Re: [R-pkg-devel] failing S3 dispatch

2021-10-21 Thread Duncan Murdoch 

On 21/10/2021 1:23 p.m., Jens Oehlschlägel wrote:

Thanks Duncan,

I finally found the reason for the mysterious dispatch-failure: I had an
unwanted and unexported replicated definition of the 'clone' generic in
ff's namespace (a left-over).

I still don't understand how this prevented the proper dispatch since
the duplicate in ff's namespace it was *not* called. I further
experimented and *any* non-exported object matching the name of the
generic caused the problem. Scary, maybe worth a check!


Your NAMESPACE file contains

  S3method("clone",ff)

When R installs your package, it has to figure out where "clone" lives. 
 You imported a copy of it from bit, and then overwrote that imported 
copy with the replicated definition.


That created a new generic belonging to ff, and that's the one that your 
clone.ff method was attached to.


When you called clone(x), you called the bit::clone generic which never 
received the registration, so dispatch to clone.ff never happened.


It makes sense:  you don't want a generic in one package to interfere 
with an unrelated generic in another package that happens to have the 
same name.


Duncan Murdoch




Anyhow, removing the non-exported object solved the problem.

Best regards

Jens


On 20.10.21 13:43, Jens Oehlschlägel wrote:

Thank you Duncan,

bit NAMESPACE has

S3method(clone,default)
export(clone)

ff NAMESPACE has

import(bit)
# wish of CRAN maintainers: export another time here (now maintained
and exported in bit)
# without this R CMD CHECK complained, but with it R CMD CHECK
complains also, how to export again and why?
# clone
#,clone.default
  clone.ff
,clone.ffdf
S3method("clone",ff)
S3method(clone, ffdf)
# wish of CRAN maintainers: export another time here (now maintained
and exported in bit)
#S3method(clone, default)

Best

Jens



On 20.10.21 11:02, Duncan Murdoch wrote:

On 19/10/2021 3:43 p.m., Jens Oehlschlägel wrote:

I didn't find an answer elsewhere:

My package 'bit' creates a S3 generic 'clone' and exports it.
Furthermore it registers a S3 method 'clone.default' (not exported).

My package 'ff' imports package 'bit' and exports and registers a
new S3
method 'clone.ff'. However, calling 'clone(ffobj)' dispatches to
clone.default instead of clone.ff !? Why?


You should show us the NAMESPACE entries involving clone and clone.ff
from ff.

Some comments that may or may not be relevant:

  - Normally you wouldn't export clone.ff, it's enough to register it
using S3method().

  - You may have created a new generic named clone, and that's what
clone.ff would attach itself to.  You can have bit::clone and
ff::clone as different generics and that would cause problems.



What is the recommended way to create new S3-methods that get
dispatched? In earlier versions of the packages I simply exported
everything - that worked.


I import the generic and use S3method(generic, method).  I don't
export the methods, so I wouldn't be able to call z <- clone.ff(a).

Duncan Murdoch



Best


Jens


   > require(ff)
   >
   > a <- as.ff(0:9)
   > class(x)
[1] "ff_vector" "ff"
   >
   > x <- clone(a)
   > y <- bit:::clone.default(a)
   > z <- clone.ff(a)
   >
   > # cloned ffobjects should have different filenames>

   > filename(a)  # original
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
   >
   > filename(x)  # unexpected equal (dispatch to clone.default)
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
   >
   > filename(y)  # expected equal
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
   >
   > filename(z)  # OK
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed551d3ee66.ff"

   > version
      _
platform   x86_64-pc-linux-gnu
arch   x86_64
os linux-gnu
system x86_64, linux-gnu
status
major  4
minor  1.1
year   2021
month  08
day    10
svn rev    80725
language   R
version.string R version 4.1.1 (2021-08-10)
nickname   Kick Things

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Re: [R-pkg-devel] failing S3 dispatch

2021-10-21 Thread Jens Oehlschlägel 

Thanks Duncan,

I finally found the reason for the mysterious dispatch-failure: I had an 
unwanted and unexported replicated definition of the 'clone' generic in 
ff's namespace (a left-over).


I still don't understand how this prevented the proper dispatch since 
the duplicate in ff's namespace it was *not* called. I further 
experimented and *any* non-exported object matching the name of the 
generic caused the problem. Scary, maybe worth a check!


Anyhow, removing the non-exported object solved the problem.

Best regards

Jens


On 20.10.21 13:43, Jens Oehlschlägel wrote:

Thank you Duncan,

bit NAMESPACE has

S3method(clone,default)
export(clone)

ff NAMESPACE has

import(bit)
# wish of CRAN maintainers: export another time here (now maintained 
and exported in bit)
# without this R CMD CHECK complained, but with it R CMD CHECK 
complains also, how to export again and why?

# clone
#,clone.default
 clone.ff
,clone.ffdf
S3method("clone",ff)
S3method(clone, ffdf)
# wish of CRAN maintainers: export another time here (now maintained 
and exported in bit)

#S3method(clone, default)

Best

Jens



On 20.10.21 11:02, Duncan Murdoch wrote:

On 19/10/2021 3:43 p.m., Jens Oehlschlägel wrote:

I didn't find an answer elsewhere:

My package 'bit' creates a S3 generic 'clone' and exports it.
Furthermore it registers a S3 method 'clone.default' (not exported).

My package 'ff' imports package 'bit' and exports and registers a 
new S3

method 'clone.ff'. However, calling 'clone(ffobj)' dispatches to
clone.default instead of clone.ff !? Why?


You should show us the NAMESPACE entries involving clone and clone.ff 
from ff.


Some comments that may or may not be relevant:

 - Normally you wouldn't export clone.ff, it's enough to register it 
using S3method().


 - You may have created a new generic named clone, and that's what 
clone.ff would attach itself to.  You can have bit::clone and 
ff::clone as different generics and that would cause problems.




What is the recommended way to create new S3-methods that get
dispatched? In earlier versions of the packages I simply exported
everything - that worked.


I import the generic and use S3method(generic, method).  I don't 
export the methods, so I wouldn't be able to call z <- clone.ff(a).


Duncan Murdoch



Best


Jens


  > require(ff)
  >
  > a <- as.ff(0:9)
  > class(x)
[1] "ff_vector" "ff"
  >
  > x <- clone(a)
  > y <- bit:::clone.default(a)
  > z <- clone.ff(a)
  >
  > # cloned ffobjects should have different filenames>

  > filename(a)  # original
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
  >
  > filename(x)  # unexpected equal (dispatch to clone.default)
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
  >
  > filename(y)  # expected equal
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
  >
  > filename(z)  # OK
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed551d3ee66.ff"

  > version
     _
platform   x86_64-pc-linux-gnu
arch   x86_64
os linux-gnu
system x86_64, linux-gnu
status
major  4
minor  1.1
year   2021
month  08
day    10
svn rev    80725
language   R
version.string R version 4.1.1 (2021-08-10)
nickname   Kick Things

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel





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Re: [R-pkg-devel] failing S3 dispatch

2021-10-20 Thread Jens Oehlschlägel 

Thank you Duncan,

bit NAMESPACE has

S3method(clone,default)
export(clone)

ff NAMESPACE has

import(bit)
# wish of CRAN maintainers: export another time here (now maintained and 
exported in bit)
# without this R CMD CHECK complained, but with it R CMD CHECK complains 
also, how to export again and why?

# clone
#,clone.default
 clone.ff
,clone.ffdf
S3method("clone",ff)
S3method(clone, ffdf)
# wish of CRAN maintainers: export another time here (now maintained and 
exported in bit)

#S3method(clone, default)

Best

Jens



On 20.10.21 11:02, Duncan Murdoch wrote:

On 19/10/2021 3:43 p.m., Jens Oehlschlägel wrote:

I didn't find an answer elsewhere:

My package 'bit' creates a S3 generic 'clone' and exports it.
Furthermore it registers a S3 method 'clone.default' (not exported).

My package 'ff' imports package 'bit' and exports and registers a new S3
method 'clone.ff'. However, calling 'clone(ffobj)' dispatches to
clone.default instead of clone.ff !? Why?


You should show us the NAMESPACE entries involving clone and clone.ff 
from ff.


Some comments that may or may not be relevant:

 - Normally you wouldn't export clone.ff, it's enough to register it 
using S3method().


 - You may have created a new generic named clone, and that's what 
clone.ff would attach itself to.  You can have bit::clone and 
ff::clone as different generics and that would cause problems.




What is the recommended way to create new S3-methods that get
dispatched? In earlier versions of the packages I simply exported
everything - that worked.


I import the generic and use S3method(generic, method).  I don't 
export the methods, so I wouldn't be able to call z <- clone.ff(a).


Duncan Murdoch



Best


Jens


  > require(ff)
  >
  > a <- as.ff(0:9)
  > class(x)
[1] "ff_vector" "ff"
  >
  > x <- clone(a)
  > y <- bit:::clone.default(a)
  > z <- clone.ff(a)
  >
  > # cloned ffobjects should have different filenames>

  > filename(a)  # original
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
  >
  > filename(x)  # unexpected equal (dispatch to clone.default)
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
  >
  > filename(y)  # expected equal
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
  >
  > filename(z)  # OK
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed551d3ee66.ff"

  > version
     _
platform   x86_64-pc-linux-gnu
arch   x86_64
os linux-gnu
system x86_64, linux-gnu
status
major  4
minor  1.1
year   2021
month  08
day    10
svn rev    80725
language   R
version.string R version 4.1.1 (2021-08-10)
nickname   Kick Things

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel





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Re: [R-pkg-devel] failing S3 dispatch

2021-10-20 Thread Duncan Murdoch 

On 19/10/2021 3:43 p.m., Jens Oehlschlägel wrote:

I didn't find an answer elsewhere:

My package 'bit' creates a S3 generic 'clone' and exports it.
Furthermore it registers a S3 method 'clone.default' (not exported).

My package 'ff' imports package 'bit' and exports and registers a new S3
method 'clone.ff'. However, calling 'clone(ffobj)' dispatches to
clone.default instead of clone.ff !? Why?


You should show us the NAMESPACE entries involving clone and clone.ff 
from ff.


Some comments that may or may not be relevant:

 - Normally you wouldn't export clone.ff, it's enough to register it 
using S3method().


 - You may have created a new generic named clone, and that's what 
clone.ff would attach itself to.  You can have bit::clone and ff::clone 
as different generics and that would cause problems.




What is the recommended way to create new S3-methods that get
dispatched? In earlier versions of the packages I simply exported
everything - that worked.


I import the generic and use S3method(generic, method).  I don't export 
the methods, so I wouldn't be able to call z <- clone.ff(a).


Duncan Murdoch



Best


Jens


  > require(ff)
  >
  > a <- as.ff(0:9)
  > class(x)
[1] "ff_vector" "ff"
  >
  > x <- clone(a)
  > y <- bit:::clone.default(a)
  > z <- clone.ff(a)
  >
  > # cloned ffobjects should have different filenames>

  > filename(a)  # original
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
  >
  > filename(x)  # unexpected equal (dispatch to clone.default)
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
  >
  > filename(y)  # expected equal
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
  >
  > filename(z)  # OK
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed551d3ee66.ff"

  > version
     _
platform   x86_64-pc-linux-gnu
arch   x86_64
os linux-gnu
system x86_64, linux-gnu
status
major  4
minor  1.1
year   2021
month  08
day    10
svn rev    80725
language   R
version.string R version 4.1.1 (2021-08-10)
nickname   Kick Things

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



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[R-pkg-devel] failing S3 dispatch

2021-10-19 Thread Jens Oehlschlägel 

I didn't find an answer elsewhere:

My package 'bit' creates a S3 generic 'clone' and exports it. 
Furthermore it registers a S3 method 'clone.default' (not exported).


My package 'ff' imports package 'bit' and exports and registers a new S3 
method 'clone.ff'. However, calling 'clone(ffobj)' dispatches to 
clone.default instead of clone.ff !? Why?


What is the recommended way to create new S3-methods that get 
dispatched? In earlier versions of the packages I simply exported 
everything - that worked.


Best


Jens


> require(ff)
>
> a <- as.ff(0:9)
> class(x)
[1] "ff_vector" "ff"
>
> x <- clone(a)
> y <- bit:::clone.default(a)
> z <- clone.ff(a)
>
> # cloned ffobjects should have different filenames>

> filename(a)  # original
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
>
> filename(x)  # unexpected equal (dispatch to clone.default)
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
>
> filename(y)  # expected equal
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed54cbb5060.ff"
>
> filename(z)  # OK
[1] "/tmp/Rtmpk17JRZ/ff/clone1ed551d3ee66.ff"

> version
   _
platform   x86_64-pc-linux-gnu
arch   x86_64
os linux-gnu
system x86_64, linux-gnu
status
major  4
minor  1.1
year   2021
month  08
day    10
svn rev    80725
language   R
version.string R version 4.1.1 (2021-08-10)
nickname   Kick Things

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel