BLAST 2.2.27

Closes #15147.

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

1 files changed, 9 insertions, 79 deletions

diff --git a/Library/Formula/blast.rb b/Library/Formula/blast.rb
index e59059d72..99edc4c3f 100644
--- a/Library/Formula/blast.rb
+++ b/Library/Formula/blast.rb
@@ -2,22 +2,19 @@ require 'formula'
 
 class Blast < Formula
   homepage 'http://blast.ncbi.nlm.nih.gov/'
-  url 'ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.2.25/ncbi-blast-2.2.25+-src.tar.gz'
-  version '2.2.25'
-  sha1 '95bc29cd3cdcccaac24bc4dd489d8ad6b4500d33'
-
-  fails_with :clang do
-    build 421
+  url 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz'
+  version '2.2.27'
+  sha1 '51529c9fada67e890b994213d26f4177fa3d23d8'
+
+  fails_with :llvm do
+    build 5658
+    cause <<-EOS.undent
+      Compiler segfaults.
+    EOS
   end
 
   option 'with-dll', "Create dynamic binaries instead of static"
 
-  # fixes to 2.2.25 acknowledged upstream by Aaron U. per email
-  # inform configure about -Os
-  def patches
-    DATA
-  end
-
   def install
     args = ["--prefix=#{prefix}"]
     args << "--with-dll" if build.include? 'with-dll'
@@ -40,70 +37,3 @@ class Blast < Formula
     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
-