Difference between cp -r and cp -R (copy command)

While -R is posix well-defined, -r is not portable!

On Linux, in the GNU and BusyBox implementations of cp, -r and -R are equivalent.

On the other side, as you can read in the POSIX manual page of cp, -r behavior is implementation-defined.

    * If  neither  the  -R  nor  -r  options were specified, cp shall take
      actions based on the type and contents of the file referenced by the
      symbolic link, and not by the symbolic link itself.

    * If the -R option was specified:

       * If  none  of  the  options  -H,  -L, nor -P were specified, it is
         unspecified which of -H, -L, or -P will be used as a default.

       * If the -H option was specified, cp shall take  actions based on
         the type and contents of the file referenced by any symbolic link
         specified as a source_file operand.

       * If the -L option was specified, cp shall take  actions based  on
         the type and contents of the file referenced by any symbolic link
         specified as a source_file operand or any symbolic links encoun-
         tered during traversal of a file hierarchy.

       * If  the  -P option was specified, cp shall copy any symbolic link
         specified as a source_file operand and any symbolic links encoun-
         tered  during traversal of a file hierarchy, and shall not follow
         any symbolic links.

    * If the -r option was  specified,  the  behavior  is implementation-
      defined.

Lowercase -r was an older option, introduced in 4.1BSD, which would simply copy all non-directories as files. That is, if it encountered a device or FIFO, it would open it, read the contents, and create a file at the destination with the contents.

Uppercase -R was a standardized option (introduced to BSD in 4.4BSD, though earlier versions had it as a synonym to -r) which would, on encountering a device, FIFO, or other special file, make an equivalent special file at the destination.

Many implementations do still maintain this distinction, but some (including the GNU version typical to Linux) only provide the -R semantics, with -r as a synonym.

The difference is that one uses a lowercase "R" and the other uses a capital "R". Beyond that, no difference. Same thing if you use the --recursive long option.