blast: add option for dynamic linking, support -Os

fixes to 2.2.25 acknowledged upstream by Aaron U. per email

Signed-off-by: Adam Vandenberg <flangy@gmail.com>

1 files changed, 98 insertions, 1 deletions

diff --git a/Library/Formula/blast.rb b/Library/Formula/blast.rb
index ef5f40e6c..4efa5c6e6 100644
--- a/Library/Formula/blast.rb
+++ b/Library/Formula/blast.rb
@@ -6,11 +6,108 @@ class Blast < Formula
   version '2.2.25'
   md5 '01256b808e3af49a5087945b6a8c8293'
 
+  def options
+    [['--with-dll', "Create dynamic binaries instead of static"]]
+  end
+
+  # fixes to 2.2.25 acknowledged upstream by Aaron U. per email
+  # inform configure about -Os
+  def patches
+    DATA
+  end
+
   def install
+    # FIXME This should be replaced with fails_with_clang once available
+    if ENV.compiler == :clang
+      opoo "Formula will not build with Clang, using LLVM."
+      ENV.llvm
+    end
+
+    args = ["--prefix=#{prefix}"]
+    args << "--with-dll" if ARGV.include? '--with-dll'
+
     cd 'c++' do
-      system "./configure", "--prefix=#{prefix}"
+      system "./configure", *args
       system "make"
       system "make install"
     end
   end
+
+  def caveats; <<-EOS.undent
+    Using the option '--with-dll' will create dynamic binaries instead of
+    static. NCBI Blast static binaries are approximately 28-times larger
+    than dynamic binaries.
+
+    Static binaries should be used for speed if the executable requires
+    fast startup time, such as if another program is frequently restarting
+    the blast executables.
+    EOS
+  end
 end
+
+__END__
+---
+ c++/src/build-system/configure |   24 ++++++++++++------------
+ 1 file changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/c++/src/build-system/configure b/c++/src/build-system/configure
+index 2f467a2..a2d14c7 100755
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -8538,29 +8538,29 @@ fi
+ if test "$compiler" != "MSVC" ; then
+    if test "$with_debug" = "no" ; then
+       with_optimization=${with_optimization:="yes"}
+-      CFLAGS=`  echo " $CFLAGS"   | sed 's/[ 	]-g[0-9]*//g'`
+-      CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ 	]-g[0-9]*//g'`
+-      LDFLAGS=` echo " $LDFLAGS"  | sed 's/[ 	]-g[0-9]*//g'`
++      CFLAGS=`  echo " $CFLAGS"   | sed 's/[ 	]-g[0-9s]*//g'`
++      CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ 	]-g[0-9s]*//g'`
++      LDFLAGS=` echo " $LDFLAGS"  | sed 's/[ 	]-g[0-9s]*//g'`
+       CPPFLAGS="-DNDEBUG $CPPFLAGS"
+    else
+       with_optimization=${with_optimization:="no"}
+-      if echo " $CFLAGS"   |grep -v >/dev/null '[ 	]-g[0-9]*' ; then
++      if echo " $CFLAGS"   |grep -v >/dev/null '[ 	]-g[0-9s]*' ; then
+          CFLAGS="$CFLAGS -g"     ; fi
+-      if echo " $CXXFLAGS" |grep -v >/dev/null '[ 	]-g[0-9]*' ; then
++      if echo " $CXXFLAGS" |grep -v >/dev/null '[ 	]-g[0-9s]*' ; then
+          CXXFLAGS="$CXXFLAGS -g" ; fi
+       if test "${with_tcheck=no}" = "no" ; then
+          CPPFLAGS="-D_DEBUG $CPPFLAGS"
+       else
+          CPPFLAGS="-DNDEBUG $CPPFLAGS"
+       fi
+-      if echo " $LDFLAGS"  |grep -v >/dev/null '[ 	]-g[0-9]*' ;
++      if echo " $LDFLAGS"  |grep -v >/dev/null '[ 	]-g[0-9s]*' ;
+          then LDFLAGS="$LDFLAGS -g" ; fi
+       STRIP="@:"
+    fi
+
+-   NOPT_CFLAGS=`  echo " $CFLAGS"    | sed 's/[ 	]-x*O[0-9]*//g'`
+-   NOPT_CXXFLAGS=`echo " $CXXFLAGS"  | sed 's/[ 	]-x*O[0-9]*//g'`
+-   NOPT_LDFLAGS=` echo " $LDFLAGS"   | sed 's/[ 	]-x*O[0-9]*//g'`
++   NOPT_CFLAGS=`  echo " $CFLAGS"    | sed 's/[ 	]-x*O[0-9s]*//g'`
++   NOPT_CXXFLAGS=`echo " $CXXFLAGS"  | sed 's/[ 	]-x*O[0-9s]*//g'`
++   NOPT_LDFLAGS=` echo " $LDFLAGS"   | sed 's/[ 	]-x*O[0-9s]*//g'`
+    if test "${with_tcheck-no}" != "no"; then
+       # Suppress warnings when building with ICC.
+       NOPT_CFLAGS="$NOPT_CFLAGS -O0"
+@@ -8575,11 +8575,11 @@ if test "$compiler" != "MSVC" ; then
+       FAST_CXXFLAGS="$CXXFLAGS"
+       FAST_LDFLAGS="$LDFLAGS"
+    else
+-      if echo " $CFLAGS"   |grep -v >/dev/null '[ 	]-x*O[0-9]*' ; then
++      if echo " $CFLAGS"   |grep -v >/dev/null '[ 	]-x*O[0-9s]*' ; then
+          CFLAGS="$CFLAGS -O" ; fi
+-      if echo " $CXXFLAGS" |grep -v >/dev/null '[ 	]-x*O[0-9]*' ; then
++      if echo " $CXXFLAGS" |grep -v >/dev/null '[ 	]-x*O[0-9s]*' ; then
+          CXXFLAGS="$CXXFLAGS -O" ; fi
+-      if echo " $LDFLAGS"  |grep -v >/dev/null '[ 	]-x*O[0-9]*' ; then
++      if echo " $LDFLAGS"  |grep -v >/dev/null '[ 	]-x*O[0-9s]*' ; then
+          LDFLAGS="$LDFLAGS -O" ; fi
+       FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
+       FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
+--
+1.7.9.2
+