From gmbecker at ucdavis.edu  Wed Feb 18 15:36:03 2015
From: gmbecker at ucdavis.edu (Gabriel Becker)
Date: Wed, 18 Feb 2015 06:36:03 -0800
Subject: [Rd] Different serialization of functions in interactive vs.
 batch mode
In-Reply-To: <CAFDswJsiEw+zZ0HibzQzA02JqyVKtgDpr0Bz7SLjhPiJ7YRjoA@mail.gmail.com>
References: <CAFDswJvq5T2sZNQyE1pDP_F9CGBFQfxrXHbzfKhB4CZPgXNO8g@mail.gmail.com>
	<alpine.DEB.2.02.1502180804090.2336@luke-Latitude>
	<CAFDswJsiEw+zZ0HibzQzA02JqyVKtgDpr0Bz7SLjhPiJ7YRjoA@mail.gmail.com>
Message-ID: <CADwqtCPV0h6gH6nO8=WZubhXXPRsHTxHPhk99FUPmMd+27Ow+A@mail.gmail.com>

Holger,

For me (see session info) using

digest(as.list(f))

gets around this problem.

~G

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] digest_0.6.8




On Wed, Feb 18, 2015 at 6:22 AM, Holger Hoefling <hhoeflin at gmail.com> 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
>
> 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>


-- 
Gabriel Becker, PhD
Computational Biologist
Bioinformatics and Computational Biology
Genentech, Inc.

	[[alternative HTML version deleted]]



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