R devel - Jan 2024 - Choices to remove `srcref` (and its buddies) when serializing objects

On 1/12/24 06:11, Dipterix Wang wrote:
> Dear R devs,
>
> I was digging into a package issue today when I realized R serialize
function not always generate the same results on equivalent objects when users
choose to run differently. For example, the following code
>
> serialize(with(new.env(), { function(){} }), NULL, TRUE)
>
> generates different results when I copy-paste into console vs when I use
ctrl+shift+enter to source the file in RStudio.
>
> With a deeper inspect into the cause, I found that function and language
get source reference when getOption("keep.source") is TRUE. This means
the source reference will make the functions different while in most cases,
whether keeping function source might not impact how a function behaves.
>
> While it's OK that function serialize generates different results,
functions such as `rlang::hash` and `digest::digest`, which depend on
`serialize` might eventually deliver false positives on same inputs. I've
checked source code in digest package hoping to get around this issue (for
example serialize(..., refhook = ...)). However, my workaround did not work. It
seems that the markers to the objects are different even if I used `refhook` to
force srcref to be the same. I also tried `removeSource` and
`rlang::zap_srcref`. None of them works directly on nested environments with
multiple functions.
>
> I wonder how hard it would be to have options to discard source when
serializing R objects?
>
> Currently my analyses heavily depend on digest function to generate file
caches and automatically schedule pipelines (to update cache) when changes are
detected. The pipelines save the hashes of source code, inputs, and outputs
together so other people can easily verify the calculation without accessing the
original data (which could be sensitive), or running hour-long analyses, or
having to buy servers. All of these require `serialize` to produce the same
results regardless of how users choose to run the code.
>
> It would be great if this feature could be in the future R. Other pipeline
packages such as `targets` and `drake` can also benefit from it.
I don't think such functionality would belong to serialize(). This 
function is not meant to produce stable results based on the input, the 
serialized representation may even differ based on properties not seen 
by users.

I think an option to ignore source code would belong to a function that 
computes the hash, as other options of identical().

Tomas

> Thanks,
>
> - Dipterix
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Could you recommend any packages/functions that compute hash such that the
source references and sexpinfo_struct are ignored? Basically a version of
`serialize` that convert R objects to raw without storing the ancillary source
reference and sexpinfo.

I think most people would think of `digest` but that package uses `serialize`
(see discussion
https://github.com/eddelbuettel/digest/issues/200#issuecomment-1894289875)
> On Jan 12, 2024, at 11:33?AM, Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
> 
> 
> On 1/12/24 06:11, Dipterix Wang wrote:
>> Dear R devs,
>> 
>> I was digging into a package issue today when I realized R serialize
function not always generate the same results on equivalent objects when users
choose to run differently. For example, the following code
>> 
>> serialize(with(new.env(), { function(){} }), NULL, TRUE)
>> 
>> generates different results when I copy-paste into console vs when I
use ctrl+shift+enter to source the file in RStudio.
>> 
>> With a deeper inspect into the cause, I found that function and
language get source reference when getOption("keep.source") is TRUE.
This means the source reference will make the functions different while in most
cases, whether keeping function source might not impact how a function behaves.
>> 
>> While it's OK that function serialize generates different results,
functions such as `rlang::hash` and `digest::digest`, which depend on
`serialize` might eventually deliver false positives on same inputs. I've
checked source code in digest package hoping to get around this issue (for
example serialize(..., refhook = ...)). However, my workaround did not work. It
seems that the markers to the objects are different even if I used `refhook` to
force srcref to be the same. I also tried `removeSource` and
`rlang::zap_srcref`. None of them works directly on nested environments with
multiple functions.
>> 
>> I wonder how hard it would be to have options to discard source when
serializing R objects?
>> 
>> Currently my analyses heavily depend on digest function to generate
file caches and automatically schedule pipelines (to update cache) when changes
are detected. The pipelines save the hashes of source code, inputs, and outputs
together so other people can easily verify the calculation without accessing the
original data (which could be sensitive), or running hour-long analyses, or
having to buy servers. All of these require `serialize` to produce the same
results regardless of how users choose to run the code.
>> 
>> It would be great if this feature could be in the future R. Other
pipeline packages such as `targets` and `drake` can also benefit from it.
> 
> I don't think such functionality would belong to serialize(). This
function is not meant to produce stable results based on the input, the
serialized representation may even differ based on properties not seen by users.
> 
> I think an option to ignore source code would belong to a function that
computes the hash, as other options of identical().
> 
> Tomas
> 
> 
>> Thanks,
>> 
>> - Dipterix
>> 	[[alternative HTML version deleted]]
>> 
>> ______________________________________________
>> R-devel at r-project.org <mailto:R-devel at r-project.org>
mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel

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