sci-biology/ncbi-tools++-9.0.0: although masked a not passing repoman checks this ebuild works for me, finally. All patches from upstream.

5 files changed, 259 insertions, 0 deletions

diff --git a/sci-biology/ncbi-tools++/files/make_install.patch b/sci-biology/ncbi-tools++/files/make_install.patch
new file mode 100644
index 000000000..081d99bea
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/make_install.patch
@@ -0,0 +1,22 @@
+The C++ Toolkit now includes a copy of the SRA Toolkit, which
+establishes an ncbi/ hierarchy under lib, which previously had no
+subdirectories.  Please try the following patch to the top Makefile (and
+its progenitor, src/build-system/Makefile.in.top):
+
+Index: Makefile.in.top
+===================================================================
+--- Makefile.in.top     (revision 358093)
++++ Makefile.in.top     (working copy)
+@@ -39,7 +39,10 @@
+        -$(RMDIR) $(pincludedir)
+        $(INSTALL) -d $(bindir) $(libdir) $(pincludedir)
+        $(INSTALL) $(lbindir)/* $(bindir)
+-       $(INSTALL) -m 644 $(llibdir)/* $(libdir)
++       $(INSTALL) -m 644 $(llibdir)/*.* $(libdir)
++       if test -d $(llibdir)/ncbi; then \
++           cp -pPR $(llibdir)/ncbi $(libdir)/; \
++       fi
+        -rm -f $(libdir)/lib*-static.a
+        cd $(libdir)  && \
+            for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
+
diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch
new file mode 100644
index 000000000..41240c330
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch
@@ -0,0 +1,64 @@
+--- trunk/c++/src/build-system/configure.ac     2012/12/27 15:43:29     56694
++++ trunk/c++/src/build-system/configure.ac     2013/01/03 03:16:14     56754
+@@ -605,7 +605,8 @@
+ fi
+ 
+ case "$with_projects" in
+- "") if test -r projects; then
++ ""|yes)
++     if test -r projects; then
+         AC_MSG_NOTICE([using default projects file "projects".])
+         with_projects=projects
+         AC_SUBST(PROJECTS, "\$(top_srcdir)/projects")
+@@ -623,6 +624,16 @@
+  * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;;
+ esac
+ 
++if test -n "$with_projects"; then
++   case "$with_projects" in
++      /* ) abs_projects=$with_projects         ;;
++      yes) abs_projects=$srcdir/projects       ;;
++      *  ) abs_projects=$srcdir/$with_projects ;;
++   esac
++   test -r "$abs_projects"  ||  \
++      AC_MSG_ERROR([unable to read requested projects file "$abs_projects".])
++fi
++
+ # Check for custom optimization flags before potentially going with defaults.
+ skip_fast_flags=no
+ if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
+@@ -6379,7 +6390,7 @@
+      sep=", "
+    fi
+    if test -n "$reason" -a "$with_internal" = "yes"; then
+-      if test -z "$with_projects"  -o  "$with_projects" = "no"; then
++      if test -z "$with_projects"; then
+          AC_MSG_ERROR([--with-internal:  Cannot build INTERNAL projects: missing $reason])
+       else
+          AC_MSG_WARN([--with-internal:  Cannot build all INTERNAL projects: missing $reason])
+@@ -6982,11 +6993,9 @@
+    else
+       cfm_flags='-remoteptb'
+    fi
+-   case "$with_projects" in
+-      yes     ) cfm_flags="$cfm_flags -p projects" ;;
+-      no | '' ) ;;
+-      *       ) cfm_flags="$cfm_flags -p $with_projects" ;;
+-   esac
++   if test -n "$with_projects"; then
++      cfm_flags="$cfm_flags -p $with_projects"
++   fi
+    if test "$with_configure_dialog" = yes; then
+       cfm_flags="$cfm_flags -cfg"
+    fi
+@@ -7029,7 +7038,8 @@
+ esac
+ 
+ if test -n "$with_projects"; then
+-    build_proj="To build selected projects:  cd $builddir && make all_p"
++    build_proj="To build selected projects (as listed in \"$with_projects\"):
++  cd $builddir && make all_p"
+ fi
+ 
+ cat << EOCONF
+
diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch
new file mode 100644
index 000000000..0c1b2d227
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch
@@ -0,0 +1,66 @@
+-- trunk/c++/src/build-system/configure 2012/12/27 15:43:29     56694
++++ trunk/c++/src/build-system/configure        2013/01/03 03:16:14     56754
+@@ -3125,7 +3125,8 @@
+ fi
+ 
+ case "$with_projects" in
+- "") if test -r projects; then
++ ""|yes)
++     if test -r projects; then
+         { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5
+ echo "$as_me: using default projects file \"projects\"." >&6;}
+         with_projects=projects
+@@ -3151,6 +3152,18 @@
+  ;;
+ esac
+ 
++if test -n "$with_projects"; then
++   case "$with_projects" in
++      /* ) abs_projects=$with_projects         ;;
++      yes) abs_projects=$srcdir/projects       ;;
++      *  ) abs_projects=$srcdir/$with_projects ;;
++   esac
++   test -r "$abs_projects"  ||  \
++      { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5
++echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;}
++   { (exit 1); exit 1; }; }
++fi
++
+ # Check for custom optimization flags before potentially going with defaults.
+ skip_fast_flags=no
+ if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
+@@ -33825,7 +33838,7 @@
+      sep=", "
+    fi
+    if test -n "$reason" -a "$with_internal" = "yes"; then
+-      if test -z "$with_projects"  -o  "$with_projects" = "no"; then
++      if test -z "$with_projects"; then
+          { { echo "$as_me:$LINENO: error: --with-internal:  Cannot build INTERNAL projects: missing $reason" >&5
+ echo "$as_me: error: --with-internal:  Cannot build INTERNAL projects: missing $reason" >&2;}
+    { (exit 1); exit 1; }; }
+@@ -36062,11 +36075,9 @@
+    else
+       cfm_flags='-remoteptb'
+    fi
+-   case "$with_projects" in
+-      yes     ) cfm_flags="$cfm_flags -p projects" ;;
+-      no | '' ) ;;
+-      *       ) cfm_flags="$cfm_flags -p $with_projects" ;;
+-   esac
++   if test -n "$with_projects"; then
++      cfm_flags="$cfm_flags -p $with_projects"
++   fi
+    if test "$with_configure_dialog" = yes; then
+       cfm_flags="$cfm_flags -cfg"
+    fi
+@@ -36110,7 +36121,8 @@
+ esac
+ 
+ if test -n "$with_projects"; then
+-    build_proj="To build selected projects:  cd $builddir && make all_p"
++    build_proj="To build selected projects (as listed in \"$with_projects\"):
++  cd $builddir && make all_p"
+ fi
+ 
+ cat << EOCONF
+
diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch
new file mode 100644
index 000000000..89dae23ad
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch
@@ -0,0 +1,54 @@
+--- trunk/c++/src/build-system/configure.ac     2012/12/21 15:12:14     56664
++++ trunk/c++/src/build-system/configure.ac     2012/12/27 15:43:29     56694
+@@ -623,6 +623,13 @@
+  * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;;
+ esac
+ 
++# Check for custom optimization flags before potentially going with defaults.
++skip_fast_flags=no
++if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
++   case " $CFLAGS $CXXFLAGS" in
++      *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
++   esac
++fi
+ 
+ #### Always define this
+ AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
+@@ -1431,7 +1438,7 @@
+ wsrx="[[$wschars]]"
+ 
+ #### Flags to enable (potentially unsafe) extra optimization.
+-if test -z "$DEF_FAST_FLAGS"  -o  -z "$FAST_CXXFLAGS" ; then
++if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then
+    case "$compiler:$compiler_version" in
+       GCC:2* | GCC:344 )
+         # GCC 2.9x sometimes experiences internal errors at high optimization;
+@@ -1502,8 +1509,6 @@
+         DEF_FAST_FLAGS="-O"
+         ;;
+    esac
+-else
+-   DEF_FAST_FLAGS="-O"
+ fi
+ 
+ : ${FAST_CFLAGS="$DEF_FAST_FLAGS"}
+@@ -2608,9 +2613,15 @@
+          CXXFLAGS="$CXXFLAGS -O" ; fi
+       if echo " $LDFLAGS "  | grep -v "$optrx" >/dev/null ; then
+          LDFLAGS="$LDFLAGS -O" ; fi
+-      FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
+-      FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
+-      FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
++      if test "$skip_fast_flags" = yes ; then
++         FAST_CFLAGS="$CFLAGS"
++         FAST_CXXFLAGS="$CXXFLAGS"
++         FAST_LDFLAGS="$LDFLAGS"
++      else
++         FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
++         FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
++         FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
++      fi
+    fi
+ changequote([, ])dnl
+ fi
+
diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch
new file mode 100644
index 000000000..669b31722
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch
@@ -0,0 +1,53 @@
+--- trunk/c++/src/build-system/configure        2012/12/21 15:12:14     56664
++++ trunk/c++/src/build-system/configure        2012/12/27 15:43:29     56694
+@@ -3151,6 +3151,13 @@
+  ;;
+ esac
+ 
++# Check for custom optimization flags before potentially going with defaults.
++skip_fast_flags=no
++if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then
++   case " $CFLAGS $CXXFLAGS" in
++      *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
++   esac
++fi
+ 
+ #### Always define this
+ 
+@@ -5715,7 +5722,7 @@
+ wsrx="[$wschars]"
+ 
+ #### Flags to enable (potentially unsafe) extra optimization.
+-if test -z "$DEF_FAST_FLAGS"  -o  -z "$FAST_CXXFLAGS" ; then
++if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then
+    case "$compiler:$compiler_version" in
+       GCC:2* | GCC:344 )
+         # GCC 2.9x sometimes experiences internal errors at high optimization;
+@@ -5786,8 +5793,6 @@
+         DEF_FAST_FLAGS="-O"
+         ;;
+    esac
+-else
+-   DEF_FAST_FLAGS="-O"
+ fi
+ 
+ : ${FAST_CFLAGS="$DEF_FAST_FLAGS"}
+@@ -8936,9 +8941,15 @@
+          CXXFLAGS="$CXXFLAGS -O" ; fi
+       if echo " $LDFLAGS "  | grep -v "$optrx" >/dev/null ; then
+          LDFLAGS="$LDFLAGS -O" ; fi
+-      FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
+-      FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
+-      FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
++      if test "$skip_fast_flags" = yes ; then
++         FAST_CFLAGS="$CFLAGS"
++         FAST_CXXFLAGS="$CXXFLAGS"
++         FAST_LDFLAGS="$LDFLAGS"
++      else
++         FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
++         FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
++         FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS"
++      fi
+    fi
+ fi
+