MacOS – Difficulties with El Capitan SIP

On installing the new OS a problem with logging on after the machine has been asleep started immediately. Occasionally my keyboard input is ignored and, after a brief pause, junk was loaded into the login input field. When I extend the time-out before the machine goes to sleep I get the same occasional reaction when I go back in without needing to login, but this time it's with typing into URLs in the browser. When the happens I always have to reboot!

Technical people at Apple, who placed 'Capture Data' app on my desktop, say the problem originates with home-brew, my package manager! I've since reinstalled homebrew as suggested on several sites so it will work with El Captain.

http://coolestguidesontheplanet.com/installing-homebrew-on-os-x-el-capitan-10-11-package-manager-for-unix-apps/

http://digitizor.com/fix-homebrew-permissions-osx-el-capitan/

I still get this issue occurring in a random fashion about 10%+ of the time.

Related to this issue? I can't install all that I need to set up IPython. Here pip doesn't always work.

pip install readline Ends up displaying :clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes arch x86_64 -DHAVE_RL_CALLBACK -DHAVE_RL_CATCH_SIGNAL -DHAVE_RL_COMPLETION_APPEND_CHARACTER -DHAVE_RL_COMPLETION_DISPLAY_MATCHES_HOOK -DHAVE_RL_COMPLETION_MATCHES -DHAVE_RL_COMPLETION_SUPPRESS_APPEND -DHAVE_RL_PRE_INPUT_HOOK -I. -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c Modules/2.x/readline.c -o build/temp.macosx-10.11-x86_64-2.7/Modules/2.x/readline.o -Wno-strict-prototypes
clang: error: no such file or directory: 'arch'
clang: error: no such file or directory: 'x86_64'
error: command 'clang' failed with exit status 1

----------------------------------------

Command "/usr/local/opt/python/bin/python2.7 -c "import setuptools, tokenize;file='/private/var/folders/bj/chzjff753fz0hr1l5r9kcc1c0000gn/T/pip-build-OS8w2B/readline/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install –record /var/folders/bj/chzjff753fz0hr1l5r9kcc1c0000gn/T/pip-selOV9-record/install-record.txt –single-version-externally-managed –compile" failed with error code 1 in /private/var/folders/bj/chzjff753fz0hr1l5r9kcc1c0000gn/T/pip-build-OS8w2B/readline

Same results when I try to install psycopg2!

Any suggestions on fixing the initial problems and getting stuff installed?

Thanks!!