[R] md5sum issues

Duncan Murdoch murdoch@dunc@n @end|ng |rom gm@||@com
Wed Feb 3 11:48:56 CET 2021

On 03/02/2021 4:42 a.m., Ivan Calandra wrote:
> Thank you Ivan and Duncan for your help.
> I understand your point Duncan, but the thing is that I do have an issue
> here.
> Is it then due to RStudio or even Windows? If it is, I can forget about
> a solution on that end, so I would focus on what I can do, and this Git
> setting seems to be the best place to start.

In my opinion, you should run

  git config --global core.autocrlf false

in an RStudio terminal session.  That will set the git options so they 
don't mess up the md5sum values.

You should also go to the RStudio options, and in the Code section, 
Saving tab, choose Serialization to be Posix (LF) and default text 
encoding to be UTF-8.

Unfortunately, RStudio will still mess up the .Rproj file (see 
https://github.com/rstudio/rstudio/issues/1929); there's not much you 
can do about that.  Just try not to commit the Windows version to the 
repository if any non-Windows users are sharing it.

But do note that other people have different opinions.  They argue that 
files should be converted to Windows native format by git.  That works 
in some narrow use cases, but as soon as you try to extract a file from 
git on one system and work on it on another, it breaks.

Duncan Murdoch

> Or am I missing something (I am still a newbie on these things...)?
> Ivan C
> --
> Dr. Ivan Calandra
> TraCEr, laboratory for Traceology and Controlled Experiments
> MONREPOS Archaeological Research Centre and
> Museum for Human Behavioural Evolution
> Schloss Monrepos
> 56567 Neuwied, Germany
> +49 (0) 2631 9772-243
> https://www.researchgate.net/profile/Ivan_Calandra
> On 03/02/2021 10:06, Duncan Murdoch wrote:
>> On 03/02/2021 2:14 a.m., Ivan Krylov wrote:
>>> On Tue, 2 Feb 2021 17:01:05 +0100
>>> Ivan Calandra <calandra using rgzm.de> wrote:
>>>> This happens to all text-based files (Rmd, MD, CSV...) but not to
>>>> non-editable files (PDF, XLSX...).
>>> This is probably caused by Git helpfully converting text files from LF
>>> (0x10) line endings to CR LF (0x13 0x10) when checking out the
>>> repository clone on Windows (and back when checking in).
>>> This configuration option is described in Pro Git:
>>> https://git-scm.com/book/en/v2/Customizing-Git-Git-Configuration#_core_autocrlf
>> I agree with Ivan K, but don't agree with the advice in that book.
>> It's best to just leave files alone, not to convert between LF and
>> CR-LF.  I don't think this confuses many Windows editors these days,
>> but if your editor forces files into CR-LF form, you should fix the
>> editor, not try to work around it.
>> In my opinion everyone should run
>>   git config --global core.autocrlf false
>> Some more arguments for this (in the context of Github Actions) are here:
>> https://github.community/t/git-config-core-autocrlf-should-default-to-false/16140
>> Duncan Murdoch
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