From hhoeflin at gmail.com  Wed Feb 18 16:02:05 2015
From: hhoeflin at gmail.com (Holger Hoefling)
Date: Wed, 18 Feb 2015 16:02:05 +0100
Subject: [Rd] Different serialization of functions in interactive vs.
 batch mode
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	<alpine.DEB.2.02.1502180804090.2336@luke-Latitude>
	<CAFDswJsiEw+zZ0HibzQzA02JqyVKtgDpr0Bz7SLjhPiJ7YRjoA@mail.gmail.com>
	<alpine.LFD.2.11.1502180851280.32711@itasca.stat.uiowa.edu>
Message-ID: <CAFDswJuOCkZUTmVbtf339fvZfByJ4+XOmVyOWGmc8O2p0cEgGw@mail.gmail.com>

Luke, thank you so much - that solves my problem!

Holger

On Wed, Feb 18, 2015 at 3:56 PM,  <luke-tierney at uiowa.edu> wrote:
> 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



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