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Diffstat (limited to 'sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch')
-rw-r--r--sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch213
1 files changed, 0 insertions, 213 deletions
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch
deleted file mode 100644
index 820960354..000000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-conf-opts.patch
+++ /dev/null
@@ -1,213 +0,0 @@
- src/build-system/configure | 34 +++++++++++++++++++++++-----------
- src/build-system/configure.ac | 33 ++++++++++++++++++++++-----------
- 2 files changed, 45 insertions(+), 22 deletions(-)
-
-diff --git a/src/build-system/configure b/src/build-system/configure
-index 82fc9ef..d31a4f2 100755
---- a/src/build-system/configure
-+++ b/src/build-system/configure
-@@ -924,7 +924,7 @@ Optional Packages:
- --without-distcc do not automatically use distcc if available
- --without-ncbi-c do not use NCBI C Toolkit
- --without-sss do not use NCBI SSS libraries
-- --without-utils do not use NCBI SSS UTIL library
-+ --without-sssutils do not use NCBI SSS UTIL library
- --without-sssdb do not use NCBI SSS DB library
- --with-included-sss use the in-tree copy of SSS
- --with-z=DIR use zlib installation in DIR
-@@ -2835,12 +2835,12 @@ check ncbi-public strip pch caution ccache distcc \
- ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
- geo included-geo \
- z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \
--ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \
-+ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \
- bdb python jni sqlite3 icu boost boost-tag \
- sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \
- gif jpeg tiff png xpm magic curl 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench"
-+serial objects dbapi app ctools gui algo internal gbench x"
-
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
-
-@@ -2864,6 +2864,7 @@ for x_arg in "$@" ; do
- case "$x_arg" in
- --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \
- | --cache-file= | --build= | --host= | --target= | --with-runpath= \
-+ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \
- | --with-relative-runpath= | --x-includes= | --x-libraries= )
- { { echo "$as_me:$LINENO: error: $x_arg: requires value; use --help to show usage" >&5
- echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;}
-@@ -2876,6 +2877,7 @@ echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;}
- | --with-universal=* | --with-tcheck=* \
- | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
- | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
-+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \
- | [A-Z]*=* \
- | --with-z=* | --with-bz2=* | --with-lzo=* \
- | --with-pcre=* \
-@@ -3023,7 +3025,8 @@ echo "$as_me: error: --without-extra-action is not allowed" >&2;}
- 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
-@@ -3049,6 +3052,16 @@ echo "$as_me: WARNING: default projects file \"projects\" is a dangling link." >
- ;;
- esac
-
-+if test -n "$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" || \
-+ as_fn_error $? "unable to read requested projects file \"$abs_projects\"." "$LINENO" 5
-+fi
-+
-
- #### Always define this
-
-@@ -32712,7 +32725,7 @@ else
- sep=", "
- fi
- if test -n "$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 $reason" >&2;}
- { (exit 1); exit 1; }; }
-@@ -34949,11 +34962,9 @@ if test "$with_flat_makefile" != "no"; then
- 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="$cfm_flags -cfg"
- fi
-@@ -34997,7 +35008,8 @@ lib)
- esac
-
- if test -n "$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 $builddir && make all_p"
- fi
-
- cat << EOCONF
-diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac
-index 7b733af..3b55bf5 100644
---- a/src/build-system/configure.ac
-+++ b/src/build-system/configure.ac
-@@ -222,7 +222,7 @@ AC_ARG_WITH(ncbi-c,
- AC_ARG_WITH(sss,
- [ --without-sss do not use NCBI SSS libraries])
- AC_ARG_WITH(sssutils,
-- [ --without-utils do not use NCBI SSS UTIL library])
-+ [ --without-sssutils do not use NCBI SSS UTIL library])
- AC_ARG_WITH(sssdb,
- [ --without-sssdb do not use NCBI SSS DB library])
- AC_ARG_WITH(included-sss,
-@@ -462,12 +462,12 @@ check ncbi-public strip pch caution ccache distcc \
- ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
- geo included-geo \
- z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \
--ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \
-+ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \
- bdb python jni sqlite3 icu boost boost-tag \
- sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \
- gif jpeg tiff png xpm magic curl 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench"
-+serial objects dbapi app ctools gui algo internal gbench x"
-
- changequote(, )dnl
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
-@@ -493,6 +493,7 @@ for x_arg in "$@" ; do
- case "$x_arg" in
- --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \
- | --cache-file= | --build= | --host= | --target= | --with-runpath= \
-+ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \
- | --with-relative-runpath= | --x-includes= | --x-libraries= )
- AC_MSG_ERROR([$x_arg: requires value; use --help to show usage])
- ;;
-@@ -503,6 +504,7 @@ for x_arg in "$@" ; do
- | --with-universal=* | --with-tcheck=* \
- | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
- | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
-+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \
- | [[A-Z]*=*] \
- | --with-z=* | --with-bz2=* | --with-lzo=* \
- | --with-pcre=* \
-@@ -581,7 +583,8 @@ if test "$with_extra_action" = "no" ; then
- fi
-
- case "$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")
-@@ -599,6 +602,15 @@ case "$with_projects" in
- * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$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
-
- #### Always define this
- AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
-@@ -6198,7 +6210,7 @@ else
- 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 $reason])
-@@ -6807,11 +6819,9 @@ if test "$with_flat_makefile" != "no"; then
- 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="$cfm_flags -cfg"
- fi
-@@ -6854,7 +6864,8 @@ lib)
- esac
-
- if test -n "$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