R devel - Jul 2016 - 3 minor issues with getClass 'resolve.msg' arg

Hi,

It turns out that two packages (1 Bioconductor, 1 CRAN) define an
S4 class called "Annotated":

   library(S4Vectors)  # see (*) at bottom for how to install
   library(RNeXML)

1st issue
---------

getClass() issues the same warning twice:

   tmp <- getClass("Annotated")
   Found more than one class "Annotated" in cache; using the first,
from
namespace 'S4Vectors'
   Found more than one class "Annotated" in cache; using the first,
from
namespace 'S4Vectors'

2nd issue
---------

It would be very helpful if the warning message was giving the name of
the other package. I was in a session with 50+ packages attached or
loaded via a namespace when I saw the warning. Took me a while to
identify the other package, which I finally managed to do with:

   names(.Call(methods:::C_R_getClassFromCache, "Annotated", 
methods:::.classTable))

3rd issue
---------

Calling getClass() with 'resolve.msg=FALSE' only removes one of the 2
warnings:

   > tmp <- getClass("Annotated", resolve.msg=FALSE)
   Found more than one class "Annotated" in cache; using the first,
from
namespace 'S4Vectors'

Thanks,
H.

(*) Install S4Vectors with:

   source("https://bioconductor.org/biocLite.R")
   biocLite("S4Vectors")

-- 
Herv? Pag?s

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: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

>>>>> Herv? Pag?s <hpages at fredhutch.org>
>>>>>     on Sun, 26 Jun 2016 13:21:00 -0700 writes:
    > Hi,
    > It turns out that two packages (1 Bioconductor, 1 CRAN) define an
    > S4 class called "Annotated":

    > library(S4Vectors)  # see (*) at bottom for how to install
    > library(RNeXML)

    > 1st issue
    > ---------

    > getClass() issues the same warning twice:

    > tmp <- getClass("Annotated")
    > Found more than one class "Annotated" in cache; using the
first, from
    > namespace 'S4Vectors'
    > Found more than one class "Annotated" in cache; using the
first, from
    > namespace 'S4Vectors'

    > 2nd issue
    > ---------

    > It would be very helpful if the warning message was giving the name of
    > the other package. I was in a session with 50+ packages attached or
    > loaded via a namespace when I saw the warning. Took me a while to
    > identify the other package, which I finally managed to do with:

    > names(.Call(methods:::C_R_getClassFromCache, "Annotated", 
    > methods:::.classTable))

    > 3rd issue
    > ---------

    > Calling getClass() with 'resolve.msg=FALSE' only removes one of
the 2
    > warnings:

    >> tmp <- getClass("Annotated", resolve.msg=FALSE)
    > Found more than one class "Annotated" in cache; using the
first, from
    > namespace 'S4Vectors'


Indeed, R-core had found this to be buggy ourselves, and changes
happened then to clean up this behavior; specifically it was

------------------------------------------------------------------------
r70554 | lawrence | 2016-04-27 06:05:07 +0200 (Wed, 27 Apr 2016)

better resolve multiple hits in the class cache
------------------------------------------------------------------------

Because the changes would have potential effects that were not
so easy to predict, and I think it *does* entail changed
*behavior* (not just messages) in some cases, the change have not
been ported to R 3.3.x patched, but remained in "R-devel".
Here is the NEWS entry (2nd entry of 'BUG FIXES) :

o When a class name matches multiple classes in the cache,
  perform a dynamic search in order to obey namespace
  imports. This should eliminate annoying messages about multiple
  hits in the class cache. Also, pass along the package from the
  ClassExtends object when looking up superclasses in the cache.

    > Thanks,
    > H.

You are welcome,
Martin


    > (*) Install S4Vectors with:

    > source("https://bioconductor.org/biocLite.R")
    > biocLite("S4Vectors")

    > -- 
    > Herv? Pag?s

    > 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: hpages at fredhutch.org
    > Phone:  (206) 667-5791
    > Fax:    (206) 667-1319

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

Hi Martin,

Thanks for the heads up and thanks Michael for making this change.

FWIW I just tried this with R-devel and indeed it seems to be doing
a much better job at handling multiple hits in the cache class. In
particular the Annotated class defined in the RNeXML package doesn't
get in the way anymore because it's not exported. Perfect!

Cheers,
H.

On 07/11/2016 03:30 AM, Martin Maechler wrote:
>>>>>> Herv? Pag?s <hpages at fredhutch.org>
>>>>>>      on Sun, 26 Jun 2016 13:21:00 -0700 writes:
>
>      > Hi,
>      > It turns out that two packages (1 Bioconductor, 1 CRAN) define an
>      > S4 class called "Annotated":
>
>      > library(S4Vectors)  # see (*) at bottom for how to install
>      > library(RNeXML)
>
>      > 1st issue
>      > ---------
>
>      > getClass() issues the same warning twice:
>
>      > tmp <- getClass("Annotated")
>      > Found more than one class "Annotated" in cache; using
the first, from
>      > namespace 'S4Vectors'
>      > Found more than one class "Annotated" in cache; using
the first, from
>      > namespace 'S4Vectors'
>
>      > 2nd issue
>      > ---------
>
>      > It would be very helpful if the warning message was giving the
name of
>      > the other package. I was in a session with 50+ packages attached
or
>      > loaded via a namespace when I saw the warning. Took me a while to
>      > identify the other package, which I finally managed to do with:
>
>      > names(.Call(methods:::C_R_getClassFromCache,
"Annotated",
>      > methods:::.classTable))
>
>      > 3rd issue
>      > ---------
>
>      > Calling getClass() with 'resolve.msg=FALSE' only removes
one of the 2
>      > warnings:
>
>      >> tmp <- getClass("Annotated", resolve.msg=FALSE)
>      > Found more than one class "Annotated" in cache; using
the first, from
>      > namespace 'S4Vectors'
>
>
> Indeed, R-core had found this to be buggy ourselves, and changes
> happened then to clean up this behavior; specifically it was
>
> ------------------------------------------------------------------------
> r70554 | lawrence | 2016-04-27 06:05:07 +0200 (Wed, 27 Apr 2016)
>
> better resolve multiple hits in the class cache
> ------------------------------------------------------------------------
>
> Because the changes would have potential effects that were not
> so easy to predict, and I think it *does* entail changed
> *behavior* (not just messages) in some cases, the change have not
> been ported to R 3.3.x patched, but remained in "R-devel".
> Here is the NEWS entry (2nd entry of 'BUG FIXES) :
>
> o When a class name matches multiple classes in the cache,
>    perform a dynamic search in order to obey namespace
>    imports. This should eliminate annoying messages about multiple
>    hits in the class cache. Also, pass along the package from the
>    ClassExtends object when looking up superclasses in the cache.
>
>      > Thanks,
>      > H.
>
> You are welcome,
> Martin
>
>
>      > (*) Install S4Vectors with:
>
>      > source("https://bioconductor.org/biocLite.R")
>      > biocLite("S4Vectors")
>
>      > --
>      > Herv? Pag?s
>
>      > 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: hpages at fredhutch.org
>      > Phone:  (206) 667-5791
>      > Fax:    (206) 667-1319
>
>      > ______________________________________________
>      > R-devel at r-project.org mailing list
>      > https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Herv? Pag?s

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: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319