diff options
Diffstat (limited to 'sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch')
| -rw-r--r-- | sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch | 216 |
1 files changed, 0 insertions, 216 deletions
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch deleted file mode 100644 index d44993da2..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch +++ /dev/null @@ -1,216 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/configure.ori 2014-06-25 23:47:05.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/configure 2014-06-25 23:52:35.000000000 +0200 -@@ -927,7 +927,7 @@ - --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 -@@ -2965,13 +2965,13 @@ - ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ - geo included-geo \ - z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ --ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ -+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ - bdb python perl jni sqlite3 icu boost boost-tag \ - sp expat sablot libxml libxslt libexslt xerces xalan zorba \ - oechem sge muparser hdf5 \ - gif jpeg tiff png xpm magic curl mimetic 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'` - -@@ -2995,6 +2995,7 @@ - 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: $x_arg: requires value; use --help to show usage" >&2;} -@@ -3007,6 +3008,7 @@ - | --with-universal=* | --with-tcheck=* \ - | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ - | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ -+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | [A-Z]*=* \ - | --with-z=* | --with-bz2=* | --with-lzo=* \ - | --with-pcre=* \ -@@ -3201,6 +3203,17 @@ - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$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 \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi - - #### Always define this - -@@ -17878,68 +17891,6 @@ - fi - - --echo "$as_me:$LINENO: checking for std::is_sorted<> in <algorithm>" >&5 --echo $ECHO_N "checking for std::is_sorted<> in <algorithm>... $ECHO_C" >&6 --if test "${ncbi_cv_func_is_sorted+set}" = set; then -- echo $ECHO_N "(cached) $ECHO_C" >&6 --else -- cat >conftest.$ac_ext <<_ACEOF --/* confdefs.h. */ --_ACEOF --cat confdefs.h >>conftest.$ac_ext --cat >>conftest.$ac_ext <<_ACEOF --/* end confdefs.h. */ --#include <algorithm> --int --main () --{ --int a[2]; return std::is_sorted(a, a+2) ? 0 : 1; -- ; -- return 0; --} --_ACEOF --rm -f conftest.$ac_objext --if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 -- (eval $ac_compile) 2>conftest.er1 -- ac_status=$? -- grep -v '^ *+' conftest.er1 >conftest.err -- rm -f conftest.er1 -- cat conftest.err >&5 -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); } && -- { ac_try='test -z "$ac_cxx_werror_flag" -- || test ! -s conftest.err' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; } && -- { ac_try='test -s conftest.$ac_objext' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; }; then -- ncbi_cv_func_is_sorted=yes --else -- echo "$as_me: failed program was:" >&5 --sed 's/^/| /' conftest.$ac_ext >&5 -- --ncbi_cv_func_is_sorted=no --fi --rm -f conftest.err conftest.$ac_objext conftest.$ac_ext --fi --echo "$as_me:$LINENO: result: $ncbi_cv_func_is_sorted" >&5 --echo "${ECHO_T}$ncbi_cv_func_is_sorted" >&6 --if test "$ncbi_cv_func_is_sorted" = yes; then -- --cat >>confdefs.h <<\_ACEOF --#define HAVE_IS_SORTED 1 --_ACEOF -- --fi -- -- - - echo "$as_me:$LINENO: checking for SysV semaphores" >&5 - echo $ECHO_N "checking for SysV semaphores... $ECHO_C" >&6 -@@ -18550,7 +18501,7 @@ - echo $ECHO_N "(cached) $ECHO_C" >&6 - else - ncbi_cv_c_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_c_restrict" = "no" || break - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ -@@ -18620,7 +18571,7 @@ - echo $ECHO_N "(cached) $ECHO_C" >&6 - else - ncbi_cv_cxx_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_cxx_restrict" = "no" || break - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ -@@ -19046,67 +18997,6 @@ - _ACEOF - - fi -- --echo "$as_me:$LINENO: checking whether $CXX supports C++0x nullptr" >&5 --echo $ECHO_N "checking whether $CXX supports C++0x nullptr... $ECHO_C" >&6 --if test "${ncbi_cv_cxx_nullptr+set}" = set; then -- echo $ECHO_N "(cached) $ECHO_C" >&6 --else -- cat >conftest.$ac_ext <<_ACEOF --/* confdefs.h. */ --_ACEOF --cat confdefs.h >>conftest.$ac_ext --cat >>conftest.$ac_ext <<_ACEOF --/* end confdefs.h. */ -- --int --main () --{ --void * p = nullptr; -- ; -- return 0; --} --_ACEOF --rm -f conftest.$ac_objext --if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 -- (eval $ac_compile) 2>conftest.er1 -- ac_status=$? -- grep -v '^ *+' conftest.er1 >conftest.err -- rm -f conftest.er1 -- cat conftest.err >&5 -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); } && -- { ac_try='test -z "$ac_cxx_werror_flag" -- || test ! -s conftest.err' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; } && -- { ac_try='test -s conftest.$ac_objext' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; }; then -- ncbi_cv_cxx_nullptr=yes --else -- echo "$as_me: failed program was:" >&5 --sed 's/^/| /' conftest.$ac_ext >&5 -- --ncbi_cv_cxx_nullptr=no --fi --rm -f conftest.err conftest.$ac_objext conftest.$ac_ext --fi --echo "$as_me:$LINENO: result: $ncbi_cv_cxx_nullptr" >&5 --echo "${ECHO_T}$ncbi_cv_cxx_nullptr" >&6 --if test "$ncbi_cv_cxx_nullptr" = yes; then -- --cat >>confdefs.h <<\_ACEOF --#define HAVE_NULLPTR 1 --_ACEOF -- --fi - - ### Check for the availability of other packages - ### -------------------------------------------- |