From: "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/
Date: Wed, 25 Jun 2014 15:00:47 +0000 (UTC) [thread overview]
Message-ID: <1403708413.10e04f5023b0d6d66f63f277104707e2aea0fda7.mmokrejs@gentoo> (raw)
commit: 10e04f5023b0d6d66f63f277104707e2aea0fda7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 25 15:00:13 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jun 25 15:00:13 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=10e04f50
more changes to get ncbi-tools++-12.0.0 compiled
---
.../files/ncbi-tools++-12.0.0-linking.patch | 52 +
.../files/ncbi-tools++-12.0.0-linking2.patch | 10 +
.../files/ncbi-tools++-12.0.0-more-patches.patch | 136 ++
...ncbi-tools++-12.0.0-support-autoconf-2.60.patch | 1512 +-------------------
...tools++-12.0.0-support-autoconf-2.60.patch.bad} | 0
.../ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 46 +-
6 files changed, 308 insertions(+), 1448 deletions(-)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
new file mode 100644
index 0000000..196f3a4
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
@@ -0,0 +1,52 @@
+--- ncbi_cxx--12_0_0/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib.ori (revision 400707)
++++ ncbi_cxx--12_0_0/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib (working copy)
+@@ -10,6 +10,6 @@
+ LIB_OR_DLL = both
+
+ # Dependencies for shared library
+-DLL_LIB = ncbi_xreader$(DLL)
++DLL_LIB = $(GENBANK_LDEP)
+
+ WATCHERS = vasilche
+--- ncbi_cxx--12_0_0/src/app/grid/util/Makefile.ncfetch.app.ori (revision 400707)
++++ ncbi_cxx--12_0_0/src/app/grid/util/Makefile.ncfetch.app (working copy)
+@@ -5,7 +5,7 @@
+ APP = ncfetch.cgi
+ SRC = ncfetch
+
+-LIB = xcgi xconnserv xconnect xutil xncbi
++LIB = xcgi xconnserv xthrserv xconnect xutil xncbi
+ LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+
+ WATCHERS = kazimird
+--- ncbi_cxx--12_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori (revision 400707)
++++ ncbi_cxx--12_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app (working copy)
+@@ -4,7 +4,7 @@
+ SRC = netcache_cgi_sample
+
+ ### BEGIN COPIED SETTINGS
+-LIB = xconnserv xconnect xcgi xhtml xutil xncbi
++LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi
+
+ LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+ ### END COPIED SETTINGS
+--- ncbi_cxx--12_0_0/src/misc/grid_cgi/Makefile.xgridcgi.lib.ori 2014-06-24 21:42:11.000000000 +0200
++++ ncbi_cxx--12_0_0/src/misc/grid_cgi/Makefile.xgridcgi.lib 2014-06-24 21:42:29.000000000 +0200
+@@ -10,4 +10,4 @@
+
+ WATCHERS = vakatov
+
+-DLL_LIB = xncbi xcgi xconnserv xhtml
++DLL_LIB = xhtml xcgi xconnserv
+--- ncbi_cxx--12_0_0/src/sra/sdk/libs/vfs/Makefile.vfs.lib.ori 2014-06-24 22:54:55.000000000 +0200
++++ ncbi_cxx--12_0_0/src/sra/sdk/libs/vfs/Makefile.vfs.lib 2014-06-24 22:55:05.000000000 +0200
+@@ -8,6 +8,7 @@
+ CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \
+ $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE $(ORIG_CPPFLAGS)
+
+-DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL)
++DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) krypto$(DLL) \
++ kfg$(DLL) kfs$(DLL) klib$(DLL)
+
+ LIB_OR_DLL = both
+
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
new file mode 100644
index 0000000..5507b84
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
@@ -0,0 +1,10 @@
+--- ncbi_cxx--12_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori 2014-06-24 21:50:43.000000000 +0200
++++ ncbi_cxx--12_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app 2014-06-24 21:50:48.000000000 +0200
+@@ -11,7 +11,7 @@
+ # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
+
+ ### BEGIN COPIED SETTINGS
+-LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi
++LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi
+
+ LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch
new file mode 100644
index 0000000..449bbc5
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch
@@ -0,0 +1,136 @@
+--- ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h.ori 2013/09/30 13:46:04 59961
++++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h 2013/09/30 14:10:44 59962
+@@ -62,10 +62,6 @@
+ #define HAVE_SYS_TYPES_H 1
+ #define HAVE_VSNPRINTF 1
+
+-#if _MSC_VER >= 1600
+-# define HAVE_IS_SORTED 1
+-#endif
+-
+ #if _MSC_VER < 1500
+ # define vsnprintf _vsnprintf
+ #endif
+@@ -136,10 +132,6 @@
+
+ #endif
+
+-#if _MSC_VER >= 1600
+-# define HAVE_NULLPTR 1
+-#endif
+-
+ /* Windows XP and above */
+ #define NCBI_WIN32_WINNT 0x0501
+ #if !defined(_WIN32_WINNT)
+--- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2013/09/30 13:46:04 59961
++++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2013/09/30 14:10:44 59962
+@@ -258,9 +258,6 @@
+ /* Define to 1 if you have `ios(_base)::register_callback'. */
+ #define HAVE_IOS_REGISTER_CALLBACK 1
+
+-/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
+-/* #undef HAVE_IS_SORTED */
+-
+ /* Define to 1 if you have the `lchown' function. */
+ /* #undef HAVE_LCHOWN */
+
+@@ -595,9 +592,6 @@
+ /* Define to 1 if wxWidgets is available. */
+ /* #undef HAVE_WXWIDGETS */
+
+-/* Define to 1 if nullptr keyword is available. */
+-/* #undef HAVE_NULLPTR */
+-
+ /* Define as const if the declaration of iconv() needs const. */
+ #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */
+ # define ICONV_CONST
+--- ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h.ori 2013/09/30 13:46:04 59961
++++ ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h 2013/09/30 14:10:44 59962
+@@ -115,6 +115,11 @@
+ || defined(__GXX_EXPERIMENTAL_CPP0X__)
+ # define NCBI_HAVE_CXX11 1
+ # endif
++# if defined(NCBI_HAVE_CXX11) \
++ || (defined(NCBI_COMPILER_MSVC) && _MSC_VER >= 1600)
++# define HAVE_IS_SORTED 1
++# define HAVE_NULLPTR 1
++# endif
+ #endif
+
+ #include <common/ncbi_skew_guard.h>
+--- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2013/09/30 13:46:04 59961
++++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2013/09/30 14:10:44 59962
+@@ -179,9 +179,6 @@
+ /* Define to 1 if you have `ios(_base)::register_callback'. */
+ #undef HAVE_IOS_REGISTER_CALLBACK
+
+-/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
+-#undef HAVE_IS_SORTED
+-
+ /* Define to 1 if you have the `lchown' function. */
+ #undef HAVE_LCHOWN
+
+@@ -391,9 +388,6 @@
+ /* Define to 1 if `min'/`max' templates are not implemented. */
+ #undef HAVE_NO_MINMAX_TEMPLATE
+
+-/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */
+-#undef HAVE_NULLPTR
+-
+ /* Define to 1 if ODBC libraries are available. */
+ #undef HAVE_ODBC
+
+--- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2013/09/30 13:46:04 59961
++++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2013/09/30 14:10:44 59962
+@@ -3351,17 +3351,6 @@
+ fi
+
+
+-AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted,
+- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
+- [[#include <algorithm>]],
+- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])],
+- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])])
+-if test "$ncbi_cv_func_is_sorted" = yes; then
+- AC_DEFINE(HAVE_IS_SORTED, 1,
+- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.])
+-fi
+-
+-
+
+ AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores,
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h>
+@@ -3498,7 +3487,7 @@
+ AC_CACHE_CHECK([whether the C compiler supports C99 restrict],
+ ncbi_cv_c_restrict,
+ [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
+ AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
+ [ncbi_cv_c_restrict=$restrict], [])
+@@ -3518,7 +3507,7 @@
+ AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict],
+ ncbi_cv_cxx_restrict,
+ [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
+ AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
+ [ncbi_cv_cxx_restrict=$restrict], [])
+@@ -3623,14 +3612,6 @@
+ unaligned addresses.])
+ fi
+
+-AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr,
+- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])],
+- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])])
+-if test "$ncbi_cv_cxx_nullptr" = yes; then
+- AC_DEFINE(HAVE_NULLPTR, 1,
+- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.])
+-fi
+-
+ ### Check for the availability of other packages
+ ### --------------------------------------------
+
+
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch
index 80b23e9..9047c33 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch
@@ -1,1337 +1,6 @@
---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014-06-23 17:35:47.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014-06-23 17:36:41.000000000 +0200
-@@ -1,5 +1,5 @@
- #############################################################################
--# $Id: configure.ac 398256 2013-05-03 19:14:07Z rafanovi $
-+# $Id$
- # Derived from configure.in version 1.173.
- # ==========================================================================
- #
-@@ -38,7 +38,7 @@
- #
- #############################################################################
-
--AC_PREREQ(2.59)
-+AC_PREREQ(2.60)
-
- dnl Early setup, most crucially for locking. The diversion magic lets
- dnl this occur before AC_INIT, which already interferes with other
-@@ -71,7 +71,7 @@
- python, perl, jni, sqlite3, mimetic, sge, icu, sp, expat,
- sablot, libxml, libxslt, libexslt, xerces, xalan, zorba,
- oechem, muparser, hdf5, gif, jpeg, png, tiff, xpm,
-- magic, curl],
-+ magic, curl, gsoap, mongodb],
- [if test "${[with_]X-no}" != "no"; then
- AC_MSG_ERROR([incompatible options: --with-]X[ but --without-3psw])
- else
-@@ -143,6 +143,8 @@
- [ --with-bin-release build executables suitable for public release])
- AC_ARG_WITH(mt,
- [ --with-mt compile in a MultiThread-safe manner])
-+AC_ARG_WITH(openmp,
-+ [ --with-openmp enable OpenMP extensions for all projects])
- AC_ARG_WITH(64,
- [ --with-64 compile to 64-bit code])
- AC_ARG_WITH(universal,
-@@ -220,11 +222,15 @@
-
- ## NCBI packages
- AC_ARG_WITH(ncbi-c,
-+ [ --with-ncbi-c=DIR use NCBI C Toolkit installation in DIR])
-+AC_ARG_WITH(ncbi-c2,
- [ --without-ncbi-c do not use NCBI C Toolkit])
- AC_ARG_WITH(sss,
-+ [ --with-sss=DIR use NCBI SSS installation in DIR])
-+AC_ARG_WITH(sss2,
- [ --without-sss do not use NCBI SSS libraries])
- AC_ARG_WITH(sssutils,
-- [ --without-sssutils do not use NCBI SSS UTIL library])
-+ [ --without-utils 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,
-@@ -439,6 +445,14 @@
- [ --with-mimetic=DIR use libmimetic installation in DIR])
- AC_ARG_WITH(mimetic2,
- [ --without-mimetic do not use libmimetic])
-+AC_ARG_WITH(gsoap,
-+ [ --with-gsoap=DIR use gSOAP++ installation in DIR])
-+AC_ARG_WITH(gsoap2,
-+ [ --without-gsoap do not use gSOAP++])
-+AC_ARG_WITH(mongodb,
-+ [ --with-mongodb=DIR use MongoDB installation in DIR])
-+AC_ARG_WITH(mongodb2,
-+ [ --without-mongodb do not use MongoDB])
- AC_ARG_WITH(3psw,
- [ --with-3psw=std:netopt favor standard (system) builds of the above pkgs.])
- AC_ARG_WITH(3psw2,
-@@ -479,24 +493,28 @@
- [***** See also HTML documentation in ./doc/index.html *****])
-
-
-+AC_DIVERT_PUSH(PARSE_ARGS)
-+dnl As of Autoconf 2.60, this needs to run too early for config.log,
-+dnl to which AC_MSG_ERROR normally copies its output, to be available.
-+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD])
- #### Check the passed arguments against the list of available ones
- x_with_list="\
- debug max-debug symbols optimization profiling tcheck dll static static-exe \
- plugin-auto-load bundles bin-release mt 64 universal exe runpath hard-runpath \
--lfs limited-linker \
-+lfs limited-linker openmp \
- autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \
- deactivation makefile-auto-update projects flat-makefile configure-dialog \
- 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 gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
--ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \
-+ftds mysql orbacus 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 \
-+gif jpeg tiff png xpm magic curl mimetic gsoap mongodb 3psw \
- local-lbsm ncbi-crypt connext \
--serial objects dbapi app ctools gui algo internal gbench x"
-+serial objects dbapi app ctools gui algo internal gbench"
-
- changequote(, )dnl
- x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
-@@ -522,7 +540,6 @@
- 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])
- ;;
-@@ -533,12 +550,11 @@
- | --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=* \
-+ | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \
- | --with-gcrypt=* | --with-gnutls=* | --with-openssl=* \
-- | --with-krb5=* | --with-curl=* \
-+ | --with-krb5=* | --with-curl=* | --with-gsoap=* | --with-mongodb=* \
- | --with-sybase-local=* | --with-wxwidgets=* | --with-mimetic=* \
- | --with-ftds=* | --with-mysql=* | --with-fastcgi=* \
- | --with-sqlite3=* | --with-expat=* | --with-sablot=* \
-@@ -552,7 +568,7 @@
- | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
- | --x-includes=* | --x-libraries=* | --with-3psw=* \
- | --target=* | --with-runpath=* | --with-relative-runpath=* \
-- | --no-create | --no-recursion)
-+ | --help | --no-create | --no-recursion)
- ;;
-
- * )
-@@ -560,6 +576,8 @@
- ;;
- esac
- done
-+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD])
-+AC_DIVERT_POP
-
-
- if test "$with_gbench" = "yes" ; then
-@@ -604,6 +622,13 @@
- : ${with_optimization=no}
- fi
-
-+if test "$with_openmp" = yes; then
-+ if test "$with_mt" = no; then
-+ AC_MSG_ERROR([incompatible options: --without-mt but --with-openmp])
-+ fi
-+ : ${with_mt=yes}
-+fi
-+
- #### Check for special options
- if test "$with_extra_action" = "yes" ; then
- AC_MSG_ERROR([--with-extra-action must have a value after =])
-@@ -649,15 +674,10 @@
- *\ -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 "$abs_projects" || \
-- AC_MSG_ERROR([unable to read requested projects file "$abs_projects".])
--fi
-+# Generally save any originally specified flags.
-+USER_CFLAGS=$CFLAGS
-+USER_CXXFLAGS=$CXXFLAGS
-+USER_LDFLAGS=$LDFLAGS
-
- #### Always define this
- AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
-@@ -675,6 +695,23 @@
- #### Make some provisions for traditional operation
- AC_PROG_INSTALL
-
-+#### Point ICC at a suitable GCC version ASAP.
-+case "/$CXX" in
-+ */icpc )
-+ if test -d /usr/local/gcc; then
-+ case "`$CXX -dumpversion`:$host_cpu" in
-+ *:i?86) v=4.4.5 ;;
-+ ?.* | 1[[01]].* ) v=4.0.1 ;;
-+ *) v=4.4.2 ;;
-+ esac
-+ gcc=/usr/local/gcc/$v/bin/gcc
-+ if test -x $gcc; then
-+ CC="$CC -gcc-name=$gcc"
-+ CXX="$CXX -gcc-name=$gcc"
-+ fi
-+ fi
-+ ;;
-+esac
-
- #### C and C++ compilers
- AC_LANG(C++)
-@@ -987,6 +1024,30 @@
- ;;
- * ) NCBIATOMIC_LIB=xncbi ;;
- esac
-+ case "$compiler" in
-+ GCC )
-+ if $CC -v | grep clang >/dev/null; then
-+ :
-+ # Will allegedly support -openmp at some point, but as of 3.4,
-+ # just parses it as specifying an output filename: -o penmp.
-+ else
-+ case "$compiler_version" in
-+ [[123]]?? | 4[[01]]? ) ;;
-+ * ) : ${OPENMP_FLAGS=-fopenmp} ;;
-+ esac
-+ fi
-+ ;;
-+ ICC )
-+ : ${OPENMP_FLAGS=-openmp}
-+ ;;
-+ WorkShop* )
-+ : ${OPENMP_FLAGS=-xopenmp=parallel}
-+ ;;
-+ esac
-+ if test "$with_openmp" = yes; then
-+ MT_FLAG="$MT_FLAG $OPENMP_FLAGS"
-+ OPENMP_FLAGS=
-+ fi
- mt_sfx="MT"
- NCBI_FEATURE(MT)
- else
-@@ -994,6 +1055,7 @@
- MT_FLAG=
- THREAD_LIBS=
- NCBIATOMIC_LIB=
-+ OPENMP_FLAGS=
- mt_sfx=""
- fi
- MT_SFX="${mt_sfx}"
-@@ -1006,6 +1068,9 @@
- APP_LDFLAGS=
- DLL_LDFLAGS=
-
-+### Should go before any test compiler runs
-+AC_GNU_SOURCE
-+
- case "$host_os:$compiler" in
- darwin*:GCC )
- AC_CACHE_CHECK([whether $CC supports -Wl,-rpath],
-@@ -1047,6 +1112,47 @@
- ;;
- esac
-
-+case "$compiler:$compiler_version" in
-+ GCC:4[[0-6]]? | ICC:1[[01]]?? )
-+ ncbi_cv_prog_cxx_11=no
-+ ncbi_cv_prog_c_99=no
-+ ;;
-+ ICC:* )
-+ ncbi_cv_prog_c_99='-std=gnu99 -fgnu89-inline'
-+ ;;
-+esac
-+
-+AC_CACHE_CHECK([how to enable C++ '11 features in $CXX],
-+ ncbi_cv_prog_cxx_11,
-+ [orig_CXX=$CXX
-+ ncbi_cv_prog_cxx_11=no
-+ for x in -std=gnu++11 -std=gnu++0x; do
-+ CXX="$orig_CXX $x"
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
-+ [ncbi_cv_prog_cxx_11=$x])
-+ test "x$ncbi_cv_prog_cxx_11" = "xno" || break
-+ done
-+ CXX=$orig_CXX])
-+test "$ncbi_cv_prog_cxx_11" = no || CXX="$CXX $ncbi_cv_prog_cxx_11"
-+
-+AC_LANG_PUSH(C)
-+AC_CACHE_CHECK([how to enable C '11 or at least '99 features in $CC],
-+ ncbi_cv_prog_c_99,
-+ [orig_CC=$CC
-+ ncbi_cv_prog_c_99=no
-+ for x in -xc99=all "-std=gnu11 -fgnu89-inline" \
-+ "-std=gnu1x -fgnu89-inline" \
-+ "-std=gnu99 -fgnu89-inline" \
-+ "-std=gnu9x -fgnu89-inline"; do
-+ CC="$orig_CC $x"
-+ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
-+ [ncbi_cv_prog_c_99=$x])
-+ test "x$ncbi_cv_prog_c_99" = "xno" || break
-+ done
-+ CC=$orig_CC])
-+AC_LANG_POP(C)
-+test "$ncbi_cv_prog_c_99" = no || CC="$CC $ncbi_cv_prog_c_99"
-+
- #### Provide default environment setup for known platforms/compilers
- DEPFLAGS="-M"
- DEPFLAGS_POST="" # Needed for VisualAge
-@@ -1059,7 +1165,15 @@
- ;;
-
- solaris*:GCC )
-- CPPFLAGS="-D_XOPEN_SOURCE=500 $CPPFLAGS"
-+ # On Solaris, GCC defaults to setting _XOPEN_SOURCE (to 500) only
-+ # in C++ mode. Set it for C code as well to ensure consistent
-+ # header behavior, taking care to match the C standard version
-+ # (as enforced by <sys/feature_tests.h>).
-+ case "$ncbi_cv_prog_c_99" in
-+ no) CC="$CC -D_XOPEN_SOURCE=500" ;;
-+ *) CC="$CC -D_XOPEN_SOURCE=600" ;;
-+ esac
-+
- STRIP="@:"
- ;;
-
-@@ -1202,11 +1316,19 @@
- LDFLAGS="-flat_namespace $LDFLAGS"
-
- if test "$with_ncbi_public" = yes; then
-+ sdks='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk'
-+ case "$host_os" in
-+ darwin?.* | darwin10.* ) # Mac OS X 10.6.x or older
- TARGET='-mmacosx-version-min=10.5'
-- sdks='/Developer/SDKs/MacOSX10.6.sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.6.sdk'
-+ sdks="/Developer/SDKs/MacOSX10.6.sdk"
- if test "$with_64:${with_universal-no}" != "yes:no"; then
- sdks="/Developer/SDKs/MacOSX10.5.sdk $sdks"
- fi
-+ ;;
-+ * )
-+ TARGET='-mmacosx-version-min=10.7'
-+ ;;
-+ esac
- for sdk in $sdks; do
- if test -d "$sdk"; then
- TARGET="-isysroot $sdk $TARGET"
-@@ -1487,8 +1609,8 @@
- ;;
- GCC:* )
- DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing"
-- case "$host_os" in
-- freebsd* ) ;;
-+ case "$host_os:$host_cpu:$compiler_version" in
-+ freebsd* | solaris*:*86*:* | *:4[[5-9]]? | *:[[5-9]]?? ) ;;
- * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;
- esac
- if test "$with_profiling" != "yes"; then
-@@ -1587,13 +1709,9 @@
- solaris* )
- CONF_f_runpath="-R"
- ;;
-- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
-+ linux*:[[GI]]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
- CONF_f_runpath="-Wl,-rpath,"
- ;;
-- linux*:ICC )
-- # trying to use "-Wl,-rpath," here sends "ld" to endless 100% CPU loop
-- CONF_f_runpath="-Xlinker -rpath -Xlinker "
-- ;;
- irix*:* | linux*:KCC | *:Compaq )
- CONF_f_runpath="-rpath "
- ;;
-@@ -1697,8 +1815,11 @@
- LINK="$LINK -Kc++"
- ;;
- ICC:1???:* )
-- APP_LDFLAGS="-static-intel $APP_LDFLAGS"
-- DLL_LDFLAGS="-static-intel -nodefaultlibs $DLL_LDFLAGS"
-+ # Suppress "warning #10237: -lcilkrts linked in dynamically, static
-+ # library not available" which is not a problem in practice due to
-+ # as-needed linkage.
-+ APP_LDFLAGS="-static-intel -diag-disable 10237 $APP_LDFLAGS"
-+ DLL_LDFLAGS="-static-intel -diag-disable 10237 -nodefaultlibs $DLL_LDFLAGS"
- # Redundant for apps, but necessary for plugins to be adequately
- # self-contained, at least on 32-bit Linux.
- LIBS="$LIBS -lstdc++"
-@@ -1817,18 +1938,6 @@
-
- #### Intel compiler:: common flags and definitions
- if test "$compiler" = "ICC" ; then
-- if test -d /usr/local/gcc; then
-- case "$compiler_version:$HOST_CPU" in
-- *:i?86) v=4.4.5 ;;
-- ???:* | 1[[01]]??:* ) v=4.0.1 ;;
-- *) v=4.4.2 ;;
-- esac
-- gcc=/usr/local/gcc/$v/bin/gcc
-- if test -x $gcc; then
-- CC="$CC -gcc-name=$gcc"
-- CXX="$CXX -gcc-name=$gcc"
-- fi
-- fi
- if test -n "$icc_license" ; then
- icc_CC="$CC"
- icc_CXX="$CXX"
-@@ -2073,6 +2182,7 @@
- fi
-
- AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
-+dnl AC_PATH_PROG(GREP, grep)
- AC_PROG_EGREP
- AC_MSG_CHECKING([how to run $EGREP quietly])
- if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
-@@ -2086,6 +2196,16 @@
-
- AC_CHECK_PROG(VALGRIND_PATH, valgrind, valgrind)
-
-+AC_PATH_PROG(LDD, ldd)
-+if test -n "$LDD"; then
-+ AC_MSG_CHECKING([whether $LDD accepts -r])
-+ if $LDD -r /bin/ls >/dev/null 2>&1; then
-+ AC_MSG_RESULT(yes)
-+ LDD_R="$LDD -r"
-+ else
-+ AC_MSG_RESULT(no)
-+ fi
-+fi
-
- #### Check if "${build_root}" is defined; provide a default one
- if test -n "${with_build_root}" ; then
-@@ -2170,9 +2290,6 @@
- fi
-
-
--### Should go before any test compiler runs
--AC_GNU_SOURCE
--
- #### Determine whether this is implicitly a 64-bit platform
- AC_TYPE_SIZE_T
- if test "${with_universal-no}" = "no"; then
-@@ -2342,7 +2459,7 @@
- fi
- ;;
- *:ICC )
-- runpath="$runpath -Xlinker -rpath-link -Xlinker \$(libdir)"
-+ runpath="$runpath -Wl,-rpath-link,\$(libdir)"
- ;;
- esac
- elif test "$with_runpath" = "yes" -o "$with_dll" != "no" ; then
-@@ -2658,15 +2775,30 @@
- dbgrx1="$wsrx-g[^cx$wschars]*$wsrx"
- dbgrx2="$wsrx-gx*coff[0-9+]*$wsrx"
- optrx="$wsrx-x*O[0-9s]*$wsrx"
-+ NDEB_CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+ NDEB_CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+ NDEB_LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
- if test "$with_symbols" = "no" ; then
-- CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-- CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-- LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
-+ CFLAGS=$NDEB_CFLAGS
-+ CXXFLAGS=$NDEB_CXXFLAGS
-+ LDFLAGS=$NDEB_LDFLAGS
- else
- echo " $CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || CFLAGS="$CFLAGS -g"
- echo " $CXXFLAGS "| $EGREP_Q "$dbgrx1|$dbgrx2" || CXXFLAGS="$CXXFLAGS -g"
- echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g"
- STRIP="@:"
-+ case "$compiler:$compiler_version" in
-+ GCC:4[89]? | GCC:[5-9]? | GCC:???? )
-+ # GCC 4.8 defaults to DWARF 4, which Totalview for one
-+ # can't handle; roll back to version 3 by default.
-+ echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+ CFLAGS="$NDEB_CFLAGS -gdwarf-3"
-+ echo " $USER_CXXFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+ CXXFLAGS="$NDEB_CXXFLAGS -gdwarf-3"
-+ echo " $USER_LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
-+ LDFLAGS="$NDEB_LDFLAGS -gdwarf-3"
-+ ;;
-+ esac
- fi
-
- NOPT_CFLAGS=` echo " $CFLAGS " | sed "s/$optrx/ /g"`
-@@ -3024,9 +3156,9 @@
- ### Check for other standard library functions
-
- AC_FUNC_VPRINTF
--AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getpagesize \
-- getpass getpassphrase getpwuid getrusage gettimeofday \
-- getuid memrchr readpassphrase readv usleep \
-+AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getgrouplist \
-+ getpagesize getpass getpassphrase getpwuid getrusage \
-+ gettimeofday getuid memrchr readpassphrase readv usleep \
- asprintf vasprintf vsnprintf select statfs statvfs \
- strcasecmp strlcat strlcpy strdup strndup strtok_r \
- sysmp timegm utimes lutimes writev)
-@@ -3253,17 +3385,6 @@
- fi
-
-
--AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted,
-- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
-- [[#include <algorithm>]],
-- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])],
-- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])])
--if test "$ncbi_cv_func_is_sorted" = yes; then
-- AC_DEFINE(HAVE_IS_SORTED, 1,
-- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.])
--fi
--
--
-
- AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores,
- AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h>
-@@ -3400,7 +3521,7 @@
- AC_CACHE_CHECK([whether the C compiler supports C99 restrict],
- ncbi_cv_c_restrict,
- [ncbi_cv_c_restrict=no
-- for restrict in restrict __restrict__ __restrict; do
-+ for restrict in __restrict__ __restrict restrict; do
- test "$ncbi_cv_c_restrict" = "no" || break
- AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
- [ncbi_cv_c_restrict=$restrict], [])
-@@ -3420,7 +3541,7 @@
- AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict],
- ncbi_cv_cxx_restrict,
- [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
- AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
- [ncbi_cv_cxx_restrict=$restrict], [])
-@@ -3525,14 +3646,6 @@
- unaligned addresses.])
- fi
-
--AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr,
-- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])],
-- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])])
--if test "$ncbi_cv_cxx_nullptr" = yes; then
-- AC_DEFINE(HAVE_NULLPTR, 1,
-- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.])
--fi
--
- ### Check for the availability of other packages
- ### --------------------------------------------
-
-@@ -3630,7 +3743,16 @@
- dnl NCBI_CHECK_LIBS(FUSE, fuse, fuse_loop)
- AC_SEARCH_LIBS(fuse_loop, fuse, [NCBI_PACKAGE(FUSE)])
- LIBS=$orig_LIBS
-+# Temporarily drop OpenMP flags for this test, as some toolchains count
-+# its support library's indirect use of librt when building applications
-+# but not when building shared libraries with --no-undefined.
-+orig_CXXFLAGS=$CXXFLAGS
-+orig_LDFLAGS=$LDFLAGS
-+CXXFLAGS=`echo $CXXFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
-+LDFLAGS=`echo $LDFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
- NCBI_CHECK_LIBS(RT, rt posix4, clock_gettime)
-+CXXFLAGS=$orig_CXXFLAGS
-+LDFLAGS=$orig_LDFLAGS
- NCBI_CHECK_LIBS(DEMANGLE, demangle, cplus_demangle)
- # Add to (orig_)LIBS if present for the sake of corelib and the
- # following call to AC_CHECK_FUNCS.
-@@ -3734,7 +3856,6 @@
- NCBI_PACKAGE(LocalBZ2)
- fi
-
--: ${LZO_PATH=$NCBI/lzo2}
- if test -d "$LZO_PATH"; then
- NCBI_FIX_DIR(LZO_PATH)
- fi
-@@ -3767,7 +3888,7 @@
- ## SSL/TLS libraries
- case "$with_gcrypt" in
- no ) ac_cv_path_LIBGCRYPT_CONFIG=no ;;
-- yes | '' ) : ${GCRYPT_PATH=$NCBI/gcrypt} ;;
-+ yes | '' ) ;;
- * ) GCRYPT_PATH=$with_gcrypt ;;
- esac
- if test -d "$GCRYPT_PATH"; then
-@@ -3802,13 +3923,16 @@
-
- case "$with_gnutls" in
- no ) ac_cv_path_LIBGNUTLS_CONFIG=no ;;
-- yes | '' ) : ${GNUTLS_PATH=$NCBI/gnutls} ;;
-+ yes | '' ) ;;
- * ) GNUTLS_PATH=$with_gnutls ;;
- esac
- if test -d "$GNUTLS_PATH"; then
- NCBI_FIX_DIR(GNUTLS_PATH)
-+ gnutls_config_path=${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin
-+else
-+ gnutls_config_path=$PATH
- fi
--AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin:$PATH])
-+AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [$gnutls_config_path])
-
- if test "x$with_gnutls" != xno; then
- if test -x "$LIBGNUTLS_CONFIG"; then
-@@ -3817,7 +3941,7 @@
- test "x$p" = "x/usr" || GNUTLS_PATH=$p
- fi
- else
-- LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls"
-+ LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static"
- $LIBGNUTLS_CONFIG --exists >/dev/null 2>&1 || LIBGNUTLS_CONFIG=no
- fi
- case "$LIBGNUTLS_CONFIG" in
-@@ -3846,6 +3970,10 @@
- $GNUTLS_CONFIG_LIBS $GCRYPT_LIBS)
- if test "x$with_gnutls" != xno -a -n "$GNUTLS_CONFIG_LIBS"; then
- NCBI_RPATHIFY_OUTPUT(GNUTLS_LIBS, [echo $GNUTLS_CONFIG_LIBS], [$no_usr_lib])
-+ # Conservatively build against gcrypt if available even when gnutls
-+ # uses nettle instead, because gcrypt needs explicit initialization
-+ # to be thread-safe, but gnutls's headers don't indicate which
-+ # underlying crypto library it's actually using.
- case "$GNUTLS_INCLUDE" in
- *$GCRYPT_INCLUDE* ) ;;
- * ) GNUTLS_INCLUDE="$GNUTLS_INCLUDE $GCRYPT_INCLUDE" ;;
-@@ -4108,7 +4236,8 @@
- SYBASE_DBLIBS="$SYBASE_LPATH $SYBASE_DBLIBS"
- SYBASE_DLLS="$SYBASE_DLLLIST"
-
-- AC_CACHE_CHECK([for Sybase in $SYBASE_PATH], ncbi_cv_lib_sybase,
-+ AC_CACHE_CHECK([for Sybase${SYBASE_PATH:+ in $SYBASE_PATH}],
-+ ncbi_cv_lib_sybase,
- [CPPFLAGS="$SYBASE_INCLUDE $orig_CPPFLAGS"
- LIBS="$SYBASE_LIBS $SYBASE_DLLS $SYBASE_NETWORK_LIBS $DL_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -4216,7 +4345,8 @@
- AC_MSG_NOTICE([Using bundled FreeTDS (version $ftds_ver) from $FTDS_PATH])
- else
- FTDS_LIBS="$FTDS_CTLIBS"
-- AC_CACHE_CHECK([for FreeTDS in $FTDS_PATH], ncbi_cv_lib_freetds,
-+ AC_CACHE_CHECK([for FreeTDS${FTDS_PATH:+ in $FTDS_PATH}],
-+ ncbi_cv_lib_freetds,
- [CPPFLAGS="$FTDS_INCLUDE $orig_CPPFLAGS"
- LIBS="$FTDS_LIBS $NETWORK_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -4281,7 +4411,7 @@
- # Kill off single quotes, due to later requoting
- : ${MYSQL_INCLUDE=`$mysql_config --include | tr -d \'`}
- NCBI_RPATHIFY_OUTPUT_COND(MYSQL_LIBS, $mysql_config --libs${mt_sfx:+_r},
-- [s/'//g; ])
-+ [s/'//g; $no_usr_lib])
- AC_CACHE_CHECK([whether MySQL works], ncbi_cv_lib_mysql,
- [CPPFLAGS="$MYSQL_INCLUDE $orig_CPPFLAGS"
- LIBS="$MYSQL_LIBS $orig_LIBS"
-@@ -4310,7 +4440,6 @@
- if test "$with_bdb" != "no" ; then
- case "$with_bdb" in
- yes | "" )
-- : ${BERKELEYDB_PATH:="$NCBI/BerkeleyDB"}
- ;;
- */*)
- BERKELEYDB_PATH=$with_bdb
-@@ -4351,7 +4480,8 @@
- else
- BERKELEYDB_STATIC_LIBS=${BERKELEYDB_LIBS}
- fi
-- AC_CACHE_CHECK([for Berkeley DB libraries in $BERKELEYDB_PATH],
-+ AC_CACHE_CHECK(
-+ [for Berkeley DB libraries${BERKELEYDB_PATH:+ in $BERKELEYDB_PATH}],
- ncbi_cv_lib_berkeley_db,
- [CPPFLAGS="$BERKELEYDB_INCLUDE $orig_CPPFLAGS"
- LIBS="$BERKELEYDB_LIBS $orig_LIBS"
-@@ -4450,7 +4580,8 @@
- NCBI_RPATHIFY(ODBC_LIBS, ${ODBC_LIBPATH}, [ -lodbc -lodbcinst])
- CPPFLAGS="$ODBC_INCLUDE $orig_CPPFLAGS"
- LIBS="$ODBC_LIBS $orig_LIBS"
-- AC_CACHE_CHECK([for ODBC libraries in $ODBC_PATH], ncbi_cv_lib_odbc,
-+ AC_CACHE_CHECK([for ODBC libraries${ODBC_PATH:+ in $ODBC_PATH}],
-+ ncbi_cv_lib_odbc,
- [AC_LINK_IFELSE([AC_LANG_PROGRAM(
- [[#include <sql.h>]],
- [[SQLHDBC hdbc; SQLCHAR* cp = (SQLCHAR*) "x";
-@@ -4542,7 +4673,7 @@
- AC_PATH_PROG(PERL, perl, [], [$PERL_PATH/bin:$PATH])
- if test -x "$PERL"; then
- PERL_ARCHLIB=`$PERL -MConfig -e 'print \$Config{archlibexp};'`
-- PERL_FLAGS=`$PERL -MConfig -e 'print \$Config{cppflags};'`
-+ PERL_FLAGS=`$PERL -MConfig -e 'print join " ", grep /^-[[DI]]/, split /\\s+/, \$Config{cppflags};'`
- PERL_INCLUDE="-I$PERL_ARCHLIB/CORE $PERL_FLAGS"
- PERL_DEPS=`$PERL -MConfig -e 'print \$Config{libs};'`
- NCBI_RPATHIFY(PERL_LIBS, $PERL_ARCHLIB/CORE, [ -lperl $PERL_DEPS])
-@@ -4603,9 +4734,7 @@
-
- ## Boost
- if test "$with_boost" != "no"; then
-- if test "${with_boost-yes}" = yes; then
-- : ${BOOST_PATH=$NCBI/boost}
-- else
-+ if test "${with_boost-yes}" != yes; then
- BOOST_PATH=$with_boost
- fi
- if test -d "$BOOST_PATH"; then
-@@ -4644,17 +4773,22 @@
- if test -d `echo $BOOST_INCLUDE | sed -e 's/^-I//'`/boost-${ncbi_cv_lib_boost_version}/boost; then
- BOOST_INCLUDE=$BOOST_INCLUDE/boost-${ncbi_cv_lib_boost_version}
- fi
-- case "$ncbi_compiler" in
-- MIPSPRO)
-+ case "$compiler:$ncbi_compiler_ver" in
-+ MIPSpro*)
- BOOST_INCLUDE="$BOOST_INCLUDE $BOOST_INCLUDE/boost/compatibility/cpp_c_headers"
- ;;
-- WORKSHOP)
-+ WorkShop*)
- # Boost.Test's macros yield a *lot* of spurious "should not initialize
- # a non-const reference with a temporary" warnings, to the point of
- # overwhelming the compiler in some cases; turn them off altogether
- # when using Boost at all.
- BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp"
- ;;
-+ GCC*:4[[7-9]]* | GCC*:5*)
-+ # Some portions of Boost also have a lot of "unused" typedefs
-+ # from concept checking.
-+ BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs"
-+ ;;
- esac
- case "$ncbi_cv_lib_boost_version" in
- 0_* | 1_[[0-9]] | 1_[[0-9]]_* | 1_[[0-2]][[0-9]] | 1_[[0-2]][[0-9]]_* ) ;;
-@@ -4666,7 +4800,7 @@
- fi
- with_boost=no
- ;;
-- 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-2]] | 1_5[[0-2]]_* ) ;;
-+ 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-3]] | 1_5[[0-3]]_* ) ;;
- '' ) with_boost=no ;;
- * )
- AC_MSG_WARN(
-@@ -4751,7 +4885,9 @@
- BOOST_REGEX_STATIC_LIBS=$BOOST_REGEX_LIBS
- fi
-
-- AC_CACHE_CHECK([for Boost.Regex in $BOOST_PATH], ncbi_cv_lib_boost_regex,
-+ in_path=${BOOST_PATH:+ in $BOOST_PATH}
-+
-+ AC_CACHE_CHECK([for Boost.Regex$in_path], ncbi_cv_lib_boost_regex,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$BOOST_LIBPATH $BOOST_REGEX_LIBS $RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4759,7 +4895,7 @@
- [[throw boost::regex_error(boost::regex_constants::error_stack);]])],
- [ncbi_cv_lib_boost_regex=yes], [ncbi_cv_lib_boost_regex=no])])
-
-- AC_CACHE_CHECK([for Boost.Spirit in $BOOST_PATH], ncbi_cv_lib_boost_spirit,
-+ AC_CACHE_CHECK([for Boost.Spirit$in_path], ncbi_cv_lib_boost_spirit,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4774,7 +4910,7 @@
- BOOST_SYSTEM_STATIC_LIBS=$BOOST_SYSTEM_LIBS
- fi
-
-- AC_CACHE_CHECK([for Boost.System in $BOOST_PATH], ncbi_cv_lib_boost_system,
-+ AC_CACHE_CHECK([for Boost.System$in_path], ncbi_cv_lib_boost_system,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$BOOST_LIBPATH $BOOST_SYSTEM_LIBS $RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4785,6 +4921,24 @@
- BOOST_SYSTEM_LIBS=
- BOOST_SYSTEM_STATIC_LIBS=])])
-
-+ boost_fs_lib=-lboost_filesystem${BOOST_TAG}
-+ if test -f "$BOOST_LIBPATH_/libboost_filesystem${BOOST_TAG}-static.a"; then
-+ boost_fs_static_lib=-lboost_filesystem${BOOST_TAG}-static
-+ else
-+ boost_fs_static_lib=$boost_fs_lib
-+ fi
-+ BOOST_FILESYSTEM_LIBS="$boost_fs_lib $BOOST_SYSTEM_LIBS"
-+ BOOST_FILESYSTEM_STATIC_LIBS="$boost_fs_static_lib $BOOST_SYSTEM_STATIC_LIBS"
-+
-+ AC_CACHE_CHECK([for Boost.Filesystem$in_path], ncbi_cv_lib_boost_filesystem,
-+ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
-+ LIBS="$BOOST_LIBPATH $BOOST_FILESYSTEM_LIBS $RT_LIBS $orig_LIBS"
-+ [AC_LINK_IFELSE(
-+ [AC_LANG_PROGRAM([[#include <boost/filesystem.hpp>]],
-+ [[return boost::filesystem::portable_name("foo");]])],
-+ [ncbi_cv_lib_boost_filesystem=yes],
-+ [ncbi_cv_lib_boost_filesystem=no])])
-+
- BOOST_TEST_PEM_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}
- if test -f "$BOOST_LIBPATH_/libboost_prg_exec_monitor${BOOST_TAG}-static.a"; then
- BOOST_TEST_PEM_STATIC_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}-static
-@@ -4813,7 +4967,7 @@
- BOOST_TEST_TEM_LIBS=$BOOST_TEST_TEM_STATIC_LIBS
- BOOST_TEST_UTF_LIBS=$BOOST_TEST_UTF_STATIC_LIBS
-
-- AC_CACHE_CHECK([for Boost.Test in $BOOST_PATH], ncbi_cv_lib_boost_test,
-+ AC_CACHE_CHECK([for Boost.Test$in_path], ncbi_cv_lib_boost_test,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$RT_LIBS $orig_LIBS"
- found=
-@@ -4853,7 +5007,7 @@
- BOOST_THREAD_STATIC_LIBS=$BOOST_THREAD_LIBS
- fi
-
-- AC_CACHE_CHECK([for Boost.Threads in $BOOST_PATH], ncbi_cv_lib_boost_thread,
-+ AC_CACHE_CHECK([for Boost.Threads$in_path], ncbi_cv_lib_boost_thread,
- CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
- LIBS="$BOOST_LIBPATH $BOOST_THREAD_LIBS $RT_LIBS $orig_LIBS"
- [AC_LINK_IFELSE(
-@@ -4864,12 +5018,25 @@
- BOOST_INCLUDE=
- BOOST_LIBPATH=
- BOOST_TAG=
-+ ncbi_cv_lib_boost_filesystem=no
- ncbi_cv_lib_boost_regex=no
- ncbi_cv_lib_boost_spirit=no
-+ ncbi_cv_lib_boost_system=no
- ncbi_cv_lib_boost_test=no
- ncbi_cv_lib_boost_thread=no
- fi
-
-+if test "$ncbi_cv_lib_boost_filesystem" != "no"; then
-+ dnl AC_DEFINE(HAVE_BOOST_FILESYSTEM, 1,
-+ dnl [Define to 1 if the `Boost.Filesystem' library is available.])
-+ NCBI_PACKAGE(Boost.Filesystem)
-+else
-+ boost_fs_lib=
-+ boost_fs_static_lib=
-+ BOOST_FILESYSTEM_LIBS=
-+ BOOST_FILESYSTEM_STATIC_LIBS=
-+fi
-+
- if test "$ncbi_cv_lib_boost_regex" != "no"; then
- AC_DEFINE(HAVE_BOOST_REGEX, 1,
- [Define to 1 if the `Boost.Regex' library is available.])
-@@ -4927,7 +5094,10 @@
-
- ## NCBI C Toolkit
- if test "$with_ncbi_c" != "no" ; then
-- NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"}
-+ if test "${with_ncbi_c-yes}" != yes; then
-+ NCBI_C_PATH=$with_ncbi_c
-+ fi
-+ : ${NCBI_C_PATH="$NCBI"}
- if test "$ncbi_compiler" = ICC -a -d "$NCBI_C_PATH/ncbi_icc"; then
- NCBI_C_PATH=$NCBI_C_PATH/ncbi_icc
- fi
-@@ -4949,7 +5119,8 @@
- NCBI_C_ncbi="-lncbi"
- fi
- NCBI_C_LIBPATH="-L$NCBI_C_LIBPATH"
-- AC_CACHE_CHECK([for the NCBI C toolkit in $NCBI_C_PATH], ncbi_cv_lib_ctools,
-+ AC_CACHE_CHECK([for the NCBI C toolkit${NCBI_C_PATH:+ in $NCBI_C_PATH}],
-+ ncbi_cv_lib_ctools,
- [CPPFLAGS="$NCBI_C_INCLUDE $orig_CPPFLAGS"
- LIBS="$NCBI_C_LIBPATH $NCBI_C_ncbi $NETWORK_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -5000,11 +5171,7 @@
-
- ## OpenGL
- if test "$with_opengl" != "no"; then
-- if test "${with_opengl-yes}" = yes; then
-- if test -d $NCBI/MesaGL; then
-- : ${OPENGL_PATH=$NCBI/MesaGL}
-- fi
-- else
-+ if test "${with_opengl-yes}" != yes; then
- OPENGL_PATH=$with_opengl
- fi
- if test -d "$OPENGL_PATH"; then
-@@ -5101,7 +5268,6 @@
- else
- OSMESA_STATIC_LIBS=$OSMESA_LIBS
- fi
-- : ${GLUT_PATH=$NCBI/glut}
- if test "$with_glut" != "no"; then
- if test "${with_glut-yes}" != "yes"; then
- GLUT_PATH=$with_glut
-@@ -5121,7 +5287,6 @@
- NCBI_MISSING_PACKAGE(glut)
- fi
- fi
-- : ${GLEW_PATH=$NCBI/glew}
- if test "$with_glew" != "no"; then
- if test "${with_glew-yes}" != "yes"; then
- GLEW_PATH=$with_glew
-@@ -5214,7 +5379,7 @@
- : ${with_wxwidgets_ucs=no}
- if test "$with_wxwidgets" != "no" ; then
- case "$with_wxwidgets" in
-- yes | "" ) : ${WXWIDGETS_PATH=$NCBI/wxwidgets} ;;
-+ yes | "" ) ;;
- * ) WXWIDGETS_PATH=$with_wxwidgets ;;
- esac
- if test -d "$WXWIDGETS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-@@ -5283,12 +5448,13 @@
- libsed=$basesed
- ;;
- esac
-- AC_CACHE_CHECK([for wxWidgets in $WXWIDGETS_ARCH_PATH],
-+ AC_CACHE_CHECK(
-+ [for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}],
- ncbi_cv_lib_wxwidgets,
- [if test -x "$wxconf" ; then
- WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
- NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, ["$wxconf" $wxcfflags --libs],
-- [$libsed; ])
-+ [$libsed; s/ -lm / /g;])
-
- CPPFLAGS="$WXWIDGETS_INCLUDE $orig_CPPFLAGS"
- LIBS="$WXWIDGETS_LIBS $orig_LIBS"
-@@ -5315,12 +5481,12 @@
- else
- NCBI_PACKAGE(wxWidgets)
- case "`"$wxconf" $wxcfflags --version`" in
-- 2.[[89]].* | 2.[[0-9]][[0-9]]* )
-- NCBI_PACKAGE(wx2.8)
-- wxlibs=std,richtext,aui
-+ 1.* | 2.[[0-7]].*)
-+ wxlibs=std
- ;;
- *)
-- wxlibs=std
-+ NCBI_PACKAGE(wx2.8)
-+ wxlibs=std,richtext,aui,propgrid
- ;;
- esac
- # The "yes" may have been cached; get the actual settings again if needed
-@@ -5328,9 +5494,9 @@
- WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
- fi
- NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, [$wxconf $wxcfflags --libs $wxlibs],
-- [$libsed; ])
-+ [$libsed; s/ -lm / /g;])
- WXWIDGETS_STATIC_LIBS=`"$wxconf" $wxcfflags --libs --static $wxlibs \
-- 2>/dev/null | sed -e "$basesed"`
-+ 2>/dev/null | sed -e "$basesed; s/ -lm / /g;"`
- if test -n "$WXWIDGETS_STATIC_LIBS"; then
- # Allow direct use of underlying libraries with strict linkers
- WXWIDGETS_LIBS="$WXWIDGETS_LIBS `echo $WXWIDGETS_STATIC_LIBS | sed -e 's/.*\.a *//'`"
-@@ -5350,7 +5516,7 @@
- ## In-house Fast-CGI library
- if test "$with_fastcgi" != "no" ; then
- case "$with_fastcgi" in
-- yes | "" ) : ${FASTCGI_PATH:="$NCBI/fcgi-current"} ;;
-+ yes | "" ) ;;
- */* ) FASTCGI_PATH=$with_fastcgi ;;
- * ) FASTCGI_PATH=$NCBI/fcgi-${with_fastcgi} ;;
- esac
-@@ -5366,7 +5532,8 @@
- NCBI_RPATHIFY(FASTCGI_LIBS, $FASTCGI_LIBDIR, [ -lfcgi $NETWORK_LIBS])
- FASTCGI_OBJS="fcgibuf"
- LIBS="$FASTCGI_LIBS $orig_LIBS"
-- AC_CACHE_CHECK([for FastCGI libraries in $FASTCGI_PATH], ncbi_cv_lib_fcgi,
-+ AC_CACHE_CHECK([for FastCGI libraries${FASTCGI_PATH:+ in $FASTCGI_PATH}],
-+ ncbi_cv_lib_fcgi,
- [CPPFLAGS="$FASTCGI_INCLUDE $orig_CPPFLAGS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
- [[#include <fcgiapp.h>]],
-@@ -5416,7 +5583,11 @@
- else
- with_included_sss=no
- fi
-+ if test "${with_sss-yes}" = yes; then
- NCBI_SSS_PATH=${NCBI_SSS_PATH:="$NCBI/sss/BUILD"}
-+ else
-+ NCBI_SSS_PATH=$with_sss
-+ fi
- NCBI_SSS_INCLUDE=${NCBI_SSS_INCLUDE:="$NCBI_SSS_PATH/include"}
- if test -z "$NCBI_SSS_LIBPATH" ; then
- NCBI_SSS_LIBPATH="${NCBI_SSS_PATH}/lib/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}"
-@@ -5424,7 +5595,8 @@
- NCBI_SSS_LIBPATH="${NCBI_SSS_LIBPATH}mt"
- fi
- fi
-- AC_MSG_CHECKING([for NCBI SSS directories in $NCBI_SSS_PATH])
-+ AC_MSG_CHECKING(
-+ [for NCBI SSS directories${NCBI_SSS_PATH:+ in $NCBI_SSS_PATH}])
- if test "$with_included_sss" = "yes"; then
- AC_MSG_RESULT([yes]) # duh
- elif test ! -d "${NCBI_SSS_LIBPATH}" -o ! -d "${NCBI_SSS_INCLUDE}" ; then
-@@ -5510,7 +5682,6 @@
-
- # SP
- if test "$with_sp" != "no" ; then
-- SP_PATH=${SP_PATH:="$NCBI/SP"}
- if test -n "$SP_INCLUDE"; then
- SP_GENERIC="$SP_INCLUDE/../generic"
- else
-@@ -5520,7 +5691,7 @@
- if test -z "$SP_LIBPATH" ; then
- SP_LIBPATH="${SP_PATH}/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}"
- fi
-- AC_MSG_CHECKING([for SP directories in $SP_PATH])
-+ AC_MSG_CHECKING([for SP directories${SP_PATH:+ in $SP_PATH}])
- if test ! -d "${SP_LIBPATH}" -o ! -d "${SP_INCLUDE}" ; then
- AC_MSG_RESULT([no])
- NCBI_MISSING_PACKAGE(sp)
-@@ -5558,19 +5729,13 @@
-
-
- ## ORBacus CORBA
--if test "${with_orbacus:-yes}" = yes; then
-- if test -d $NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT; then
-- : ${ORBACUS_PATH=$NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT}
-- else
-- : ${ORBACUS_PATH=$NCBI/corba/OB-4.0.1}
-- fi
--elif test "$with_orbacus" != no; then
-+if test "$with_orbacus" != no; then
-+ if test "$with_orbacus" != yes; then
- ORBACUS_PATH=$with_orbacus
- fi
- if test -d "$ORBACUS_PATH"; then
- NCBI_FIX_DIR(ORBACUS_PATH)
- fi
--if test "$with_orbacus" != no; then
- fullpath=${ORBACUS_PATH}/${DEBUG_SFX}${mt_sfx}${bit64_sfx}
- if test -f ${fullpath}/inc/OB/Config.h ; then
- : ${ORBACUS_INCLUDE="-I$ORBACUS_PATH/include -I$fullpath/inc"}
-@@ -5594,7 +5759,8 @@
- LIBIMR=
- ;;
- esac
-- AC_CACHE_CHECK([for ORBacus in $ORBACUS_PATH], ncbi_cv_lib_orbacus,
-+ AC_CACHE_CHECK([for ORBacus${ORBACUS_PATH:+ in $ORBACUS_PATH}],
-+ ncbi_cv_lib_orbacus,
- [CPPFLAGS="$ORBACUS_INCLUDE $orig_CPPFLAGS"
- LIBS="$ORBACUS_LIBPATH $LIBOB $NETWORK_LIBS $DL_LIBS $orig_LIBS"
- AC_LINK_IFELSE([AC_LANG_PROGRAM(
-@@ -5633,7 +5799,7 @@
-
- if test "$with_icu" != "no" ; then
- case "$with_icu" in
-- yes | "" ) : ${ICU_PATH=$NCBI/icu} ;;
-+ yes | "" ) ;;
- * ) ICU_PATH=$with_icu ;;
- esac
- if test -d "$ICU_PATH/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}${mt_sfx}/lib" \
-@@ -5648,7 +5814,8 @@
- ICU_BINPATH=${ICU_BINPATH:="$ICU_ARCH_PATH/bin"}
- ICU_LIBPATH=${ICU_LIBPATH:="$ICU_ARCH_PATH/lib"}
- ICU_INCLUDE=
-- AC_CACHE_CHECK([for ICU in $ICU_ARCH_PATH], ncbi_cv_lib_icu,
-+ AC_CACHE_CHECK([for ICU${ICU_ARCH_PATH:+ in $ICU_ARCH_PATH}],
-+ ncbi_cv_lib_icu,
- [ICU_CONFIG=`$ICU_BINPATH/icu-config --bindir 2>/dev/null`/icu-config
- if test -x "$ICU_CONFIG" ; then
- ICU_INCLUDE=`$ICU_CONFIG --cppflags-searchpath`
-@@ -5690,9 +5857,6 @@
-
-
- ### XML/XSL libraries
--if test -d "$NCBI/expat/include"; then
-- : ${EXPAT_PATH=$NCBI/expat}
--fi
- NCBI_CHECK_THIRD_PARTY_LIB(expat,
- AC_LANG_PROGRAM([#include <expat.h>],
- [XML_Parser parser = XML_ParserCreate("utf-8");]))
-@@ -5701,7 +5865,6 @@
- else
- EXPAT_STATIC_LIBS=${EXPAT_LIBS}
- fi
--: ${SABLOT_PATH=$NCBI/Sablot}
- vpath="$SABLOT_PATH/${compiler_vpfx}build"
- test -d "$vpath" && SABLOT_PATH=$vpath
- if test -d "$SABLOT_PATH"; then
-@@ -5718,7 +5881,6 @@
- SABLOT_STATIC_LIBS=${SABLOT_LIBS}
- fi
-
--: ${LIBXML_PATH=$NCBI/libxml}
- # test -d "$LIBXML_PATH" || LIBXML_PATH=`xml2-config --prefix 2>/dev/null`
- if test "$with_libxml" != "no"; then
- case "$with_libxml" in
-@@ -5813,7 +5975,6 @@
- LIBEXSLT_STATIC_LIBS=${LIBEXSLT_LIBS}
- fi
-
--: ${XERCES_PATH=$NCBI/xerces}
- if test "$with_xerces" != no; then
- if test "${with_xerces-yes}" != yes; then
- XERCES_PATH=$with_xerces
-@@ -5838,7 +5999,7 @@
- NCBI_FIX_DIR(XERCES_LIBPATH)
- fi
- fi
-- if test -d $XERCES_PATH; then
-+ if test -d "$XERCES_PATH"; then
- in_path=" in $XERCES_PATH"
- : ${XERCES_INCLUDE=-I$XERCES_PATH/include}
- : ${XERCES_LIBPATH=$XERCES_PATH/lib}
-@@ -5875,7 +6036,6 @@
- XERCES_STATIC_LIBS=
- fi
-
--: ${XALAN_PATH=$NCBI/xalan}
- if test "$with_xalan" != no; then
- if test "${with_xalan-yes}" != yes; then
- XALAN_PATH=$with_xalan
-@@ -5900,7 +6060,7 @@
- NCBI_FIX_DIR(XALAN_LIBPATH)
- fi
- fi
-- if test -d $XALAN_PATH; then
-+ if test -d "$XALAN_PATH"; then
- in_path=" in $XALAN_PATH"
- : ${XALAN_INCLUDE=-I$XALAN_PATH/include}
- : ${XALAN_LIBPATH=$XALAN_PATH/lib}
-@@ -5937,7 +6097,6 @@
-
- test -d SunWS_cache && rm -r SunWS_cache
-
--: ${ZORBA_PATH=$NCBI/zorba}
- if test "$with_zorba" != no; then
- if test "${with_zorba-yes}" != yes; then
- ZORBA_PATH=$with_zorba
-@@ -5967,7 +6126,7 @@
- ZORBA_PATH=`$ZORBA_CONFIG --prefix`
- : ${ZORBA_INCLUDE=`$ZORBA_CONFIG --cppflags`}
- fi
-- if test -d $ZORBA_PATH; then
-+ if test -d "$ZORBA_PATH"; then
- in_path=" in $ZORBA_PATH"
- : ${ZORBA_INCLUDE=-I$ZORBA_PATH/include}
- : ${ZORBA_LIBPATH=$ZORBA_PATH/lib}
-@@ -6010,7 +6169,7 @@
-
- ### SQLite
- case "$with_sqlite3" in
-- yes | '' ) : ${SQLITE3_PATH=$NCBI/sqlite3} ;;
-+ yes | '' ) ;;
- * ) SQLITE3_PATH=$with_sqlite3 ;;
- esac
-
-@@ -6048,7 +6207,6 @@
- ### OEChem
- # somewhat kludgish, as we now wanto to add in oeiupac and oedepict,
- # which depend on oechem....
--: ${OECHEM_PATH=$NCBI/oechem}
- NCBI_CHECK_THIRD_PARTY_LIB(oechem,
- AC_LANG_PROGRAM([#include <oechem.h>],
- [OEChem::OEMol mol; OEChem::OEConfBase* c = mol.GetActive();]),
-@@ -6091,7 +6249,7 @@
-
- ### muParser
- case "$with_muparser" in
-- yes | '' ) : ${MUPARSER_PATH=$NCBI/muParser} ;;
-+ yes | '' ) ;;
- * ) MUPARSER_PATH=$with_muparser ;;
- esac
-
-@@ -6111,7 +6269,7 @@
-
- ### hdf5
- case "$with_hdf5" in
-- yes | '' ) : ${HDF5_PATH=$NCBI/hdf5} ;;
-+ yes | '' ) ;;
- * ) HDF5_PATH=$with_hdf5 ;;
- esac
-
-@@ -6176,7 +6334,7 @@
- GIF_LIBS=$UNGIF_LIBS
- fi
-
--test -n "$x_libraries" && : ${XPM_PATH=`dirname "$x_libraries"`}
-+case "$x_libraries" in */*) : ${XPM_PATH=`dirname "$x_libraries"`} ;; esac
- NCBI_CHECK_THIRD_PARTY_LIB(Xpm,
- AC_LANG_PROGRAM([#include <X11/xpm.h>],
- [XpmImage image; XpmInfo info;
-@@ -6241,7 +6399,7 @@
- fi
-
- case "$with_ftgl" in
-- yes | '' ) : ${FTGL_PATH=$NCBI/ftgl} ;;
-+ yes | '' ) ;;
- * ) FTGL_PATH=$with_ftgl ;;
- esac
-
-@@ -6268,7 +6426,7 @@
-
- # Mimetic
- case "$with_mimetic" in
-- yes | '' ) : ${MIMETIC_PATH=$NCBI/mimetic} ;;
-+ yes | '' ) ;;
- * ) MIMETIC_PATH=$with_mimetic ;;
- esac
- if test -d "$MIMETIC_PATH"; then
-@@ -6293,6 +6451,88 @@
- [mimetic::MimeEntity me;])])
-
-
-+# gSOAP++
-+case "$with_gsoap" in
-+ yes | '' ) ;;
-+ * ) GSOAP_PATH=$with_gsoap ;;
-+esac
-+if test -d "$GSOAP_PATH"; then
-+ NCBI_FIX_DIR(GSOAP_PATH)
-+fi
-+for d in "$GSOAP_LIBDIR" \
-+ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-+ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
-+ "$GSOAP_PATH/lib${bit64_sfx}" \
-+ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}/lib" \
-+ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}/lib" \
-+ "$GSOAP_PATH/lib"; do
-+ if test -d "$d"; then
-+ GSOAP_LIBDIR=$d
-+ NCBI_FIX_DIR(GSOAP_LIBDIR)
-+ break
-+ fi
-+done
-+NCBI_RPATHIFY(GSOAP_LIBPATH, $GSOAP_LIBDIR)
-+
-+: ${GSOAP_BINDIR=`dirname "$GSOAP_LIBDIR"`/bin}
-+AC_PATH_PROG(GSOAP_SOAPCPP2, soapcpp2, [], $GSOAP_BINDIR:$PATH)
-+AC_PATH_PROG(GSOAP_WSDL2H, wsdl2h, [], $GSOAP_BINDIR:$PATH)
-+
-+NCBI_CHECK_THIRD_PARTY_LIB_EX(gsoap, GSOAP, gsoapssl++,
-+ [AC_LANG_PROGRAM([#include <stdsoap2.h>
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultcode(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultsubcode(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultstring(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultdetail(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultsubcode(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultdetail(struct soap*)
-+ { return NULL; }
-+ SOAP_FMAC3 void SOAP_FMAC4 soap_serializeheader(struct soap*) { }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_putheader(struct soap*) { return 0; }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_getheader(struct soap*) { return 0; }
-+ SOAP_FMAC3 void SOAP_FMAC4 soap_serializefault(struct soap*) { }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_putfault(struct soap*) { return 0; }
-+ SOAP_FMAC3 int SOAP_FMAC4 soap_getfault(struct soap*) { return 0; }],
-+ [soap s;])],
-+ $OPENSSL_LIBS $Z_LIBS)
-+
-+case "$with_sqlite3" in
-+ yes | '' ) ;;
-+ * ) SQLITE3_PATH=$with_sqlite3 ;;
-+esac
-+
-+
-+# MongoDB
-+if test -d "$MONGODB_PATH"; then
-+ NCBI_FIX_DIR(MONGODB_PATH)
-+fi
-+if test -d $MONGODB_PATH/lib${bit64_sfx}; then
-+ MONGODB_LIBDIR=$MONGODB_PATH/lib${bit64_sfx}
-+else
-+ MONGODB_LIBDIR=$MONGODB_PATH/lib
-+fi
-+# need Boost rpath
-+NCBI_RPATHIFY(MONGODB_LIBPATH, $MONGODB_LIBDIR)
-+NCBI_CHECK_THIRD_PARTY_LIB_EX(mongodb, MONGODB, mongoclient,
-+ [AC_LANG_PROGRAM([#include <mongo/client/dbclient.h>],
-+ [std::vector<mongo::HostAndPort> v;
-+ mongo::DBClientReplicaSet client("foo", v);
-+ client.connect();])],
-+ [$BOOST_LIBPATH $boost_fs_lib $BOOST_THREAD_LIBS], [],
-+ [$BOOST_INCLUDE])
-+# MongoDB's own library is normally static, but its supporting Boost
-+# libraries might not be by default.
-+if test -n "$MONGODB_LIBS"; then
-+ MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongodb $BOOST_LIBPATH $boost_fs_static_lib $BOOST_THREAD_STATIC_LIBS"
-+else
-+ MONGODB_STATIC_LIBS=
-+fi
-+
- ### Restore original compiler/linker flags
- LIBS="$orig_LIBS"
- CPPFLAGS="$orig_CPPFLAGS"
-@@ -6499,16 +6739,6 @@
- fi
-
-
--## Sequence Read Archive SDK, which may be attached on either the
--## public or the internal side
--
--if test -f "${real_srcdir}/src/sra/sdk/Makefile.sra_macros.mk"; then
-- sra=sra
--else
-- sra=
--fi
--
--
- ## `internal' project cluster
-
- if test "$with_internal" = "no" \
-@@ -6781,6 +7011,7 @@
- AC_SUBST(C_LINK)
- AC_SUBST(TAIL_N)
- AC_SUBST(EGREP_Q)
-+AC_SUBST(LDD_R)
-
- AC_SUBST(CFLAGS)
- AC_SUBST(FAST_CFLAGS)
-@@ -6829,7 +7060,6 @@
- AC_SUBST(algo)
- AC_SUBST(app)
- AC_SUBST(internal)
--AC_SUBST(sra)
-
- AC_SUBST(check)
- AC_SUBST(CHECK_ARG)
-@@ -6865,6 +7095,7 @@
-
- AC_SUBST(THREAD_LIBS)
- AC_SUBST(NCBIATOMIC_LIB)
-+AC_SUBST(OPENMP_FLAGS)
- AC_SUBST(NETWORK_LIBS)
- AC_SUBST(NETWORK_PURE_LIBS)
- AC_SUBST(RESOLVER_LIBS)
-@@ -6902,6 +7133,8 @@
- AC_SUBST(BOOST_INCLUDE)
- AC_SUBST(BOOST_LIBPATH)
- AC_SUBST(BOOST_TAG)
-+AC_SUBST(BOOST_FILESYSTEM_LIBS)
-+AC_SUBST(BOOST_FILESYSTEM_STATIC_LIBS)
- AC_SUBST(BOOST_REGEX_LIBS)
- AC_SUBST(BOOST_REGEX_STATIC_LIBS)
- AC_SUBST(BOOST_SYSTEM_LIBS)
-@@ -6968,6 +7201,8 @@
- AC_SUBST(SQLITE3_STATIC_LIBS)
- AC_SUBST(FREETYPE_INCLUDE)
- AC_SUBST(FREETYPE_LIBS)
-+AC_SUBST(GSOAP_PATH)
-+AC_SUBST(MONGODB_STATIC_LIBS)
- AC_SUBST(ncbi_xreader_pubseqos)
- AC_SUBST(ncbi_xreader_pubseqos2)
- AC_SUBST(UNLESS_PUBSEQOS)
-@@ -7194,7 +7429,9 @@
-
- cat << EOCONF
- ===============================================================================
--NCBI C++ Toolkit documentation: doc/index.html, doc/config.html#ref_Running
-+NCBI C++ Toolkit documentation:
-+ Online: http://www.ncbi.nlm.nih.gov/toolkit/doc/book/
-+ Local: ./doc/public/index.html
- For the available configuration flags run: ./configure --help
-
- CFLAGS = $CFLAGS
---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014-06-23 17:36:18.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014-06-23 17:36:59.000000000 +0200
-@@ -1,126 +1,45 @@
+--- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014/05/05 12:38:59 62744
++++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014/05/05 13:59:33 62745
+@@ -1,126 +1,44 @@
-# Hacked up in various ways, since Autoconf's version doesn't quite
-# suit our (unusual) conventions. (Originally from status.m4)
-m4_define([_AC_SRCPATHS],
@@ -1380,13 +49,11 @@
-AS_SET_CATFILE([ac_abs_builddir], [$builddir], [$1])
-AS_SET_CATFILE([ac_abs_top_builddir],
- [$ac_abs_builddir], [${ac_top_builddir}.])
- AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir])
+-AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir])
-AS_SET_CATFILE([ac_abs_srcdir], [$ac_abs_top_srcdir], [$ac_dir_suffix])
-])# _AC_SRCPATHS
-
-+ac_builddir=$builddir
-+])
-
+-
-# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a
-# last resort due to issues with sourcing .bashrc.
-m4_define([_AS_LINENO_PREPARE],
@@ -1426,7 +93,7 @@
- esac
- done]);;
- esac
-
+-
- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
- # uniformly replaced by the line number. The first 'sed' inserts a
- # line-number line before each line; the second 'sed' does the real
@@ -1456,6 +123,10 @@
- exit
-}
-])# _AS_LINENO_PREPARE
++ac_builddir=$builddir
++])
++
++
+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both
+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make
+# bash a last resort due to issues with sourcing .bashrc while entirely
@@ -1485,7 +156,7 @@
AC_DEFUN(NCBI_FIX_DIR,
-@@ -158,7 +77,7 @@
+@@ -158,7 +76,7 @@
AC_MSG_WARN([Proceeding without questions per --without-caution]) ;;
* )
echo "$1 [[y/N]]"
@@ -1494,59 +165,69 @@
case "$answer" in
[[Yy]]* ) AC_MSG_WARN([Proceeding at your own risk...]) ;;
* ) AC_MSG_ERROR([Configuration has been canceled by user.]) ;;
---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014-06-23 17:38:56.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014-06-23 17:39:04.000000000 +0200
-@@ -98,6 +98,9 @@
- /* Define to 1 if you have the `getaddrinfo' function. */
- #undef HAVE_GETADDRINFO
+--- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014/05/05 12:38:59 62744
++++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014/05/05 13:59:33 62745
+@@ -38,7 +38,7 @@
+ #
+ #############################################################################
-+/* Define to 1 if you have the `getgrouplist' function. */
-+#undef HAVE_GETGROUPLIST
-+
- /* If you have the `gethostbyaddr_r' function, define to the number of
- arguments it takes (normally 7 or 8). */
- #undef HAVE_GETHOSTBYADDR_R
-@@ -176,9 +179,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #undef HAVE_IOS_REGISTER_CALLBACK
+-AC_PREREQ(2.59)
++AC_PREREQ(2.60)
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--#undef HAVE_IS_SORTED
--
- /* Define to 1 if you have the `lchown' function. */
- #undef HAVE_LCHOWN
+ dnl Early setup, most crucially for locking. The diversion magic lets
+ dnl this occur before AC_INIT, which already interferes with other
+@@ -493,6 +493,10 @@
+ [***** See also HTML documentation in ./doc/index.html *****])
-@@ -234,6 +234,9 @@
- /* Define to 1 if libgnutls is available. */
- #undef HAVE_LIBGNUTLS
-+/* Define to 1 if libgsoapssl++ is available. */
-+#undef HAVE_LIBGSOAP
-+
- /* Define to 1 if libhdf5_cpp is available. */
- #undef HAVE_LIBHDF5
++AC_DIVERT_PUSH(PARSE_ARGS)
++dnl As of Autoconf 2.60, this needs to run too early for config.log,
++dnl to which AC_MSG_ERROR normally copies its output, to be available.
++m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD])
+ #### Check the passed arguments against the list of available ones
+ x_with_list="\
+ debug max-debug symbols optimization profiling tcheck dll static static-exe \
+@@ -564,7 +568,7 @@
+ | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
+ | --x-includes=* | --x-libraries=* | --with-3psw=* \
+ | --target=* | --with-runpath=* | --with-relative-runpath=* \
+- | --no-create | --no-recursion)
++ | --help | --no-create | --no-recursion)
+ ;;
-@@ -260,6 +263,9 @@
- /* Define to 1 if libmimetic is available. */
- #undef HAVE_LIBMIMETIC
+ * )
+@@ -572,6 +576,8 @@
+ ;;
+ esac
+ done
++m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD])
++AC_DIVERT_POP
-+/* Define to 1 if libmongoclient is available. */
-+#undef HAVE_LIBMONGODB
-+
- /* Define to 1 if libmuparser is available. */
- #undef HAVE_LIBMUPARSER
-@@ -382,9 +388,6 @@
- /* Define to 1 if `min'/`max' templates are not implemented. */
- #undef HAVE_NO_MINMAX_TEMPLATE
+ if test "$with_gbench" = "yes" ; then
+@@ -2176,7 +2182,7 @@
+ fi
+
+ AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
+-AC_PATH_PROG(GREP, grep)
++dnl AC_PATH_PROG(GREP, grep)
+ AC_PROG_EGREP
+ AC_MSG_CHECKING([how to run $EGREP quietly])
+ if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
+--- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014/05/05 14:10:55 62749
++++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014/05/05 14:23:49 62750
+@@ -694,7 +694,7 @@
+ /* Define to empty if `const' does not conform to ANSI C. */
+ /* #undef const */
--/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */
--#undef HAVE_NULLPTR
--
- /* Define to 1 if ODBC libraries are available. */
- #undef HAVE_ODBC
+-/* Define to `unsigned' if <sys/types.h> does not define. */
++/* Define to `unsigned int' if <sys/types.h> does not define. */
+ /* #undef size_t */
-@@ -799,37 +802,37 @@
+ /*
+--- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014/05/05 14:10:55 62749
++++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014/05/05 14:23:49 62750
+@@ -802,37 +802,37 @@
by a signal. */
#undef SELECT_UPDATES_TIMEOUT
@@ -1595,66 +276,21 @@
#undef SIZEOF___INT64
/* Define to 1 if the stack grows down. */
-@@ -870,5 +873,5 @@
+@@ -873,5 +873,5 @@
/* Define to empty if `const' does not conform to ANSI C. */
#undef const
-/* Define to `unsigned' if <sys/types.h> does not define. */
+/* Define to `unsigned int' if <sys/types.h> does not define. */
#undef size_t
---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014-06-23 17:40:40.000000000 +0200
-+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014-06-23 17:40:57.000000000 +0200
-@@ -1,4 +1,4 @@
--/* $Id: ncbiconf_xcode.h 361821 2012-05-04 14:28:13Z ucko $
-+/* $Id$
- * By Vlad Lebedev, NCBI (lebedev@ncbi.nlm.nih.gov)
- *
- * Mac OS X - xCode Build
-@@ -258,9 +258,6 @@
- /* Define to 1 if you have `ios(_base)::register_callback'. */
- #define HAVE_IOS_REGISTER_CALLBACK 1
-
--/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
--/* #undef HAVE_IS_SORTED */
--
- /* Define to 1 if you have the `lchown' function. */
- /* #undef HAVE_LCHOWN */
-
-@@ -358,6 +355,9 @@
- /* Define to 1 if you have the `lutimes' function. */
- /* #undef HAVE_LUTIMES */
-
-+/* Define to 1 if you have the `madvise' function. */
-+#define HAVE_MADVISE 1
-+
- /* Define to 1 if you have the <malloc.h> header file. */
- /* #undef HAVE_MALLOC_H */
-
-@@ -589,15 +589,15 @@
- /* Define to 1 if you have the <windows.h> header file. */
- /* #undef HAVE_WINDOWS_H */
-
-+/* Define to 1 if you have the `writev' function. */
-+#define HAVE_WRITEV 1
-+
- /* Define to 1 if the system has the type `wstring'. */
- #define HAVE_WSTRING 1
-
- /* Define to 1 if wxWidgets is available. */
- /* #undef HAVE_WXWIDGETS */
+--- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014/05/06 13:12:18 62759
++++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014/05/06 13:42:48 62760
+@@ -11,6 +11,7 @@
--/* Define to 1 if nullptr keyword is available. */
--/* #undef HAVE_NULLPTR */
--
- /* Define as const if the declaration of iconv() needs const. */
- #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */
- # define ICONV_CONST
-@@ -694,7 +694,7 @@
- /* Define to empty if `const' does not conform to ANSI C. */
- /* #undef const */
+ NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
--/* Define to `unsigned' if <sys/types.h> does not define. */
-+/* Define to `unsigned int' if <sys/types.h> does not define. */
- /* #undef size_t */
++AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir])
+ ac_builddir=$builddir
+ ])
- /*
+
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch.bad
similarity index 100%
copy from sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch
copy to sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch.bad
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 2a77c11..ecb94f0 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -112,9 +112,12 @@ src_prepare() {
"${FILESDIR}"/${P}-fix-creaders-linking.patch
"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
"${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
- "${FILESDIR}"/${P}-support-autoconf-2.60.patch
- "${FILESDIR}"/${P}-configure.patch
+ "${FILESDIR}"/${P}-more-patches.patch
+ "${FILESDIR}"/${P}-linking.patch
+ "${FILESDIR}"/${P}-linking2.patch
)
+ # "${FILESDIR}"/${P}-support-autoconf-2.60.patch
+ # "${FILESDIR}"/${P}-configure.patch
epatch ${PATCHES[@]}
# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
# https://bugs.gentoo.org/show_bug.cgi?id=514706
@@ -248,7 +251,8 @@ src_configure() {
$(use_with xerces xerces "${EPREFIX}/usr")
$(use_with hdf5 hdf5 "${EPREFIX}/usr")
$(use_with xalan xalan "${EPREFIX}/usr")
-# $(use_with gif gif "${EPREFIX}/usr")
+# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
+ --without-gif
$(use_with jpeg jpeg "${EPREFIX}/usr")
$(use_with tiff tiff "${EPREFIX}/usr")
$(use_with png png "${EPREFIX}/usr")
@@ -263,7 +267,7 @@ src_configure() {
# TODO
# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
- # otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
+ # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
@@ -274,6 +278,7 @@ src_configure() {
--srcdir="${S}" \
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
+ --with-flat-makefile \
${myconf[@]} || die
#--without-debug \
# --with-bin-release \
@@ -291,12 +296,33 @@ src_configure() {
}
src_compile() {
- # all_r would ignore the --with-projects contents and build more
- # emake all_r -C GCC*-Release*/build || die
- # all_p with compile only selected/required components
-# cd "${S}"_build &&\
- emake all_p -C "${S}"_build/build
-# emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
+ ## all_r would ignore the --with-projects contents and build more
+ ## emake all_r -C GCC*-Release*/build || die
+ ## all_p with compile only selected/required components
+ ##cd "${S}"_build &&\
+ ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
+ #emake all_p -C "${S}"_build/build
+
+ #
+ # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
+ #
+ # The next release should automatically address such underlinking, albeit
+ # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to
+ # add or extend more DLL_LIB settings, to which end you may find the
+ # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
+ # helpful. For instance,
+ #
+ # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
+ #
+ # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
+ #
+ # DLL_LIB = xncbi
+ #
+ # (You can find the path to that makefile by examining
+ # .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
+ #
+ # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
+ emake -C "${S}"_build/build -f Makefile.flat
}
src_install() {
next reply other threads:[~2014-06-25 15:01 UTC|newest]
Thread overview: 30+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-06-25 15:00 Martin Mokrejs [this message]
-- strict thread matches above, loose matches on Subject: below --
2023-05-02 12:15 [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/ Andrew Ammerlaan
2019-04-05 15:27 Martin Mokrejs
2017-03-27 0:44 Martin Mokrejs
2017-03-26 22:48 Martin Mokrejs
2017-03-26 20:37 Martin Mokrejs
2017-03-23 21:28 Martin Mokrejs
2017-03-23 18:28 Martin Mokrejs
2017-03-23 17:17 Martin Mokrejs
2017-03-22 22:36 Martin Mokrejs
2016-12-02 23:28 Martin Mokrejs
2014-09-16 4:07 Christoph Junghans
2014-06-26 20:42 Martin Mokrejs
2014-06-25 23:24 Martin Mokrejs
2014-06-25 21:57 Martin Mokrejs
2014-06-25 20:59 Martin Mokrejs
2014-06-23 20:34 Martin Mokrejs
2014-06-23 16:10 Martin Mokrejs
2014-01-25 16:25 Justin Lecher
2013-09-14 8:17 Martin Mokrejs
2013-09-13 22:17 Martin Mokrejs
2013-09-13 22:05 Martin Mokrejs
2013-09-13 21:27 Martin Mokrejs
2013-09-13 16:51 Martin Mokrejs
2013-09-13 16:45 Martin Mokrejs
2013-09-13 16:08 Martin Mokrejs
2013-01-30 17:08 Justin Lecher
2013-01-07 22:13 Martin Mokrejs
2013-01-07 17:09 Martin Mokrejs
2012-12-28 19:19 Martin Mokrejs
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