Catch up with upstream audit changes

amos.rb

@@ -19,11 +19,11 @@ class Amos < Formula
   def install
     ENV.deparallelize
     system "./configure", "--prefix=#{prefix}",
-      "--with-Boost-dir=#{Formula.factory('boost').opt_prefix}",
-      "--with-qmake-qt4=#{Formula.factory('qt').opt_prefix}/bin/qmake",
-      "BLAT=#{Formula.factory('blat').opt_prefix}/bin/blat",
-      "DELTAFILTER=#{Formula.factory('mummer').opt_prefix}/libexec/delta-filter",
-      "SHOWCOORDS=#{Formula.factory('mummer').opt_prefix}/libexec/show-coords"
+      "--with-Boost-dir=#{Formula["boost"].opt_prefix}",
+      "--with-qmake-qt4=#{Formula["qt"].opt_prefix}/bin/qmake",
+      "BLAT=#{Formula["blat"].opt_prefix}/bin/blat",
+      "DELTAFILTER=#{Formula["mummer"].opt_prefix}/libexec/delta-filter",
+      "SHOWCOORDS=#{Formula["mummer"].opt_prefix}/libexec/show-coords"
     system "make install"
   end
 

arpack.rb

@@ -18,7 +18,7 @@ def install
     args << '--enable-mpi' if build.with? :mpi
     if build.with? 'openblas'
       ['blas', 'lapack'].each do |pkg|
-        args << "--with-#{pkg}=-L#{Formula.factory('openblas').lib} -lopenblas"
+        args << "--with-#{pkg}=-L#{Formula["openblas"].lib} -lopenblas"
       end
     end
 

bam-readcount.rb

@@ -10,7 +10,7 @@ class BamReadcount < Formula
   depends_on 'samtools'
 
   def install
-    samtools = Formula.factory('samtools').opt_prefix
+    samtools = Formula["samtools"].opt_prefix
     ENV['SAMTOOLS_ROOT'] = "#{samtools}:#{samtools}/include/bam"
     system 'cmake', '.', *std_cmake_args
     system 'make'

beetl.rb

@@ -24,8 +24,8 @@ def patches
   end
 
   def install
-    boost = Formula.factory('boost').opt_prefix
-    seqan = Formula.factory('seqan').opt_prefix/'include'
+    boost = Formula["boost"].opt_prefix
+    seqan = Formula["seqan"].opt_prefix/'include'
     args = [
       '--disable-dependency-tracking',
       '--disable-silent-rules',

cppad.rb

@@ -35,13 +35,13 @@ def install
       cppad_testvector = 'boost'
     elsif build.with? 'eigen'
       cppad_testvector = 'eigen'
-      cmake_args << "-Deigen_prefix=#{Formula.factory('eigen').prefix}"
-      cmake_args << "-Dcppad_cxx_flags=-I" + Formula.factory('eigen').include + '/eigen3'
+      cmake_args << "-Deigen_prefix=#{Formula["eigen"].prefix}"
+      cmake_args << "-Dcppad_cxx_flags=-I#{Formula["eigen"].include}/eigen3"
     elsif build.include? 'with-std'
       cppad_testvector = 'std'
     end
     cmake_args << "-Dcppad_testvector=#{cppad_testvector}"
-    cmake_args << "-Dadolc_prefix=#{Formula.factory('adol-c').prefix}" if build.with? 'adol-c'
+    cmake_args << "-Dadolc_prefix=#{Formula["adol-c"].prefix}" if build.with? 'adol-c'
 
     mkdir 'build' do
       system "cmake", "..", *cmake_args

cufflinks.rb

@@ -15,7 +15,7 @@ class Cufflinks < Formula
   end
 
   def install
-    ENV['EIGEN_CPPFLAGS'] = '-I'+Formula.factory('eigen').include/'eigen3'
+    ENV['EIGEN_CPPFLAGS'] = "-I#{Formula["eigen"].include}/eigen3"
     ENV.append 'LIBS', '-lboost_system-mt -lboost_thread-mt'
     cd 'src' do
       # Fixes 120 files redefining `foreach` that break building with boost

dssp.rb

@@ -9,7 +9,7 @@ class Dssp < Formula
 
   def install
     # Create a make.config file that contains the configuration for boost
-    boost = Formula.factory('boost').opt_prefix
+    boost = Formula["boost"].opt_prefix
     File.open('make.config', 'w') do |makeconf|
       makeconf.puts "BOOST_LIB_SUFFIX = -mt"
       makeconf.puts "BOOST_LIB_DIR = #{boost / 'lib'}"

ipopt.rb

@@ -32,13 +32,13 @@ def install
     # See whether the parallel or sequential MUMPS library was built.
     if @@mumps_options.include? 'without-mpi'
       mumps_libs << '-lmpiseq'
-      mumps_incdir = Formula.factory('mumps').libexec / 'include'
+      mumps_incdir = Formula["mumps"].libexec / 'include'
     else
       # The MPI libs were installed as a MUMPS dependency.
       mumps_libs += %w[-lmpi_cxx -lmpi_mpifh]
-      mumps_incdir = Formula.factory('mumps').include
+      mumps_incdir = Formula["mumps"].include
     end
-    mumps_libcmd = "-L#{Formula.factory('mumps').lib} " + mumps_libs.join(' ')
+    mumps_libcmd = "-L#{Formula["mumps"].lib} " + mumps_libs.join(' ')
 
     args = ["--disable-debug",
             "--disable-dependency-tracking",
@@ -49,15 +49,15 @@ def install
             "--enable-static"]
 
     if build.with? 'openblas'
-      args << "--with-blas-incdir=#{Formula.factory('openblas').include}"
-      args << "--with-blas-lib=-L#{Formula.factory('openblas').lib} -lopenblas"
-      args << "--with-lapack-incdir=#{Formula.factory('openblas').include}"
-      args << "--with-lapack-lib=-L#{Formula.factory('openblas').lib} -lopenblas"
+      args << "--with-blas-incdir=#{Formula["openblas"].include}"
+      args << "--with-blas-lib=-L#{Formula["openblas"].lib} -lopenblas"
+      args << "--with-lapack-incdir=#{Formula["openblas"].include}"
+      args << "--with-lapack-lib=-L#{Formula["openblas"].lib} -lopenblas"
     end
 
     if build.with? 'asl'
-      args << "--with-asl-incdir=#{Formula.factory('asl').include}/asl"
-      args << "--with-asl-lib=-L#{Formula.factory('asl').lib} -lasl -lfuncadd0"
+      args << "--with-asl-incdir=#{Formula["asl"].include}/asl"
+      args << "--with-asl-lib=-L#{Formula["asl"].lib} -lasl -lfuncadd0"
     end
 
     system "./configure", *args

lammps.rb

@@ -107,7 +107,7 @@ def install
     end
 
     # Assuming gfortran library
-    ENV.append 'LDFLAGS', "-L#{Formula.factory('gfortran').opt_prefix}/gfortran/lib -lgfortran"
+    ENV.append 'LDFLAGS', "-L#{Formula["gfortran"].opt_prefix}/gfortran/lib -lgfortran"
 
     # build the lammps program and library
     cd "src" do
@@ -126,12 +126,12 @@ def install
         s.change_make_var! "LINK" , ENV["CXX"]
 
         # installing with FFTW and JPEG
-        s.change_make_var! "FFT_INC"  , "-DFFT_FFTW3 -I#{Formula.factory('fftw').opt_prefix}/include"
-        s.change_make_var! "FFT_PATH" , "-L#{Formula.factory('fftw').opt_prefix}/lib"
+        s.change_make_var! "FFT_INC"  , "-DFFT_FFTW3 -I#{Formula["fftw"].opt_prefix}/include"
+        s.change_make_var! "FFT_PATH" , "-L#{Formula["fftw"].opt_prefix}/lib"
         s.change_make_var! "FFT_LIB"  , "-lfftw3"
 
-        s.change_make_var! "JPG_INC"  , "-DLAMMPS_JPEG -I#{Formula.factory('jpeg').opt_prefix}/include"
-        s.change_make_var! "JPG_PATH" , "-L#{Formula.factory('jpeg').opt_prefix}/lib"
+        s.change_make_var! "JPG_INC"  , "-DLAMMPS_JPEG -I#{Formula["jpeg"].opt_prefix}/include"
+        s.change_make_var! "JPG_PATH" , "-L#{Formula["jpeg"].opt_prefix}/lib"
         s.change_make_var! "JPG_LIB"  , "-ljpeg"
 
         s.change_make_var! "CCFLAGS" , ENV["CFLAGS"]

mira.rb

@@ -19,8 +19,8 @@ def install
     system "./configure", "--disable-debug",
                           "--disable-dependency-tracking",
                           "--prefix=#{prefix}",
-                          "--with-expat=#{Formula.factory('expat').opt_prefix}",
-                          "--with-boost=#{Formula.factory('boost').opt_prefix}"
+                          "--with-expat=#{Formula["expat"].opt_prefix}",
+                          "--with-boost=#{Formula["boost"].opt_prefix}"
     # Link with boost_system for boost::system::system_category().
     # http://www.freelists.org/post/mira_talk/Linking-requires-boost-system
     system "make LIBS=-lboost_system-mt install"

mrbayes.rb

@@ -24,7 +24,7 @@ def install
     args = ["--disable-debug", "--prefix=#{prefix}"]
 
     if build.with? 'beagle'
-      args << "--with-beagle=#{Formula.factory('beagle').opt_prefix}"
+      args << "--with-beagle=#{Formula["beagle"].opt_prefix}"
     else
       args << "--with-beagle=no"
     end

mumps.rb

@@ -25,9 +25,9 @@ def install
     inreplace 'Makefile.inc' do |s|
       if build.with? 'scotch5'
         s.gsub! /#\s*SCOTCHDIR\s*=/, 'SCOTCHDIR = '
-        s.change_make_var! 'SCOTCHDIR', Formula.factory('scotch5').prefix
+        s.change_make_var! 'SCOTCHDIR', Formula["scotch5"].prefix
         s.gsub! /#\s*ISCOTCH\s*=/, 'ISCOTCH = '
-        s.change_make_var! 'ISCOTCH', "-I#{Formula.factory('scotch5').include}"
+        s.change_make_var! 'ISCOTCH', "-I#{Formula["scotch5"].include}"
 
         if build.with? :mpi
           s.gsub! /#\s*LSCOTCH\s*=\s*-L\$\(SCOTCHDIR\)\/lib -lptesmumps -lptscotch -lptscotcherr/, 'LSCOTCH = -L$(SCOTCHDIR)/lib -lptesmumps -lptscotch -lptscotcherr'
@@ -40,11 +40,11 @@ def install
 
       if build.with? 'metis4'
         s.gsub! /#\s*LMETISDIR\s*=/, 'LMETISDIR = '
-        s.change_make_var! 'LMETISDIR', Formula.factory('metis4').lib
+        s.change_make_var! 'LMETISDIR', Formula["metis4"].lib
         s.gsub! /#\s*IMETIS\s*=/, 'IMETIS = '
-        s.change_make_var! 'IMETIS', Formula.factory('metis4').include
+        s.change_make_var! 'IMETIS', Formula["metis4"].include
         s.sub! /#\s*LMETIS\s*=/, 'LMETIS = '
-        s.change_make_var! 'LMETIS', "-L#{Formula.factory('metis4').lib} -lmetis"
+        s.change_make_var! 'LMETIS', "-L#{Formula["metis4"].lib} -lmetis"
         orderingsf << ' -Dmetis'
       end
 
@@ -59,17 +59,17 @@ def install
         s.change_make_var! 'CC', "#{ENV['MPICC']} -fPIC"
         s.change_make_var! 'FC', "#{ENV['MPIFC']} -fPIC"
         s.change_make_var! 'FL', "#{ENV['MPIFC']} -fPIC"
-        s.change_make_var! 'SCALAP', "-L#{Formula.factory('scalapack').lib} -lscalapack"
-        s.change_make_var! 'INCPAR', "-I#{Formula.factory('open-mpi').include}"
-        s.change_make_var! 'LIBPAR', "$(SCALAP) -L#{Formula.factory('open-mpi').lib} -lmpi -lmpi_mpifh"
+        s.change_make_var! 'SCALAP', "-L#{Formula["scalapack"].lib} -lscalapack"
+        s.change_make_var! 'INCPAR', "-I#{Formula["open-mpi"].include}"
+        s.change_make_var! 'LIBPAR', "$(SCALAP) -L#{Formula["open-mpi"].lib} -lmpi -lmpi_mpifh"
       else
         s.change_make_var! 'CC', "#{ENV['CC']} -fPIC"
         s.change_make_var! 'FC', "#{ENV['FC']} -fPIC"
         s.change_make_var! 'FL', "#{ENV['FC']} -fPIC"
       end
 
       if build.with? 'openblas'
-        s.change_make_var! 'LIBBLAS', "-L#{Formula.factory('openblas').lib} -lopenblas"
+        s.change_make_var! 'LIBBLAS', "-L#{Formula["openblas"].lib} -lopenblas"
       else
         s.change_make_var! 'LIBBLAS', '-lblas -llapack'
       end

nlopt.rb

@@ -17,7 +17,7 @@ def install
     if build.with? 'octave'
       ENV['OCT_INSTALL_DIR'] = share/'nlopt/oct'
       ENV['M_INSTALL_DIR'] = share/'nlopt/m'
-      ENV['MKOCTFILE'] = "#{Formula.factory('octave').bin}/mkoctfile"
+      ENV['MKOCTFILE'] = "#{Formula["octave"].bin}/mkoctfile"
     end
     system "./configure", *args
     system "make"

octave.rb

@@ -53,7 +53,7 @@ class Octave < Formula
   def blas_flags
     flags = []
     if build.with? 'openblas'
-      flags << "-L#{Formula.factory('openblas').lib} -lopenblas"
+      flags << "-L#{Formula["openblas"].lib} -lopenblas"
     else
       flags << "-ldotwrp" if MacOS.version == :snow_leopard and MacOS.prefer_64_bit?
       # Cant use `-framework Accelerate` because `mkoctfile`, the tool used to

openimageio.rb

@@ -68,7 +68,7 @@ def install
       chdir 'localpub'
     end
 
-    j2k = Formula.factory('openjpeg').linked_keg.realpath
+    j2k = Formula["openjpeg"].linked_keg.realpath
     ENV.append 'MY_CMAKE_FLAGS', "-Wno-dev"   # stops a warning.
     ENV.append 'MY_CMAKE_FLAGS', "-DOPENJPEG_INCLUDE_DIR=#{j2k}/include/openjpeg-1.5"
     args = ["USE_TBB=1", "EMBEDPLUGINS=1"]

osgearth.rb

@@ -61,7 +61,7 @@ def install
       args << "-DV8_ICUI18N_LIBRARY=''" << "-DV8_ICUUC_LIBRARY=''"
     end
     # define libminizip paths (skips the only pkconfig dependency in cmake modules)
-    mzo = Formula.factory("minizip").opt_prefix
+    mzo = Formula["minizip"].opt_prefix
     args << "-DMINIZIP_INCLUDE_DIR=#{(build.with? "minizip") ? mzo/"include/minizip" : "''"}"
     args << "-DMINIZIP_LIBRARY=#{(build.with? "minizip") ? mzo/"lib/libminizip.dylib" : "''"}"
 
@@ -82,7 +82,7 @@ def install
   end
 
   def caveats
-    osg = Formula.factory("open-scene-graph")
+    osg = Formula["open-scene-graph"]
     osgver = (osg.linked_keg.exist?) ? osg.version : "#.#.# (version)"
     <<-EOS.undent
     This formula installs Open Scene Graph plugins. To ensure access when using

pastix.rb

@@ -53,21 +53,21 @@ def install
         s.gsub! /#\s*CFPROG\s*:=/, "CFPROG := "
 
         s.gsub! /SCOTCH_HOME\s*\?=/, "SCOTCH_HOME="
-        s.change_make_var! "SCOTCH_HOME", Formula.factory('scotch').prefix
+        s.change_make_var! "SCOTCH_HOME", Formula["scotch"].prefix
 
         s.gsub! /HWLOC_HOME\s*\?=/, "HWLOC_HOME="
-        s.change_make_var! "HWLOC_HOME", Formula.factory('hwloc').prefix
+        s.change_make_var! "HWLOC_HOME", Formula["hwloc"].prefix
 
         if build.with? 'metis4'
           s.gsub! /#\s*VERSIONORD\s*=\s*_metis/, "VERSIONORD = _metis"
           s.gsub! /#\s*METIS_HOME/, "METIS_HOME"
-          s.change_make_var! "METIS_HOME", Formula.factory('metis4').prefix
-          s.gsub! /#\s*CCPASTIX\s*:=\s*\$\(CCPASTIX\)\s+-DMETIS\s+-I\$\(METIS_HOME\)\/Lib/, "CCPASTIX := \$(CCPASTIX) -DMETIS -I#{Formula.factory('metis4').include}"
-          s.gsub! /#\s*EXTRALIB\s*:=\s*\$\(EXTRALIB\)\s+-L\$\(METIS_HOME\)\s+-lmetis/, "EXTRALIB := \$\(EXTRALIB\) -L#{Formula.factory('metis4').lib} -lmetis"
+          s.change_make_var! "METIS_HOME", Formula["metis4"].prefix
+          s.gsub! /#\s*CCPASTIX\s*:=\s*\$\(CCPASTIX\)\s+-DMETIS\s+-I\$\(METIS_HOME\)\/Lib/, "CCPASTIX := \$(CCPASTIX) -DMETIS -I#{Formula["metis4"].include}"
+          s.gsub! /#\s*EXTRALIB\s*:=\s*\$\(EXTRALIB\)\s+-L\$\(METIS_HOME\)\s+-lmetis/, "EXTRALIB := \$\(EXTRALIB\) -L#{Formula["metis4"].lib} -lmetis"
         end
 
         if build.with? 'openblas'
-          s.gsub! /#\s*BLAS_HOME\s*=\s*\/path\/to\/blas/, "BLAS_HOME = #{Formula.factory('openblas').lib}"
+          s.gsub! /#\s*BLAS_HOME\s*=\s*\/path\/to\/blas/, "BLAS_HOME = #{Formula["openblas"].lib}"
           s.change_make_var! "BLASLIB", "-lopenblas"
         end
       end

qgis.rb

@@ -42,23 +42,23 @@ def install
     # Set bundling level back to 0 (the default in all versions prior to 1.8.0)
     # so that no time and energy is wasted copying the Qt frameworks into QGIS.
     args = std_cmake_args.concat %W[
-      -DQWT_INCLUDE_DIR=#{Formula.factory('qwt').opt_prefix}/lib/qwt.framework/Headers/
-      -DQWT_LIBRARY=#{Formula.factory('qwt').opt_prefix}/lib/qwt.framework/qwt
-      -DBISON_EXECUTABLE=#{Formula.factory('bison').opt_prefix}/bin/bison
+      -DQWT_INCLUDE_DIR=#{Formula["qwt"].opt_prefix}/lib/qwt.framework/Headers/
+      -DQWT_LIBRARY=#{Formula["qwt"].opt_prefix}/lib/qwt.framework/qwt
+      -DBISON_EXECUTABLE=#{Formula["bison"].opt_prefix}/bin/bison
       -DENABLE_TESTS=NO
       -DQGIS_MACAPP_BUNDLE=0
       -DQGIS_MACAPP_DEV_PREFIX='#{prefix}/Frameworks'
       -DQGIS_MACAPP_INSTALL_DEV=YES
       -DPYTHON_LIBRARY='#{%x(python-config --prefix).chomp}/lib/libpython2.7.dylib'
     ]
 
-    args << "-DGRASS_PREFIX='#{Formula.factory('grass').opt_prefix}'" if build.with? 'grass'
+    args << "-DGRASS_PREFIX='#{Formula["grass"].opt_prefix}'" if build.with? 'grass'
 
     # So that `libintl.h` can be found
-    ENV.append 'CXXFLAGS', "-I'#{Formula.factory('gettext').opt_prefix}/include'" if build.with? 'grass'
+    ENV.append 'CXXFLAGS', "-I'#{Formula["gettext"].opt_prefix}/include'" if build.with? 'grass'
 
     # Avoid ld: framework not found QtSql (https://github.com/Homebrew/homebrew-science/issues/23)
-    ENV.append 'CXXFLAGS', "-F#{Formula.factory('qt').opt_prefix}/lib"
+    ENV.append 'CXXFLAGS', "-F#{Formula["qt"].opt_prefix}/lib"
 
     Dir.mkdir 'build'
     Dir.chdir 'build' do

rml-mmc.rb

@@ -14,7 +14,7 @@ class RmlMmc < Formula
 
   def install
     ENV.j1
-    ENV['SMLNJ_HOME'] = Formula.factory("smlnj").prefix/'SMLNJ_HOME'
+    ENV['SMLNJ_HOME'] = Formula["smlnj"].prefix/'SMLNJ_HOME'
 
     system "./configure --prefix=#{prefix}"
     system "make install"

root.rb

@@ -47,16 +47,16 @@ def install
            "--all",
            "--enable-builtin-glew",
            "#{cocoa_flag}",
-	   "#{qt_flag}", "#{qtgsi_flag}",
+           "#{qt_flag}", "#{qtgsi_flag}",
            "--prefix=#{prefix}",
            "--etcdir=#{prefix}/etc/root",
            "--mandir=#{man}"
 
     # ROOT configure script does not search for Qt framework
     if build.with? 'qt'
       inreplace "config/Makefile.config" do |s|
-	s.gsub! /^QTLIBDIR .*/, "QTLIBDIR := -F #{HOMEBREW_PREFIX}/lib"
-	s.gsub! /^QTLIB .*/, "QTLIB := -framework QtCore -framework QtGui -framework Qt3Support"
+        s.gsub! /^QTLIBDIR .*/, "QTLIBDIR := -F #{HOMEBREW_PREFIX}/lib"
+        s.gsub! /^QTLIB .*/, "QTLIB := -framework QtCore -framework QtGui -framework Qt3Support"
       end
     end
 

samtools.rb

@@ -25,7 +25,7 @@ class Samtools < Formula
   def install
     if build.devel?
       inreplace 'Makefile', 'include $(HTSDIR)/htslib.mk', ''
-      htslib = Formula.factory('Htslib').opt_prefix
+      htslib = Formula["Htslib"].opt_prefix
       system 'make', "HTSDIR=#{htslib}/include", "HTSLIB=#{htslib}/lib/libhts.a"
       system 'make', 'razip', "LDFLAGS=-L#{htslib}/lib", 'LDLIBS=-lhts -lz'
     else

sga.rb

@@ -17,8 +17,8 @@ def install
       system "./autogen.sh"
       system "./configure", "--disable-dependency-tracking",
                             "--prefix=#{prefix}",
-                            "--with-bamtools=#{Formula.factory('bamtools').opt_prefix}",
-                            "--with-sparsehash=#{Formula.factory('google-sparsehash').opt_prefix}"
+                            "--with-bamtools=#{Formula["bamtools"].opt_prefix}",
+                            "--with-sparsehash=#{Formula["google-sparsehash"].opt_prefix}"
       system "make install"
     end
   end

slepc.rb

@@ -19,7 +19,7 @@ def install
     ENV.deparallelize
     petsc_arch = 'arch-darwin-c-opt'
     ENV['SLEPC_DIR'] = Dir.getwd
-    ENV['PETSC_DIR'] = Formula.factory('petsc').prefix
+    ENV['PETSC_DIR'] = Formula["petsc"].prefix
     ENV['PETSC_ARCH'] = petsc_arch
     system "./configure", "--prefix=#{prefix}/#{petsc_arch}"
     system "make PETSC_ARCH=#{petsc_arch}"

stacks.rb

@@ -14,7 +14,7 @@ def install
     args << "--enable-sparsehash" if build.with? "google-sparsehash"
 
     if build.with? "samtools"
-      samtools = Formula.factory("samtools").opt_prefix
+      samtools = Formula["samtools"].opt_prefix
       args += ["--enable-bam",
         "--with-bam-include-path=#{samtools}/include/bam",
         "--with-bam-lib-path=#{samtools}/lib"]

suite-sparse.rb

@@ -32,7 +32,7 @@ def install
 
       if build.include? "with-metis4"
         s.remove_make_var! "METIS_PATH"
-        s.change_make_var! "METIS", Formula.factory("metis4").lib + "libmetis.a"
+        s.change_make_var! "METIS", "#{Formula["metis4"].lib}/libmetis.a"
       end
 
       s.change_make_var! "INSTALL_LIB", lib