davipatti

-I: Adding /Users/david/bin/amber14/dat/leap/prep to search path.
-I: Adding /Users/david/bin/amber14/dat/leap/lib to search path.
-I: Adding /Users/david/bin/amber14/dat/leap/parm to search path.
-I: Adding /Users/david/bin/amber14/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source tleapIn.

Welcome to LEaP!
Sourcing: ./tleapIn
----- Source: /Users/david/bin/amber14/dat/leap/cmd/leaprc.ff12SB

davipatti

#!/bin/bash

min=60

say "Testing"
sleep 1
say "Testing"
sleep 1

davipatti

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [

davipatti

dhcp-172-17-187-12:Andante david$ make
gcc   -I.  -I../../lm  -I../liborc   -c -o alloc_structures.o alloc_structures.c
gcc   -I.  -I../../lm  -I../liborc   -c -o andante.o andante.c
gcc   -I.  -I../../lm  -I../liborc   -c -o assign_radii.o assign_radii.c
gcc   -I.  -I../../lm  -I../liborc   -c -o borrow_chi.o borrow_chi.c
gcc   -I.  -I../../lm  -I../liborc   -c -o borrowed_clashes.o borrowed_clashes.c
gcc   -I.  -I../../lm  -I../liborc   -c -o build_stuff.o build_stuff.c
gcc   -I.  -I../../lm  -I../liborc   -c -o check_rotamers.o check_rotamers.c
gcc   -I.  -I../../lm  -I../liborc   -c -o clash_check.o clash_check.c
gcc   -I.  -I../../lm  -I../liborc   -c -o combo_utility.o combo_utility.c

davipatti

dhcp-172-17-187-12:Andante david$ make
gcc   -I.  -I../../lm  -I../liborc   -c -o alloc_structures.o alloc_structures.c
gcc   -I.  -I../../lm  -I../liborc   -c -o andante.o andante.c
gcc   -I.  -I../../lm  -I../liborc   -c -o assign_radii.o assign_radii.c
gcc   -I.  -I../../lm  -I../liborc   -c -o borrow_chi.o borrow_chi.c
gcc   -I.  -I../../lm  -I../liborc   -c -o build_stuff.o build_stuff.c
gcc   -I.  -I../../lm  -I../liborc   -c -o check_rotamers.o check_rotamers.c
gcc   -I.  -I../../lm  -I../liborc   -c -o combo_utility.o combo_utility.c
gcc   -I.  -I../../lm  -I../liborc   -c -o create_rotamer_library.o create_rotamer_library.c
gcc   -I.  -I../../lm  -I../liborc   -c -o d5_util1.o d5_util1.c

davipatti

1 warning generated.
mv -f .deps/tinyxmlparser.Tpo .deps/tinyxmlparser.Plo
/bin/sh ../../libtool --tag=CXX   --mode=link g++  -DNDEBUG -DUSE_TINYXML -DTIXML_USE_STL -DC99_OK -O2 -fno-common -DHAVE_ZLIB  -framework Accelerate -static  -o libtinyxml.la -rpath /Users/david/amber12/lib tinyxml.lo tinyxmlerror.lo tinystr.lo tinyxmlparser.lo  -lz 
libtool: link: ar cru .libs/libtinyxml.a  tinyxml.o tinyxmlerror.o tinystr.o tinyxmlparser.o
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libtinyxml.a(tinystr.o) has no symbols
libtool: link: ranlib .libs/libtinyxml.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libtinyxml.a(tinystr.o) has no symbols
libtool: link: ( cd ".libs" && rm -f "libtinyxml.la" && ln -s "../libtinyxml.la" "libtinyxml.la" )
Making all in Log
/bin/sh ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I./.. -I/Users/david/amber12/AmberTools/src/boost-1.38.