Rsync not copying some files with extended attributes
The problem I reproduced on many versions of MacOS X (Mountain Lion, Mavericks, Yosemite, El Capitan) which are using a much too old version
of rsync (2.6.9) and with more recent versions built with Macports (3.x) is solved with version 3.1.2.

Standard MacOS X rsync 2.6.9 → failure

••On_my_Mac••% /usr/bin/rsync -avE example example2
building file list ... done
._example
example/color-profile-1
example/._color-profile-1
example/index.xml.gz
example/Contents/
rsync: recv_generator: mkdir "/Users/Shared/tmp/example2/example/Contents" failed: Permission denied (13)
*** Skipping everything below this failed directory ***
example/QuickLook/
rsync: recv_generator: mkdir "/Users/Shared/tmp/example2/example/QuickLook" failed: Permission denied (13)
*** Skipping everything below this failed directory ***
rsync: mkstemp "/Users/Shared/tmp/example2/example/.color-profile-1.zFdjjF" failed: Permission denied (13)
rsync: mkstemp "/Users/Shared/tmp/example2/example/.._color-profile-1.ySmazZ" failed: Permission denied (13)
rsync: mkstemp "/Users/Shared/tmp/example2/example/.index.xml.gz.zB0WUl" failed: Permission denied (13)
copyfile(/dev/null, example/Contents, COPYFILE_METADATA) failed:2
copyfile(/dev/null, example/QuickLook, COPYFILE_METADATA) failed:13

sent 157793 bytes  received 120 bytes  315826.00 bytes/sec
total size is 461293  speedup is 2.92
rsync error: some files could not be transferred (code 23) at /SourceCache/rsync/rsync-45/rsync/main.c(992) [sender=2.6.9]
••On_my_Mac••%


Built rsync 3.1.2 → success

••On_my_Mac••% type rsync
rsync is /opt/local/bin/rsync
••On_my_Mac••% rsync --version
rsync  version 3.1.2  protocol version 31
Copyright (C) 1996-2015 by Andrew Tridgell, Wayne Davison, and others.
Web site: http://rsync.samba.org/
Capabilities:
    64-bit files, 64-bit inums, 64-bit timestamps, 64-bit long ints,
    socketpairs, hardlinks, symlinks, IPv6, batchfiles, inplace,
    append, ACLs, xattrs, iconv, symtimes, no prealloc, file-flags,
    HFS-compression

rsync comes with ABSOLUTELY NO WARRANTY.  This is free software, and you
are welcome to redistribute it under certain conditions.  See the GNU
General Public Licence for details.
••On_my_Mac••%




••On_my_Mac••% /usr/bin/sudo rm -rf example2
••On_my_Mac••% /opt/local/bin/rsync -avAX --fake-super example example2
sending incremental file list
created directory example2
example/
example/color-profile-1
example/index.xml.gz
example/Contents/
example/Contents/PkgInfo
example/QuickLook/
example/QuickLook/Preview.pdf
example/QuickLook/Thumbnail.jpg

sent 462,152 bytes  received 167 bytes  924,638.00 bytes/sec
total size is 461,293  speedup is 1.00
••On_my_Mac••%


2 key details to note:


the -E option changed to -AX (ACL &amp; extended attributes)
the use of --fake-super to be able to copy file inside read only
directories


How to use it on different Macs

If you want to make an rsync on a remote Mac, you will have to explictly call the built rsync on the remote Mac with the --rsync-command option:

/opt/local/bin/rsync -avAX --fake-super --rsync-command=/opt/local/bin/rsync example remote_MAC:/tmp/example2