> not export it. The methods package explicitly conditions on the warn
>>> level, so it is apparently intentional. It just looks in the global
>>> class table for duplicates, so it does not pay attention to the
>>> namespace. It's not clear to what extent the methods package assumes
>>> that there are no duplicates in the class table; probably too much work
>>> to fix.
>>>
>>> As for sharing class definitions, perhaps the methods package should
>>> define it. It already defines classes from the stats package, like
>>> "aov". We could start moving more stuff from BiocGenerics to methods.
>>>
>>
>> Sounds good. The more upstream these class definitions are the better.
>>
>> Just moved setOldClass("dist") from graph to BiocGenerics 0.13.11 and
>> exported the dist class.
>>
>> H.
>>
>>
>>>
>>>
>>> On Wed, Apr 1, 2015 at 4:29 PM, Martin Morgan >> > wrote:
>>>
>>> On 04/01/2015 03:52 PM, Hervé Pagès wrote:
>>>
>>> Hi,
>>>
>>> In the same way that we avoid having 2 packages define the same
>>> S4 generic function by moving the shared generic definitions to
>>> BiocGenerics, it seems that we should also avoid having 2
>>> packages
>>> call setOldClass on the same S3 class. Like with S4 generic
>>> functions,
>>> we've already started to do this by putting some setOldClass
>>> statements in BiocGenerics (e.g. we've done it for the
>>> 'connection'
>>> classes 'file', 'url', 'gzfile', 'bzfile', etc..., see
>>> class?gzfile).
>>> So if nobody objects we'll do this for the 'dist' class too.
>>>
>>> Then you won't need to use setOldClass in your cogena package
>>> Zhilong.
>>> You'll just need to make sure that you import BiocGenerics.
>>>
>>>
>>> This sounds like an ok work-around to me.
>>>
>>> For the hard-core...
>>>
>>> One thing is that this is not seen when the package is loaded by
>>> itself, e.g.,
>>>
>>>  > biocLite("zhilongjia/cogena")
>>>  > library(cogena)
>>>  >
>>>
>>> only when loaded by BiocCheck (on the source directory)
>>>
>>>  > BiocCheck::BiocCheck("cogena")
>>> * This is BiocCheck, version 1.3.13.
>>> * BiocCheck is a work in progress. O

Re: [Bioc-devel] issue about S4 slot has a dist object.

[Michael Lawrence]

I used my unreleased rgtags package to search for references to setOldClass
in Bioc:

library(rgtags)
classes <- sub(".*\\.", "", methods(print))
defs <- do.call(c, lapply(classes, findDefinitions))
oldClass <- lapply(expr(defs), `[[`, 1L) == quote(setOldClass)
defs[oldClass]

   tagname  path line
1 AsIs BiocGenerics/R/S3-classes-as-S4-classes.R   20
2  POSIXlt   gmapR/R/GsnapOutput-class.R   10
3 dist   MLInterfaces/R/AllClasses.R  105
4 dist MLInterfaces/inst/oldFiles/INIT.R   15
5 dist  graph/R/AllClasses.R   45
6 dist   phyloseq/R/allClasses.R  151
7  formula  biovizBase/R/facets-method.R   21
8  formula geeni/R/gdManager-class.R8
9 function   gQTLstats/R/allS4.R1
10  hclust  MLInterfaces/inst/oldFiles/classInterfaces.R   16
11  hclust   chroGPS/R/clusGPS.R2
12  kmeans  MLInterfaces/inst/oldFiles/classInterfaces.R   17
13 numeric_version AnnotationHub/R/AnnotationHubMetadata-class.R3
14 numeric_version AnnotationHubData/R/AnnotationHubMetadata-class.R   12
15  prcomp MLInterfaces/R/clDesign.R   23
16  prcomp  MLInterfaces/inst/oldFiles/classInterfaces.R   18
17 sessionInfoGGtools/R/AllClasses.R1

Note that POSIXlt, formula and function are already defined by the methods
package. I have removed the calls from gmapR and biovizBase, but the
maintainers of the other packages should be notified. It looks like "dist"
was a good choice, because it is in three packages. The rest of the classes
are somewhat specialized. What's the deal with AnnotationHub and
AnnotationHubData? I will run a similar analysis of CRAN.


On Wed, Apr 1, 2015 at 5:18 PM, Hervé Pagès  wrote:

> On 04/01/2015 05:05 PM, Michael Lawrence wrote:
>
>> So this explains why I wasn't able to figure out how that package was
>> importing graph, and, yes, I also thought it was strange that graph did
>> not export it. The methods package explicitly conditions on the warn
>> level, so it is apparently intentional. It just looks in the global
>> class table for duplicates, so it does not pay attention to the
>> namespace. It's not clear to what extent the methods package assumes
>> that there are no duplicates in the class table; probably too much work
>> to fix.
>>
>> As for sharing class definitions, perhaps the methods package should
>> define it. It already defines classes from the stats package, like
>> "aov". We could start moving more stuff from BiocGenerics to methods.
>>
>
> Sounds good. The more upstream these class definitions are the better.
>
> Just moved setOldClass("dist") from graph to BiocGenerics 0.13.11 and
> exported the dist class.
>
> H.
>
>
>>
>>
>> On Wed, Apr 1, 2015 at 4:29 PM, Martin Morgan > > wrote:
>>
>> On 04/01/2015 03:52 PM, Hervé Pagès wrote:
>>
>> Hi,
>>
>> In the same way that we avoid having 2 packages define the same
>> S4 generic function by moving the shared generic definitions to
>> BiocGenerics, it seems that we should also avoid having 2 packages
>> call setOldClass on the same S3 class. Like with S4 generic
>> functions,
>> we've already started to do this by putting some setOldClass
>> statements in BiocGenerics (e.g. we've done it for the
>> 'connection'
>> classes 'file', 'url', 'gzfile', 'bzfile', etc..., see
>> class?gzfile).
>> So if nobody objects we'll do this for the 'dist' class too.
>>
>> Then you won't need to use setOldClass in your cogena package
>> Zhilong.
>> You'll just need to make sure that you import BiocGenerics.
>>
>>
>> This sounds like an ok work-around to me.
>>
>> For the hard-core...
>>
>> One thing is that this is not seen when the package is loaded by
>> itself, e.g.,
>>
>>  > biocLite("zhilongjia/cogena")
>>  > library(cogena)
>>  >
>>
>> only when loaded by BiocCheck (on the source directory)
>>
>>  > BiocCheck::BiocCheck("cogena")
>> * This is BiocCheck, version 1.3.13.
>> * BiocCheck is a work in progress. Output and severity of issues may
>>change.
>> * Installing package...
>> Note: the specification for S3 class "dist" in package 'cogena'
>> seems equivalent to one from package 'graph': not turning on
>> duplicate class definitions for this class.
>> ^C
>>
>> This is because BiocCheck (indirectly?) Imports: graph. But the old
>> class definition seems to 'leak' (even though graph is not on the
>> search path, and the dist old class is not exported from graph, 

Re: [Bioc-devel] issue about S4 slot has a dist object.

[Hervé Pagès]

On 04/01/2015 05:05 PM, Michael Lawrence wrote:

So this explains why I wasn't able to figure out how that package was
importing graph, and, yes, I also thought it was strange that graph did
not export it. The methods package explicitly conditions on the warn
level, so it is apparently intentional. It just looks in the global
class table for duplicates, so it does not pay attention to the
namespace. It's not clear to what extent the methods package assumes
that there are no duplicates in the class table; probably too much work
to fix.

As for sharing class definitions, perhaps the methods package should
define it. It already defines classes from the stats package, like
"aov". We could start moving more stuff from BiocGenerics to methods.


Sounds good. The more upstream these class definitions are the better.

Just moved setOldClass("dist") from graph to BiocGenerics 0.13.11 and
exported the dist class.

H.





On Wed, Apr 1, 2015 at 4:29 PM, Martin Morgan mailto:mtmor...@fredhutch.org>> wrote:

On 04/01/2015 03:52 PM, Hervé Pagès wrote:

Hi,

In the same way that we avoid having 2 packages define the same
S4 generic function by moving the shared generic definitions to
BiocGenerics, it seems that we should also avoid having 2 packages
call setOldClass on the same S3 class. Like with S4 generic
functions,
we've already started to do this by putting some setOldClass
statements in BiocGenerics (e.g. we've done it for the 'connection'
classes 'file', 'url', 'gzfile', 'bzfile', etc..., see
class?gzfile).
So if nobody objects we'll do this for the 'dist' class too.

Then you won't need to use setOldClass in your cogena package
Zhilong.
You'll just need to make sure that you import BiocGenerics.


This sounds like an ok work-around to me.

For the hard-core...

One thing is that this is not seen when the package is loaded by
itself, e.g.,

 > biocLite("zhilongjia/cogena")
 > library(cogena)
 >

only when loaded by BiocCheck (on the source directory)

 > BiocCheck::BiocCheck("cogena")
* This is BiocCheck, version 1.3.13.
* BiocCheck is a work in progress. Output and severity of issues may
   change.
* Installing package...
Note: the specification for S3 class "dist" in package 'cogena'
seems equivalent to one from package 'graph': not turning on
duplicate class definitions for this class.
^C

This is because BiocCheck (indirectly?) Imports: graph. But the old
class definition seems to 'leak' (even though graph is not on the
search path, and the dist old class is not exported from graph, and
BiocCheck doesn't import the non-exported dist class, and cogena
doesn't Depend or Import graph!)

Also of interest perhaps is that the Note is only printed when
warn=1 (which BiocCheck also uses)

(new R session)

 > requireNamespace("graph")
Loading required namespace: graph
 > requireNamespace("cogena")
Loading required namespace: cogena
 > q()

(new R session:)

 > options(warn=1)
 > requireNamespace("graph")
Loading required namespace: graph
 > requireNamespace("cogena")
Loading required namespace: cogena

Note: the specification for S3 class "dist" in package 'cogena'
seems equivalent to one from package 'graph': not turning on
duplicate class definitions for this class.
 >



Cheers,
H.


On 04/01/2015 03:28 PM, Michael Lawrence wrote:

Using setOldClass is generally fine. In this case, the graph
package is
already defining the dist class, so you could just import
that. The graph
package might have to export it though.

On Wed, Apr 1, 2015 at 3:15 PM, Zhilong Jia
mailto:zhilong...@gmail.com>> wrote:

Hi,

Here is the package.
(https://tracker.bioconductor.__org/issue1204
 or
https://github.com/zhilongjia/__cogena
; ). When I
biocCheck it, there is a
note.

Note: the specification for S3 class “dist” in package
‘cogena’ seems
equivalent to one from package ‘graph’: not turning on
duplicate class
definitions for this class.


In the source code, there are two R files are related
with this issue,
cogena_class.R
and

>
dist_class.R

Re: [Bioc-devel] issue about S4 slot has a dist object.

[Michael Lawrence]

So this explains why I wasn't able to figure out how that package was
importing graph, and, yes, I also thought it was strange that graph did not
export it. The methods package explicitly conditions on the warn level, so
it is apparently intentional. It just looks in the global class table for
duplicates, so it does not pay attention to the namespace. It's not clear
to what extent the methods package assumes that there are no duplicates in
the class table; probably too much work to fix.

As for sharing class definitions, perhaps the methods package should define
it. It already defines classes from the stats package, like "aov". We could
start moving more stuff from BiocGenerics to methods.



On Wed, Apr 1, 2015 at 4:29 PM, Martin Morgan 
wrote:

> On 04/01/2015 03:52 PM, Hervé Pagès wrote:
>
>> Hi,
>>
>> In the same way that we avoid having 2 packages define the same
>> S4 generic function by moving the shared generic definitions to
>> BiocGenerics, it seems that we should also avoid having 2 packages
>> call setOldClass on the same S3 class. Like with S4 generic functions,
>> we've already started to do this by putting some setOldClass
>> statements in BiocGenerics (e.g. we've done it for the 'connection'
>> classes 'file', 'url', 'gzfile', 'bzfile', etc..., see class?gzfile).
>> So if nobody objects we'll do this for the 'dist' class too.
>>
>> Then you won't need to use setOldClass in your cogena package Zhilong.
>> You'll just need to make sure that you import BiocGenerics.
>>
>
> This sounds like an ok work-around to me.
>
> For the hard-core...
>
> One thing is that this is not seen when the package is loaded by itself,
> e.g.,
>
> > biocLite("zhilongjia/cogena")
> > library(cogena)
> >
>
> only when loaded by BiocCheck (on the source directory)
>
> > BiocCheck::BiocCheck("cogena")
> * This is BiocCheck, version 1.3.13.
> * BiocCheck is a work in progress. Output and severity of issues may
>   change.
> * Installing package...
> Note: the specification for S3 class "dist" in package 'cogena' seems
> equivalent to one from package 'graph': not turning on duplicate class
> definitions for this class.
> ^C
>
> This is because BiocCheck (indirectly?) Imports: graph. But the old class
> definition seems to 'leak' (even though graph is not on the search path,
> and the dist old class is not exported from graph, and BiocCheck doesn't
> import the non-exported dist class, and cogena doesn't Depend or Import
> graph!)
>
> Also of interest perhaps is that the Note is only printed when warn=1
> (which BiocCheck also uses)
>
> (new R session)
>
> > requireNamespace("graph")
> Loading required namespace: graph
> > requireNamespace("cogena")
> Loading required namespace: cogena
> > q()
>
> (new R session:)
>
> > options(warn=1)
> > requireNamespace("graph")
> Loading required namespace: graph
> > requireNamespace("cogena")
> Loading required namespace: cogena
>
> Note: the specification for S3 class "dist" in package 'cogena' seems
> equivalent to one from package 'graph': not turning on duplicate class
> definitions for this class.
> >
>
>
>
>> Cheers,
>> H.
>>
>>
>> On 04/01/2015 03:28 PM, Michael Lawrence wrote:
>>
>>> Using setOldClass is generally fine. In this case, the graph package is
>>> already defining the dist class, so you could just import that. The graph
>>> package might have to export it though.
>>>
>>> On Wed, Apr 1, 2015 at 3:15 PM, Zhilong Jia 
>>> wrote:
>>>
>>>  Hi,

 Here is the package. (https://tracker.bioconductor.org/issue1204 or
 https://github.com/zhilongjia/cogena; ). When I biocCheck it, there is
 a
 note.

 Note: the specification for S3 class “dist” in package ‘cogena’ seems
 equivalent to one from package ‘graph’: not turning on duplicate class
 definitions for this class.


 In the source code, there are two R files are related with this issue,
 cogena_class.R
 and  
 dist_class.R
  in
 the R
 dir. Here there is a dist slot in cogena class. In the dist_class.R
 , I
 use
 setOldClass, but it seems it is not recommended by Bioconductor.

 How to repair this issue? Thank you.

 Regards,
 Zhilong
 

  [[alternative HTML version deleted]]

 ___
 Bioc-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/bioc-devel


>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.

Re: [Bioc-devel] issue about S4 slot has a dist object.

[Martin Morgan]

On 04/01/2015 03:52 PM, Hervé Pagès wrote:

Hi,

In the same way that we avoid having 2 packages define the same
S4 generic function by moving the shared generic definitions to
BiocGenerics, it seems that we should also avoid having 2 packages
call setOldClass on the same S3 class. Like with S4 generic functions,
we've already started to do this by putting some setOldClass
statements in BiocGenerics (e.g. we've done it for the 'connection'
classes 'file', 'url', 'gzfile', 'bzfile', etc..., see class?gzfile).
So if nobody objects we'll do this for the 'dist' class too.

Then you won't need to use setOldClass in your cogena package Zhilong.
You'll just need to make sure that you import BiocGenerics.


This sounds like an ok work-around to me.

For the hard-core...

One thing is that this is not seen when the package is loaded by itself, e.g.,

> biocLite("zhilongjia/cogena")
> library(cogena)
>

only when loaded by BiocCheck (on the source directory)

> BiocCheck::BiocCheck("cogena")
* This is BiocCheck, version 1.3.13.
* BiocCheck is a work in progress. Output and severity of issues may
  change.
* Installing package...
Note: the specification for S3 class "dist" in package 'cogena' seems equivalent 
to one from package 'graph': not turning on duplicate class definitions for this 
class.

^C

This is because BiocCheck (indirectly?) Imports: graph. But the old class 
definition seems to 'leak' (even though graph is not on the search path, and the 
dist old class is not exported from graph, and BiocCheck doesn't import the 
non-exported dist class, and cogena doesn't Depend or Import graph!)


Also of interest perhaps is that the Note is only printed when warn=1 (which 
BiocCheck also uses)


(new R session)

> requireNamespace("graph")
Loading required namespace: graph
> requireNamespace("cogena")
Loading required namespace: cogena
> q()

(new R session:)

> options(warn=1)
> requireNamespace("graph")
Loading required namespace: graph
> requireNamespace("cogena")
Loading required namespace: cogena
Note: the specification for S3 class "dist" in package 'cogena' seems equivalent 
to one from package 'graph': not turning on duplicate class definitions for this 
class.

>




Cheers,
H.


On 04/01/2015 03:28 PM, Michael Lawrence wrote:

Using setOldClass is generally fine. In this case, the graph package is
already defining the dist class, so you could just import that. The graph
package might have to export it though.

On Wed, Apr 1, 2015 at 3:15 PM, Zhilong Jia  wrote:


Hi,

Here is the package. (https://tracker.bioconductor.org/issue1204 or
https://github.com/zhilongjia/cogena; ). When I biocCheck it, there is a
note.

Note: the specification for S3 class “dist” in package ‘cogena’ seems
equivalent to one from package ‘graph’: not turning on duplicate class
definitions for this class.


In the source code, there are two R files are related with this issue,
cogena_class.R
and  
dist_class.R
 in the R
dir. Here there is a dist slot in cogena class. In the dist_class.R
, I use
setOldClass, but it seems it is not recommended by Bioconductor.

How to repair this issue? Thank you.

Regards,
Zhilong


 [[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel






--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] issue about S4 slot has a dist object.

[Hervé Pagès]

Hi,

In the same way that we avoid having 2 packages define the same
S4 generic function by moving the shared generic definitions to
BiocGenerics, it seems that we should also avoid having 2 packages
call setOldClass on the same S3 class. Like with S4 generic functions,
we've already started to do this by putting some setOldClass
statements in BiocGenerics (e.g. we've done it for the 'connection'
classes 'file', 'url', 'gzfile', 'bzfile', etc..., see class?gzfile).
So if nobody objects we'll do this for the 'dist' class too.

Then you won't need to use setOldClass in your cogena package Zhilong.
You'll just need to make sure that you import BiocGenerics.

Cheers,
H.


On 04/01/2015 03:28 PM, Michael Lawrence wrote:

Using setOldClass is generally fine. In this case, the graph package is
already defining the dist class, so you could just import that. The graph
package might have to export it though.

On Wed, Apr 1, 2015 at 3:15 PM, Zhilong Jia  wrote:


Hi,

Here is the package. (https://tracker.bioconductor.org/issue1204 or
https://github.com/zhilongjia/cogena; ). When I biocCheck it, there is a
note.

Note: the specification for S3 class “dist” in package ‘cogena’ seems
equivalent to one from package ‘graph’: not turning on duplicate class
definitions for this class.


In the source code, there are two R files are related with this issue,
cogena_class.R
and  
dist_class.R
 in the R
dir. Here there is a dist slot in cogena class. In the dist_class.R
, I use
setOldClass, but it seems it is not recommended by Bioconductor.

How to repair this issue? Thank you.

Regards,
Zhilong


 [[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] issue about S4 slot has a dist object.

[Michael Lawrence]

Using setOldClass is generally fine. In this case, the graph package is
already defining the dist class, so you could just import that. The graph
package might have to export it though.

On Wed, Apr 1, 2015 at 3:15 PM, Zhilong Jia  wrote:

> Hi,
>
> Here is the package. (https://tracker.bioconductor.org/issue1204 or
> https://github.com/zhilongjia/cogena; ). When I biocCheck it, there is a
> note.
>
> Note: the specification for S3 class “dist” in package ‘cogena’ seems
> equivalent to one from package ‘graph’: not turning on duplicate class
> definitions for this class.
>
>
> In the source code, there are two R files are related with this issue,
> cogena_class.R
> and  
> dist_class.R
>  in the R
> dir. Here there is a dist slot in cogena class. In the dist_class.R
> , I use
> setOldClass, but it seems it is not recommended by Bioconductor.
>
> How to repair this issue? Thank you.
>
> Regards,
> Zhilong
> 
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] issue about S4 slot has a dist object.

[Zhilong Jia]

Hi,

Here is the package. (https://tracker.bioconductor.org/issue1204 or
https://github.com/zhilongjia/cogena; ). When I biocCheck it, there is a
note.

Note: the specification for S3 class “dist” in package ‘cogena’ seems
equivalent to one from package ‘graph’: not turning on duplicate class
definitions for this class.


In the source code, there are two R files are related with this issue,
cogena_class.R
and  
dist_class.R
 in the R
dir. Here there is a dist slot in cogena class. In the dist_class.R
, I use
setOldClass, but it seems it is not recommended by Bioconductor.

How to repair this issue? Thank you.

Regards,
Zhilong


[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel