R devel - Jan 2015 - Inspect a "delayed" assigned whose value throws an error?

Hi, I got an interesting programming challenge:

How do you inspect an object which is assigned via delayedAssign() and
that throws an error as soon as it is "touched" (=the value is
evaluated)?  Is it possible?


MINIMAL EXAMPLE:

$ R --vanilla
> delayedAssign("foo", stop("Hey!"))
(If you find this minimal example silly/obvious, please skip down to
the real example at the end)
> foo
Error: Hey!
> str(foo)
Error in str(foo) : Hey!
In addition: Warning message:
In str(foo) : restarting interrupted promise evaluation
> mode(foo)
Error in mode(foo) : Hey!
In addition: Warning message:
In mode(foo) : restarting interrupted promise evaluation
> .Internal(inspect(foo))
Error: Hey!
In addition: Warning message:
restarting interrupted promise evaluation
> traceback()
1: stop("Hey!")

Is there anyway I can inspect this object using the R API without
evaluating the value in the delayed assignment?  Is it possible to
test if this is a delayed assigned or not?


BACKGROUND:
The background to this is where I have a function in the R.oo package
that scans namespaces for functions with a certain class attribute.
For this I use is.function() and inherits() to inspect each object.
An aroma.affymetrix user reported on a problem that boiled down to the
following:

# source("http://bioconductor.org/biocLite.R");
biocLite("hgu133a.db")
> library("hgu133a.db")
> is.function(hgu133aPFAM)
Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM
  or PROSITE accessions.
> .Internal(inspect(hgu133aPFAM))
> traceback()
3: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA)
2: .Defunct(msg = msg)
1: (function ()
   {
       if (grepl("PFAM", x)) {
           bimapName <- paste0(prefix, "PFAM")
       }
       else {
           bimapName <- paste0(prefix, "PROSITE")
       }
       x <- dc[[bimapName]]
       msg = wmsg(paste0(bimapName, " is defunct. ", "Please use
select() if you
 need access to PFAM or PROSITE accessions. \n"))
       if (interactive()) {
           .Defunct(msg = msg)
       }
   })()

My immediate solution is to perform those tests using tryCatch(), but
this is interesting, because this function is such that the error is
only thrown in interactive() sessions, i.e. the following works:

$ Rscript -e "hgu133a.db::hgu133aPFAM"
[...]
NULL

This is probably also why none of my aroma.affymetrix system tests
caught this.  Without tracing the source code behind, which seems
quite nested, the above is why I believe the assignment is "delayed";
traceback() shows a body source code, the object evaluates to
different things depending on interactive().

/Henrik

If it was any other environment than the global, you could use substitute:

e <- new.env()
delayedAssign("foo", stop("Hey!"), assign.env = e)
substitute(foo, e)

delayedAssign("foo", stop("Hey!"))
substitute(foo)

Hadley

On Mon, Jan 26, 2015 at 12:53 PM, Henrik Bengtsson <hb at
biostat.ucsf.edu> wrote:
> Hi, I got an interesting programming challenge:
>
> How do you inspect an object which is assigned via delayedAssign() and
> that throws an error as soon as it is "touched" (=the value is
> evaluated)?  Is it possible?
>
>
> MINIMAL EXAMPLE:
>
> $ R --vanilla
>> delayedAssign("foo", stop("Hey!"))
>
> (If you find this minimal example silly/obvious, please skip down to
> the real example at the end)
>
>> foo
> Error: Hey!
>
>> str(foo)
> Error in str(foo) : Hey!
> In addition: Warning message:
> In str(foo) : restarting interrupted promise evaluation
>
>> mode(foo)
> Error in mode(foo) : Hey!
> In addition: Warning message:
> In mode(foo) : restarting interrupted promise evaluation
>
>> .Internal(inspect(foo))
> Error: Hey!
> In addition: Warning message:
> restarting interrupted promise evaluation
>
>> traceback()
> 1: stop("Hey!")
>
> Is there anyway I can inspect this object using the R API without
> evaluating the value in the delayed assignment?  Is it possible to
> test if this is a delayed assigned or not?
>
>
> BACKGROUND:
> The background to this is where I have a function in the R.oo package
> that scans namespaces for functions with a certain class attribute.
> For this I use is.function() and inherits() to inspect each object.
> An aroma.affymetrix user reported on a problem that boiled down to the
> following:
>
> # source("http://bioconductor.org/biocLite.R");
biocLite("hgu133a.db")
>> library("hgu133a.db")
>> is.function(hgu133aPFAM)
> Error: hgu133aPFAM is defunct. Please use select() if you need access to
PFAM
>   or PROSITE accessions.
>> .Internal(inspect(hgu133aPFAM))
>
>> traceback()
> 3: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA)
> 2: .Defunct(msg = msg)
> 1: (function ()
>    {
>        if (grepl("PFAM", x)) {
>            bimapName <- paste0(prefix, "PFAM")
>        }
>        else {
>            bimapName <- paste0(prefix, "PROSITE")
>        }
>        x <- dc[[bimapName]]
>        msg = wmsg(paste0(bimapName, " is defunct. ", "Please
use select() if you
>  need access to PFAM or PROSITE accessions. \n"))
>        if (interactive()) {
>            .Defunct(msg = msg)
>        }
>    })()
>
> My immediate solution is to perform those tests using tryCatch(), but
> this is interesting, because this function is such that the error is
> only thrown in interactive() sessions, i.e. the following works:
>
> $ Rscript -e "hgu133a.db::hgu133aPFAM"
> [...]
> NULL
>
> This is probably also why none of my aroma.affymetrix system tests
> caught this.  Without tracing the source code behind, which seems
> quite nested, the above is why I believe the assignment is
"delayed";
> traceback() shows a body source code, the object evaluates to
> different things depending on interactive().
>
> /Henrik
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


-- 
http://had.co.nz/

On Mon, Jan 26, 2015 at 12:24 PM, Hadley Wickham <h.wickham at gmail.com>
wrote:
> If it was any other environment than the global, you could use substitute:
>
> e <- new.env()
> delayedAssign("foo", stop("Hey!"), assign.env = e)
> substitute(foo, e)
>
> delayedAssign("foo", stop("Hey!"))
> substitute(foo)
Hmm... interesting and odd.

Unfortunately, this doesn't seem to help for reaching into the
namespace of hgu133a.db and inspecting 'hgu133aPFAM', e.g.
> library("hgu133a.db")
> substitute(hgu133aPFAM, env=ns)
Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM
  or PROSITE accessions.
> evalq(substitute(hgu133aPFAM), envir=ns)
Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM
  or PROSITE accessions.
> evalq(substitute(hgu133aPFAM, env=ns), envir=ns)
Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM
  or PROSITE accessions.

Thanks,

Henrik

>
> Hadley
>
> On Mon, Jan 26, 2015 at 12:53 PM, Henrik Bengtsson <hb at
biostat.ucsf.edu> wrote:
>> Hi, I got an interesting programming challenge:
>>
>> How do you inspect an object which is assigned via delayedAssign() and
>> that throws an error as soon as it is "touched" (=the value
is
>> evaluated)?  Is it possible?
>>
>>
>> MINIMAL EXAMPLE:
>>
>> $ R --vanilla
>>> delayedAssign("foo", stop("Hey!"))
>>
>> (If you find this minimal example silly/obvious, please skip down to
>> the real example at the end)
>>
>>> foo
>> Error: Hey!
>>
>>> str(foo)
>> Error in str(foo) : Hey!
>> In addition: Warning message:
>> In str(foo) : restarting interrupted promise evaluation
>>
>>> mode(foo)
>> Error in mode(foo) : Hey!
>> In addition: Warning message:
>> In mode(foo) : restarting interrupted promise evaluation
>>
>>> .Internal(inspect(foo))
>> Error: Hey!
>> In addition: Warning message:
>> restarting interrupted promise evaluation
>>
>>> traceback()
>> 1: stop("Hey!")
>>
>> Is there anyway I can inspect this object using the R API without
>> evaluating the value in the delayed assignment?  Is it possible to
>> test if this is a delayed assigned or not?
>>
>>
>> BACKGROUND:
>> The background to this is where I have a function in the R.oo package
>> that scans namespaces for functions with a certain class attribute.
>> For this I use is.function() and inherits() to inspect each object.
>> An aroma.affymetrix user reported on a problem that boiled down to the
>> following:
>>
>> # source("http://bioconductor.org/biocLite.R");
biocLite("hgu133a.db")
>>> library("hgu133a.db")
>>> is.function(hgu133aPFAM)
>> Error: hgu133aPFAM is defunct. Please use select() if you need access
to PFAM
>>   or PROSITE accessions.
>>> .Internal(inspect(hgu133aPFAM))
>>
>>> traceback()
>> 3: stop(paste(msg, collapse = ""), call. = FALSE, domain =
NA)
>> 2: .Defunct(msg = msg)
>> 1: (function ()
>>    {
>>        if (grepl("PFAM", x)) {
>>            bimapName <- paste0(prefix, "PFAM")
>>        }
>>        else {
>>            bimapName <- paste0(prefix, "PROSITE")
>>        }
>>        x <- dc[[bimapName]]
>>        msg = wmsg(paste0(bimapName, " is defunct. ",
"Please use select() if you
>>  need access to PFAM or PROSITE accessions. \n"))
>>        if (interactive()) {
>>            .Defunct(msg = msg)
>>        }
>>    })()
>>
>> My immediate solution is to perform those tests using tryCatch(), but
>> this is interesting, because this function is such that the error is
>> only thrown in interactive() sessions, i.e. the following works:
>>
>> $ Rscript -e "hgu133a.db::hgu133aPFAM"
>> [...]
>> NULL
>>
>> This is probably also why none of my aroma.affymetrix system tests
>> caught this.  Without tracing the source code behind, which seems
>> quite nested, the above is why I believe the assignment is
"delayed";
>> traceback() shows a body source code, the object evaluates to
>> different things depending on interactive().
>>
>> /Henrik
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> --
> http://had.co.nz/