[R] md5sum issues

Thu Feb 4 10:04:54 CET 2021

Dear Tim, Jeff, Duncan and Ivan,

Thank you all for your input! Actually, I am already doing what Tim 
suggested, and as Jeff said, using the checksums is redundant since I 
use Git already (which does a better job).

So I've decided to just remove the checksums from my scripts, and to 
revert the RStudio settings to default but use `git config --global 
core.autocrlf true` as mentioned in the Git guide for better 
compatibility with other platforms. I might change that in the future 
but I prefer adjusting Git rather than RStudio because I do not only use 
RStudio (I use it for R, but not necessarily or exclusively for other 
projects).

Best wishes,
Ivan

--
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 18:07, Ebert,Timothy Aaron wrote:
> Dear Ivan,
> Why not put your data file and analysis program into one folder and then provide enough description (including raw output) to enable someone to run the program (a read me file). This includes all the packages loaded into your version of R, file names, file types, and the logic behind the program. The raw output will help people check that their version is working (as you have indicated). If your data or results are critical then someone will figure out an update to keep things working on the computers of the future. Good documentation and labeling is a better path to long term reproducibility than trying to make everything generic. I tend to add documentation within a program as much as writing separate read me files.
>     R lends itself to this paradigm more than others, but many programs require that the person first have a copy of some proprietary software. I am not about to buy SPSS, but I will agree on principle that the SPSS code represents reproducible science. If I really care I will translate the SPSS code into a language that I can use.
>
> Tim
>
> -----Original Message-----
> From: R-help <r-help-bounces using r-project.org> On Behalf Of Ivan Calandra
> Sent: Wednesday, February 3, 2021 11:26 AM
> To: r-help using r-project.org
> Subject: Re: [R] md5sum issues
>
> [External Email]
>
> Dear Jeff,
>
> If I understood you correctly, it makes sense that I explain more about my goal here:
>
> I am trying to find ways to have analyses that are as reproducible as possible (knowing that it is not going to be perfect). One part is to show which file(s) I use as input and what output was created, so that potential readers/users of my analysis can check that the file they have is indeed the same that I use (and not a corrupted or modified version).
> Does that make sense?
>
> And for this purpose, I originally used file information (like creation time and so on), but I quickly realized this doesn't help much. Then I tried with MD5 and I thought it was solved, but it was obviously not solved.
>
> Duncan solution seems to work (I have not fully checked yet, though), but I am really open to other, more robust alternatives.
>
> Thanks for the input!
> Ivan
>
> --
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Ivan-5FCalandra&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=ibNvotyI5H_gn8tI80BOPNvA_3I0hXaKn8B38TS_yLY&s=EiZdNX4gKQm1kXIBD7w1MyjaAT7f3s-tk9mpNNCKW2U&e=
>
> On 03/02/2021 17:15, Jeff Newmiller wrote:
>> This CR vs LF vs CRLF newline discrepancy has been around since the 70s and the CP/M operating system. And it remains an issue in over-the-wire internet text protocols today, which actually use the CRLF version like Windows. Sorry, UNIX... world domination of LF encoding failed.
>>
>> The problem with pretending there is no issue as Duncan is advocating is that text is treated differently than binary, and every time you pretend it isn't it comes back to bite you. Applying binary algorithms like MD5 to text is one of these areas where your expectation that this will be successful is what creates the problem in the first place. A similar issue occurs in file encoding.. two files may both contain the word "Hello" but if they are encoded in UCS16 and UTF8 respectively then the MD5 results will be different.
>>
>> Git does not (currently) support differences in encoding, but it does support text vs non-text (newline) differences because they are unavoidable. Pushing forward with your expectation that text files should compare the same in binary by assuming text will always be like UNIX text just defers the problem for another day.
>>
>> Since I don't know what problem you are actually trying to solve, I cannot offer a concrete solution. But I would begin by not assuming that MD5 works the same on text and binary files... because it doesn't.
>>
>> On February 3, 2021 2:48:56 AM PST, Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rstud
>>> io_rstudio_issues_1929&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVe
>>> AsRzsn7AkP-g&m=ibNvotyI5H_gn8tI80BOPNvA_3I0hXaKn8B38TS_yLY&s=ruLgGdq-VfeMEeCAbfLgxe2bq6rlBB_wvO_A40iyuFk&e= ); 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgat
>>>> e.net_profile_Ivan-5FCalandra&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9P
>>>> EhQh2kVeAsRzsn7AkP-g&m=ibNvotyI5H_gn8tI80BOPNvA_3I0hXaKn8B38TS_yLY&s
>>>> =EiZdNX4gKQm1kXIBD7w1MyjaAT7f3s-tk9mpNNCKW2U&e=
>>>>
>>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__git-2Dscm.com_bo
>>> ok_en_v2_Customizing-2DGit-2DGit-2DConfiguration-23-5Fcore-5Fautocrlf
>>> &d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=ibNvoty
>>> I5H_gn8tI80BOPNvA_3I0hXaKn8B38TS_yLY&s=ZRHfdIX9MHy0op06VvZuG01oy2zYte
>>> 5uCSDnCUmwQfk&e=
>>>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.community
>>> _t_git-2Dconfig-2Dcore-2Dautocrlf-2Dshould-2Ddefault-2Dto-2Dfalse_161
>>> 40&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=ibNvo
>>> tyI5H_gn8tI80BOPNvA_3I0hXaKn8B38TS_yLY&s=unUVOo2qDSwSwD9el-0TZK15ERlM
>>> sU-fmqQ7TQ36LxE&e=
>>>>> Duncan Murdoch
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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>>> rg_posting-2Dguide.html&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kV
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>>> f7naPvS2_dxjXoVfkxhuWcn3VpBDGrGlhKmY&e=
>>>> and provide commented, minimal, self-contained, reproducible code.
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>>> eAsRzsn7AkP-g&m=ibNvotyI5H_gn8tI80BOPNvA_3I0hXaKn8B38TS_yLY&s=m215LP3
>>> f7naPvS2_dxjXoVfkxhuWcn3VpBDGrGlhKmY&e=
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> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=ibNvotyI5H_gn8tI80BOPNvA_3I0hXaKn8B38TS_yLY&s=65-81xtWqRiX3c1BKHs8sst32wKQHJ4tdVabERDDGnE&e=
> PLEASE do read the posting guide https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIDaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=9PEhQh2kVeAsRzsn7AkP-g&m=ibNvotyI5H_gn8tI80BOPNvA_3I0hXaKn8B38TS_yLY&s=m215LP3f7naPvS2_dxjXoVfkxhuWcn3VpBDGrGlhKmY&e=
> and provide commented, minimal, self-contained, reproducible code.