md5sum issues

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://www.researchgate.net/profile/Ivan_Calandra

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 at 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://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 at 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