From hhoeflin at gmail.com  Wed Feb 18 15:22:29 2015
From: hhoeflin at gmail.com (Holger Hoefling)
Date: Wed, 18 Feb 2015 15:22:29 +0100
Subject: [Rd] Different serialization of functions in interactive vs.
 batch mode
In-Reply-To: <alpine.DEB.2.02.1502180804090.2336@luke-Latitude>
References: <CAFDswJvq5T2sZNQyE1pDP_F9CGBFQfxrXHbzfKhB4CZPgXNO8g@mail.gmail.com>
	<alpine.DEB.2.02.1502180804090.2336@luke-Latitude>
Message-ID: <CAFDswJsiEw+zZ0HibzQzA02JqyVKtgDpr0Bz7SLjhPiJ7YRjoA@mail.gmail.com>

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

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?

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
-------------- next part --------------
library(digest)
testfun <- function() {
    return(NULL)
}
print(digest(testfun))
print(serialize(testfun, connection = NULL))
print(attributes(testfun))
attributes(testfun)$srcref <- NULL
print(attributes(testfun))
print(digest(testfun))
print(serialize(testfun, connection = NULL))
sessionInfo()



===============================================================================
Interactive mode:
$ 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
> print(attributes(testfun))
$srcref
function() {
    return(NULL)
}

> attributes(testfun)$srcref <- NULL
> print(attributes(testfun))
NULL
> print(digest(testfun))
[1] "87985c7cab8f65bc74dd8ac95d58ed32"
> 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 02 06 00 00 04 02 00 00 00 01 00 04 00 09 00 00 00 06 73 72 63 72
 [51] 65 66 00 00 00 13 00 00 00 02 00 00 03 0d 00 00 00 08 00 00 00 01 00 00 00
 [76] 17 00 00 00 01 00 00 00 17 00 00 00 17 00 00 00 17 00 00 00 01 00 00 00 01
[101] 00 00 04 02 00 00 00 01 00 04 00 09 00 00 00 07 73 72 63 66 69 6c 65 00 00
[126] 00 04 00 00 00 00 00 00 00 f2 00 00 04 02 00 00 00 01 00 04 00 09 00 00 00
[151] 0d 66 69 78 65 64 4e 65 77 6c 69 6e 65 73 00 00 00 0a 00 00 00 01 00 00 00
[176] 01 00 00 04 02 00 00 00 01 00 04 00 09 00 00 00 05 6c 69 6e 65 73 00 00 00
[201] 10 00 00 00 04 00 04 00 09 00 00 00 17 74 65 73 74 66 75 6e 20 3c 2d 20 66
[226] 75 6e 63 74 69 6f 6e 28 29 20 7b 00 04 00 09 00 00 00 10 20 20 20 20 72 65
[251] 74 75 72 6e 28 4e 55 4c 4c 29 00 04 00 09 00 00 00 01 7d 00 04 00 09 00 00
[276] 00 00 00 00 04 02 00 00 00 01 00 04 00 09 00 00 00 08 66 69 6c 65 6e 61 6d
[301] 65 00 00 00 10 00 00 00 01 00 04 00 09 00 00 00 00 00 00 00 fe 00 00 00 fe
[326] 00 00 04 02 00 00 00 01 00 04 00 09 00 00 00 05 63 6c 61 73 73 00 00 00 10
[351] 00 00 00 02 00 04 00 09 00 00 00 0b 73 72 63 66 69 6c 65 63 6f 70 79 00 04
[376] 00 09 00 00 00 07 73 72 63 66 69 6c 65 00 00 00 fe 00 00 04 02 00 00 07 ff
[401] 00 00 00 10 00 00 00 01 00 04 00 09 00 00 00 06 73 72 63 72 65 66 00 00 00
[426] fe 00 00 03 0d 00 00 00 08 00 00 00 02 00 00 00 05 00 00 00 02 00 00 00 10
[451] 00 00 00 05 00 00 00 10 00 00 00 02 00 00 00 02 00 00 04 02 00 00 02 ff 00
[476] 00 03 ff 00 00 04 02 00 00 07 ff 00 00 00 10 00 00 00 01 00 04 00 09 00 00
[501] 00 06 73 72 63 72 65 66 00 00 00 fe 00 00 04 02 00 00 02 ff 00 00 03 ff 00
[526] 00 04 02 00 00 00 01 00 04 00 09 00 00 00 0b 77 68 6f 6c 65 53 72 63 72 65
[551] 66 00 00 03 0d 00 00 00 08 00 00 00 01 00 00 00 00 00 00 00 03 00 00 00 01
[576] 00 00 00 00 00 00 00 01 00 00 00 01 00 00 00 03 00 00 04 02 00 00 02 ff 00
[601] 00 03 ff 00 00 04 02 00 00 07 ff 00 00 00 10 00 00 00 01 00 04 00 09 00 00
[626] 00 06 73 72 63 72 65 66 00 00 00 fe 00 00 00 fe 00 00 00 01 00 04 00 09 00
[651] 00 00 01 7b 00 00 00 02 00 00 00 06 00 00 00 01 00 04 00 09 00 00 00 06 72
[676] 65 74 75 72 6e 00 00 00 02 00 00 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
> 

===============================================================================
Batch mode:
$ 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
> print(attributes(testfun))
NULL
> attributes(testfun)$srcref <- NULL
> print(attributes(testfun))
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
> 


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