[Rd] Different serialization of functions in interactive vs. batch mode

luke-tierney at uiowa.edu luke-tierney at uiowa.edu
Wed Feb 18 15:56:22 CET 2015 

On Wed, 18 Feb 2015, Holger Hoefling wrote:

> Hi Luke,
>
> Ah - I see - thank you! This at least points me to a way on how to
> "fix" this. I tried setting the srcref attribute to NULL, but the hash
> value is still different and so is the serialization. So this looks
> like it is one difference, but not all of them

when source attributes are attached they are attached to calls within
the body as well, so

     > attributes(body(testfun))
     $srcref
     $srcref[[1]]
     ...

> Even if all differences were identified - it still leaves me with
> different behavior between interactive and batch-mode, though. I am
> curious as to why that is. Do you know why in interactive mode the
> attribute with the srcref is set, but not in batch mode?

I can't speak to why the default for the keep.source option is
different in the two cases, but you can set it to be the same: in
interactive mode

     > options(keep.source = FALSE)
     > testfun <- function() {return(NULL)}
     > digest(testfun)
     [1] "b03160b9250f0d5b5bcce42bd86d8e56"

Or use options(keep.source = TRUE) in the other case.

Best,

luke

>
> Thanks!
>
> Holger
>
> P.S. I attached the output I get when i set the attributes to NULL
>
>
> On Wed, Feb 18, 2015 at 3:04 PM,  <luke-tierney at uiowa.edu> wrote:
>> Add
>>
>> attributes(testfun)
>>
>> and you will see where the two functions differ.
>>
>> luke
>>
>>
>> On Wed, 18 Feb 2015, Holger Hoefling wrote:
>>
>>> Hi,
>>>
>>> I posted this question to the regular help list, but it seems to be
>>> this is probably a question that is better addressed on r-devel. Sorry
>>> for the double posting.
>>>
>>> I am using hash-values to cache certain results in R. This caching
>>> also depends on the hash-value of the function that is being cached
>>> (calculated using the digest package). I noticed that computations
>>> that should already be cached are recomputed when switching from an
>>> interactive session to a BATCH session. Therefore, I wrote a test
>>> script
>>>
>>> library(digest)
>>> testfun <- function() {
>>>    return(NULL)
>>> }
>>> testval <- "testval"
>>> print(digest(testfun))
>>> print(serialize(testfun, connection = NULL))
>>>
>>> and executed it once using input-redirection from a file (testFile.R)
>>> and once copying the code into an interactive R session. The
>>> hash-values of the functions differ. As digest internally relies on
>>> serialize, I also checked there and found that digest is not the
>>> reason for the discrepancy. Instead, the serialized value of the
>>> function already differs between the BATCH and inteactive sessions.
>>>
>>> I was wondering if someone knows if
>>> 1. Is this a feature or a bug? It feels like a bug to me as all the
>>> inputs are identical, I would expect that the output is identical as
>>> well. Is there something I am overlooking?
>>> 2. Is there a way to get consistent hash-values for functions between
>>> BATCH and interactive sessions.
>>>
>>> The output from the BATCH and interactive runs are below (as well as
>>> sessionInfo)
>>>
>>> Thank you very much for your help!
>>>
>>> Holger Hoefling
>>>
>>> ---------------------------------
>>> BATCH run (via input redirection):
>>>
>>> $ R --vanilla < testFile.R
>>>
>>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>>> Copyright (C) 2014 The R Foundation for Statistical Computing
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>> library(digest)
>>>> testfun <- function() {
>>>
>>> +     return(NULL)
>>> + }
>>>>
>>>> print(digest(testfun))
>>>
>>> [1] "b03160b9250f0d5b5bcce42bd86d8e56"
>>>>
>>>> print(serialize(testfun, connection = NULL))
>>>
>>> [1] 58 0a 00 00 00 02 00 03 01 00 00 02 03 00 00 00 04 03 00 00 00 fd 00
>>> 00 00
>>> [26] fe 00 00 00 06 00 00 00 01 00 04 00 09 00 00 00 01 7b 00 00 00 02 00
>>> 00 00
>>> [51] 06 00 00 00 01 00 04 00 09 00 00 00 06 72 65 74 75 72 6e 00 00 00 02
>>> 00 00
>>> [76] 00 fe 00 00 00 fe 00 00 00 fe
>>>>
>>>> sessionInfo()
>>>
>>> R version 3.1.0 (2014-04-10)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] digest_0.6.4
>>>>
>>>>
>>>
>>> ----------------------------------------------
>>> Interactive run:
>>>
>>> $ R --vanilla
>>>
>>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>>> Copyright (C) 2014 The R Foundation for Statistical Computing
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>> library(digest)
>>>> testfun <- function() {
>>>
>>> +     return(NULL)
>>> + }
>>>>
>>>> print(digest(testfun))
>>>
>>> [1] "fada482d2894088b079a8e56b7044862"
>>>>
>>>> print(serialize(testfun, connection = NULL))
>>>
>>>  [1] 58 0a 00 00 00 02 00 03 01 00 00 02 03 00 00 00 06 03 00 00 04 02 00
>>> 00 00
>>> [26] 01 00 04 00 09 00 00 00 06 73 72 63 72 65 66 00 00 03 0d 00 00 00 08
>>> 00 00
>>> [51] 00 01 00 00 00 0c 00 00 00 03 00 00 00 01 00 00 00 0c 00 00 00 01 00
>>> 00 00
>>> [76] 01 00 00 00 03 00 00 04 02 00 00 00 01 00 04 00 09 00 00 00 07 73 72
>>> 63 66
>>> [101] 69 6c 65 00 00 00 04 00 00 00 00 00 00 00 f2 00 00 04 02 00 00 00 01
>>> 00 04
>>> [126] 00 09 00 00 00 05 6c 69 6e 65 73 00 00 00 10 00 00 00 01 00 04 00 09
>>> 00 00
>>> [151] 00 2b 74 65 73 74 66 75 6e 20 3c 2d 20 66 75 6e 63 74 69 6f 6e 28 29
>>> 20 7b
>>> [176] 0a 20 20 20 20 72 65 74 75 72 6e 28 4e 55 4c 4c 29 0a 7d 0a 00 00 04
>>> 02 00
>>> [201] 00 00 01 00 04 00 09 00 00 00 08 66 69 6c 65 6e 61 6d 65 00 00 00 10
>>> 00 00
>>> [226] 00 01 00 04 00 09 00 00 00 00 00 00 00 fe 00 00 00 fe 00 00 04 02 00
>>> 00 00
>>> [251] 01 00 04 00 09 00 00 00 05 63 6c 61 73 73 00 00 00 10 00 00 00 02 00
>>> 04 00
>>> [276] 09 00 00 00 0b 73 72 63 66 69 6c 65 63 6f 70 79 00 04 00 09 00 00 00
>>> 07 73
>>> [301] 72 63 66 69 6c 65 00 00 00 fe 00 00 04 02 00 00 06 ff 00 00 00 10 00
>>> 00 00
>>> [326] 01 00 04 00 09 00 00 00 06 73 72 63 72 65 66 00 00 00 fe 00 00 00 fe
>>> 00 00
>>> [351] 00 fd 00 00 00 fe 00 00 02 06 00 00 04 02 00 00 01 ff 00 00 00 13 00
>>> 00 00
>>> [376] 02 00 00 03 0d 00 00 00 08 00 00 00 01 00 00 00 17 00 00 00 01 00 00
>>> 00 17
>>> [401] 00 00 00 17 00 00 00 17 00 00 00 01 00 00 00 01 00 00 04 02 00 00 02
>>> ff 00
>>> [426] 00 03 ff 00 00 04 02 00 00 06 ff 00 00 00 10 00 00 00 01 00 04 00 09
>>> 00 00
>>> [451] 00 06 73 72 63 72 65 66 00 00 00 fe 00 00 03 0d 00 00 00 08 00 00 00
>>> 02 00
>>> [476] 00 00 05 00 00 00 02 00 00 00 10 00 00 00 05 00 00 00 10 00 00 00 02
>>> 00 00
>>> [501] 00 02 00 00 04 02 00 00 02 ff 00 00 03 ff 00 00 04 02 00 00 06 ff 00
>>> 00 00
>>> [526] 10 00 00 00 01 00 04 00 09 00 00 00 06 73 72 63 72 65 66 00 00 00 fe
>>> 00 00
>>> [551] 04 02 00 00 02 ff 00 00 03 ff 00 00 04 02 00 00 00 01 00 04 00 09 00
>>> 00 00
>>> [576] 0b 77 68 6f 6c 65 53 72 63 72 65 66 00 00 03 0d 00 00 00 08 00 00 00
>>> 01 00
>>> [601] 00 00 00 00 00 00 03 00 00 00 01 00 00 00 00 00 00 00 01 00 00 00 01
>>> 00 00
>>> [626] 00 03 00 00 04 02 00 00 02 ff 00 00 03 ff 00 00 04 02 00 00 06 ff 00
>>> 00 00
>>> [651] 10 00 00 00 01 00 04 00 09 00 00 00 06 73 72 63 72 65 66 00 00 00 fe
>>> 00 00
>>> [676] 00 fe 00 00 00 01 00 04 00 09 00 00 00 01 7b 00 00 00 02 00 00 00 06
>>> 00 00
>>> [701] 00 01 00 04 00 09 00 00 00 06 72 65 74 75 72 6e 00 00 00 02 00 00 00
>>> fe 00
>>> [726] 00 00 fe 00 00 00 fe
>>>>
>>>> sessionInfo()
>>>
>>> R version 3.1.0 (2014-04-10)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] digest_0.6.4
>>>>
>>>>
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>> --
>> Luke Tierney
>> Ralph E. Wareham Professor of Mathematical Sciences
>> University of Iowa                  Phone:             319-335-3386
>> Department of Statistics and        Fax:               319-335-3017
>>    Actuarial Science
>> 241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
>> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
>

-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

More information about the R-devel mailing list