Ggtkuk

When I login, I have these messages:

-bash: $'r' : command not found
-bash: $'r' : command not found
-bash: $'r' : command not found 

It is quite clear that it is caused by Windows-style line endings in some startup script(s), so my question is:
Can I track script that causes that and how?

Bash reads a number of different files on startup, even depending on how it's started (see the manual for the description). Then there's stuff like /etc/profile.d/ that aren't directly read by the shell, but can be referenced from the other startup files in many distributions.

You'll have to go through all of those but luckily, you can just grep for the carriage return. Try e.g. something like:

grep $'r' ~/.bashrc ~/.profile ~/.bash_login ~/.bash_profile /etc/bash.bashrc /etc/profile /etc/profile.d/*

See also Is it possible to find out which files are setting/adding to environment variables, and their order of precedence? for a similar issue.

file(1) can be helpful here as well.

$file *

signin: Python script, ASCII text
signup: Python script, ASCII text, with CRLF line terminators
site_off.htm: XML 1.0 document, ASCII text
sitemaps: directory

I can see that signup needs to have those pesky Windows CRLF line-endings removed.

For a recursive directly like /home/username you could probably combine with find and xargs (and maybe a grep, too):

$ find . | xargs file | grep CR

./foo_data/V: ASCII text, with CR, LF line terminators
./foo_data/Y: ASCII text, with CR, LF line terminators

Another method is to take all of those startup scripts mentioned, and echo a string identifying each one at the start of each one.

$ head .bashrc
echo "Running bashrc"

Then, on login, you will see something like this:

running bashrc
running bash_aliases
-bash: $'r' : command not found
-bash: $'r' : command not found
-bash: $'r' : command not found 
running something_else

At that point you can conclude that, (in the example above) .bash_aliases contains the offending line endings.

Once you have identified the file, but the problem lines don't jump out at you, you can use the same method to track down the line. Echo a message halfway through the file, then 3/4ths or 1/4s through, depending on the output. That way you can track down the line, depending on whether it echoes before or after your echo.

I take the hard part of this question to be not "hwo can I find carriage returns in a file?" but "how can I find out which files my bashrc uses?"

For the second question, you can try something like this:

bash -x .bashrc

This will show you everything your bashrc does, including all the files it refers to. It's noisy, but should help you track down which files are being used.

Except in fact, my (and many other) .bashrc files exit early if not run interactively, so you have to trick it into passing that check:

bash -ix .bashrc

Here the -i forces interactive mode.

To grep out just the cases where you source a file, something like this works for me but I can't promise the regex catches everything:

bash -ix .bashrc 2> >(grep -E '^+* (.|source)')

I guess you might also want the error messages, so something like:

bash -ix .bashrc 2> >(grep -E -e '^+* (.|source)' -e 'command not found')

If for some reason none of this worked, I would resort to strace -e open bash or something like that, to find every time any file is opened by your bash session. But that's an even more heavyweight / noisy solution.