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I have two files which look identical to me (including trailing whitespaces and newlines) but diff still says they differ. Even when I do a diff -y side by side comparison the lines look exactly the same. The output from diff is the whole 2 files.

Any idea what's causing it?

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Try to compare unprintable characters. The simplest way to watch them is sed -n l filename. If it won't help, add a data example and diff output here. – rush Aug 17 '12 at 13:18
Ahh yes thank you, the lines in a file are ending with $ and in the other one ending with \r$ – MinaHany Aug 17 '12 at 13:33
A quick fix is to use dos2unix on both the files (or the one you suspect to be from a Windows machine). – chembrad Jun 2 '15 at 18:43
As a complement to existing answers: the file command will hint you about file content, including things like ASCII text, with CRLF line terminators vs ASCII text. – Stéphane Gourichon Dec 15 '15 at 16:44
up vote 13 down vote accepted

Odd .. can you try cmp? You may want to use the '-b' option too.

cmp man page - Compare two files byte by byte.

This is one of the nice things about Unix/Linux .. so many tools :)

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Thanks for that! I got: byte 19, line 1 is 15 ^M 12 ^J what does it mean? – MinaHany Aug 17 '12 at 13:22
looks like carriage return and linefeed according to this table – Levon Aug 17 '12 at 13:25

Might the differences be caused by DOS vs. UNIX line endings, or something similar?

What if you hexdump them? This might show differences more obviously, eg:

hexdump -C file1 > file1.hex
hexdump -C file2 > file2.hex
diff file1.hex file2.hex
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Well, the two hexes are different. every time there's a 0d 0a in a file the other one just has 0a – MinaHany Aug 17 '12 at 13:29
In one, you have DOS line endings (CRLF) and in the other, UNIX line endings (LF). That's why they look different to diff but not when you look at them visually. Look at en.wikipedia.org/wiki/Newline#Conversion_utilities – mrb Aug 17 '12 at 13:32
Got it! Thanks a lot. Levon's suggestion of using cmp shows the difference more clearly though :) – MinaHany Aug 17 '12 at 13:39


diff file1 file2 | cat -t

The -t option will cause cat to show any special characters clearly - eg. ^M for CR, ^I for tab.

From the man page (OS X):

 -t      Display non-printing characters (see the -v option), and display tab characters as `^I'.

 -v      Display non-printing characters so they are visible.
         Control characters print as `^X' for control-X; the delete character
         (octal 0177) prints as `^?'.  Non-ASCII characters
         (with the high bit set) are printed as `M-' (for meta) followed by the
         character for the low 7 bits.
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My first guess, which turns out to be confirmed, is that the files use different line endings. It could be some other difference in whitespace, such as the presence of trailing whitespace (but you typically wouldn't get that on many lines) or different indentation (tabs vs spaces). Use a command that prints out whitespace and control characters in a visible form, such as

diff <(cat -A file1) <(cat -A file2)
diff <(sed -n l file1) <(sed -n l file2)

You can confirm that the differences only have to do with line endings by normalizing them first. You may have a dos2unix utility; if not, remove the extra CR (^M, \r, \015) character explicitly:

diff <(tr -d '\r' <file1) <(tr -d '\r' <file2)

or, if file1 is the one with DOS endings

 tr -d '\r' <file1 | diff - file2
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