How to remove CTRL-M (^M) blue carriage return characters from a file in Linux.
How to convert plain text files in DOS/MAC format to UNIX format.
Newly created SSL Certificates not working properly.
Certs invalid or not properly configured, agents unable to use.
Application reporting obscure syntax errors and other unanticipated, unforeseen errors.
Viewing the certificate files in Linux shows ^M characters appended to every line.
The file in question was created in Windows and then copied over to Linux.
^M is the keyboard equivalent to \r or CTRL-v + CTRL-m in vim.

There are several ways to translate a file between ASCII CR+LF (DOS/Windows) and LF (Unix) newlines. The following are different options to remove, convert or translate the ^M characters:

• The simplest solution, use the dos2unix command (sometimes named fromdos, d2u or unix2dos):
  

  dos2unix filename

• Using the stream editor sed:
  

  sed -e "s/\r//g" file > newfile

  
  
• Using perl:
  

  perl -p -e 's/\r//g' file > newfile

• Using a terminal editor vi or vim:
  Inside vi [in ESC mode] type: :%s/^M//g
  Note: To enter ^M, type CTRL-V + M. That is, hold down the CTRL key then press V and M in succession.

File has been transferred between systems of different types with different newline conventions. For example, Windows-based text editors will have a special carriage return character (CR+LF) at the end of lines to denote a line return or newline, which will be displayed incorrectly in Linux (^M). This can be difficult to spot, as some applications or programs may handle the foreign newline characters properly while others do not. Thus some services may crash or not respond correctly. Often times, this is because the file is created or perhaps even edited on a Microsoft Windows machine and then uploaded or transferred to a Linux server. This typically occurs when a file is transferred from MS-DOS (or MS-Windows) without ASCII or text mode.

For debugging purposes on a Unix system, the following command will make the ^M character visible:
cat -v <filename>
Here is an example of what these hidden characters look like:

-----BEGIN CERTIFICATE-----^M
MIIDBjCCAe4CCQD3cWtEoYMtujANBgkqhkiG9w0BAQUFADBFMQswCQYDVQQGEwJB^M
VTETMBEGA1UECBMKU29tZS1TdGF0ZTEhMB8GA1UEChMYSW50ZXJuZXQgV2lkZ2l0^M
cyBQdHkgTHRkMB4XDTEzMDcxNzIxMTU0NFoXDTE1MDcxNzIxMTU0NFowRTELMAkG^M
A1UEBhMCQVUxEzARBgNVBAgTClNvbWUtU3RhdGUxITAfBgNVBAoTGEludGVybmV0^M
IFdpZGdpdHMgUHR5IEx0ZDCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEB^M
ANIQ4wo6zi9lY5WddpJbHO2OvXgbJZIB8qidksKrFm3tUMe6LiXpOb4fZAwqlUUp^M
fN+jrp+Lr7PPF52vnbKMP4dq31CWV68EtcRK3O8maLy4mpx7pCXeZIqRw3/1UwIr^M
RXzOCWTsdvudAC0Sp0DgN8U7qECojZso9nu1SBopOtBDDU/Wcdmd3ydZJN0R7waB^M
e38WNK6rUNCgcIP0obvuiwppJmUyE1hr09A3W2zGB6bMF4EqZ5uaiBoPhMyKTlDs^M
UMOd6tRXkrYEdnLuqQttUvtE6sfxZaUTmod5MCXSRrW0tAkBGhqlPBT8NvlRQzaz^M
TqzLqhCYPQ9HBihumKHRkucCAwEAATANBgkqhkiG9w0BAQUFAAOCAQEALAGKt8Bn^M
PHYPj6RNioE8eyCvx4WFG8zDIkbkFbmpBiq6SOpWliCnhGWyH5yFEDWHCOebz8L9^M
LHQTi18KDGk7PH0BpWZDpksu3JrBb3fjm+1QCpD9KWRYJVnBGAaWFFmPPpJJDoz2^M
X0MRPbzxfqsno68l46X+5l5m4H8Y2g0cOUto580x/ZlNb+gHbTzuBnwGa2Oof0bc^M
A7ZmU1IytADXWVM28h88XcBooT4dwxCVkwznNGQ8lQ+XTehjdcDEEvbTB/Jc+1M4^M
0a/OvmlDIFU34DKH/LRc7bmTe4YTTRtU5ShXTBH0ChZFuqP20vtiEsPHVn+pk4LN^M
129c5uhrxPGhNQ==^M
-----END CERTIFICATE-----^M

For an in-depth explanation of line endings, see Newline from Wikipedia.