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commit: 8d30af0e3afd031e00f5d69fce3683233a23b487 |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Mon Jun 23 16:10:25 2014 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Mon Jun 23 16:10:25 2014 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8d30af0e |
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|
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add patches for 12.0.0 to support autoconf-2.60 (so far 2.59 was needed) |
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|
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--- |
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...ncbi-tools++-12.0.0-support-autoconf-2.60.patch | 1660 ++++++++++++++++++++ |
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.../ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 10 +- |
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2 files changed, 1667 insertions(+), 3 deletions(-) |
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|
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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 |
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new file mode 100644 |
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index 0000000..80b23e9 |
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--- /dev/null |
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+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch |
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@@ -0,0 +1,1660 @@ |
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+--- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014-06-23 17:35:47.000000000 +0200 |
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++++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014-06-23 17:36:41.000000000 +0200 |
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+@@ -1,5 +1,5 @@ |
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+ ############################################################################# |
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+-# $Id: configure.ac 398256 2013-05-03 19:14:07Z rafanovi $ |
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++# $Id$ |
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+ # Derived from configure.in version 1.173. |
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+ # ========================================================================== |
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+ # |
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+@@ -38,7 +38,7 @@ |
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+ # |
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+ ############################################################################# |
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+ |
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+-AC_PREREQ(2.59) |
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++AC_PREREQ(2.60) |
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+ |
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+ dnl Early setup, most crucially for locking. The diversion magic lets |
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+ dnl this occur before AC_INIT, which already interferes with other |
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+@@ -71,7 +71,7 @@ |
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+ python, perl, jni, sqlite3, mimetic, sge, icu, sp, expat, |
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+ sablot, libxml, libxslt, libexslt, xerces, xalan, zorba, |
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+ oechem, muparser, hdf5, gif, jpeg, png, tiff, xpm, |
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+- magic, curl], |
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++ magic, curl, gsoap, mongodb], |
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+ [if test "${[with_]X-no}" != "no"; then |
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+ AC_MSG_ERROR([incompatible options: --with-]X[ but --without-3psw]) |
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+ else |
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+@@ -143,6 +143,8 @@ |
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+ [ --with-bin-release build executables suitable for public release]) |
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+ AC_ARG_WITH(mt, |
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+ [ --with-mt compile in a MultiThread-safe manner]) |
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++AC_ARG_WITH(openmp, |
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++ [ --with-openmp enable OpenMP extensions for all projects]) |
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+ AC_ARG_WITH(64, |
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+ [ --with-64 compile to 64-bit code]) |
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+ AC_ARG_WITH(universal, |
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+@@ -220,11 +222,15 @@ |
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+ |
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+ ## NCBI packages |
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+ AC_ARG_WITH(ncbi-c, |
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++ [ --with-ncbi-c=DIR use NCBI C Toolkit installation in DIR]) |
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++AC_ARG_WITH(ncbi-c2, |
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+ [ --without-ncbi-c do not use NCBI C Toolkit]) |
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+ AC_ARG_WITH(sss, |
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++ [ --with-sss=DIR use NCBI SSS installation in DIR]) |
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++AC_ARG_WITH(sss2, |
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+ [ --without-sss do not use NCBI SSS libraries]) |
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+ AC_ARG_WITH(sssutils, |
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+- [ --without-sssutils do not use NCBI SSS UTIL library]) |
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++ [ --without-utils do not use NCBI SSS UTIL library]) |
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+ AC_ARG_WITH(sssdb, |
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+ [ --without-sssdb do not use NCBI SSS DB library]) |
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+ AC_ARG_WITH(included-sss, |
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+@@ -439,6 +445,14 @@ |
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+ [ --with-mimetic=DIR use libmimetic installation in DIR]) |
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+ AC_ARG_WITH(mimetic2, |
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+ [ --without-mimetic do not use libmimetic]) |
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++AC_ARG_WITH(gsoap, |
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++ [ --with-gsoap=DIR use gSOAP++ installation in DIR]) |
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++AC_ARG_WITH(gsoap2, |
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++ [ --without-gsoap do not use gSOAP++]) |
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++AC_ARG_WITH(mongodb, |
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++ [ --with-mongodb=DIR use MongoDB installation in DIR]) |
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++AC_ARG_WITH(mongodb2, |
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++ [ --without-mongodb do not use MongoDB]) |
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+ AC_ARG_WITH(3psw, |
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+ [ --with-3psw=std:netopt favor standard (system) builds of the above pkgs.]) |
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+ AC_ARG_WITH(3psw2, |
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+@@ -479,24 +493,28 @@ |
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+ [***** See also HTML documentation in ./doc/index.html *****]) |
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+ |
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+ |
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++AC_DIVERT_PUSH(PARSE_ARGS) |
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++dnl As of Autoconf 2.60, this needs to run too early for config.log, |
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++dnl to which AC_MSG_ERROR normally copies its output, to be available. |
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++m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD]) |
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+ #### Check the passed arguments against the list of available ones |
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+ x_with_list="\ |
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+ debug max-debug symbols optimization profiling tcheck dll static static-exe \ |
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+ plugin-auto-load bundles bin-release mt 64 universal exe runpath hard-runpath \ |
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+-lfs limited-linker \ |
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++lfs limited-linker openmp \ |
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+ autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \ |
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+ deactivation makefile-auto-update projects flat-makefile configure-dialog \ |
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+ check ncbi-public strip pch caution ccache distcc \ |
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+ ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ |
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+ geo included-geo \ |
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+ z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ |
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+-ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ |
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++ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ |
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+ bdb python perl jni sqlite3 icu boost boost-tag \ |
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+ sp expat sablot libxml libxslt libexslt xerces xalan zorba \ |
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+ oechem sge muparser hdf5 \ |
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+-gif jpeg tiff png xpm magic curl mimetic 3psw \ |
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++gif jpeg tiff png xpm magic curl mimetic gsoap mongodb 3psw \ |
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+ local-lbsm ncbi-crypt connext \ |
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+-serial objects dbapi app ctools gui algo internal gbench x" |
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++serial objects dbapi app ctools gui algo internal gbench" |
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+ |
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+ changequote(, )dnl |
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+ x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` |
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+@@ -522,7 +540,6 @@ |
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+ case "$x_arg" in |
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+ --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ |
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+ | --cache-file= | --build= | --host= | --target= | --with-runpath= \ |
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+- | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ |
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+ | --with-relative-runpath= | --x-includes= | --x-libraries= ) |
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+ AC_MSG_ERROR([$x_arg: requires value; use --help to show usage]) |
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+ ;; |
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+@@ -533,12 +550,11 @@ |
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+ | --with-universal=* | --with-tcheck=* \ |
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+ | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ |
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+ | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ |
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+- | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ |
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+ | [[A-Z]*=*] \ |
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+ | --with-z=* | --with-bz2=* | --with-lzo=* \ |
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+- | --with-pcre=* \ |
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++ | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \ |
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+ | --with-gcrypt=* | --with-gnutls=* | --with-openssl=* \ |
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+- | --with-krb5=* | --with-curl=* \ |
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++ | --with-krb5=* | --with-curl=* | --with-gsoap=* | --with-mongodb=* \ |
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+ | --with-sybase-local=* | --with-wxwidgets=* | --with-mimetic=* \ |
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+ | --with-ftds=* | --with-mysql=* | --with-fastcgi=* \ |
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+ | --with-sqlite3=* | --with-expat=* | --with-sablot=* \ |
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+@@ -552,7 +568,7 @@ |
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+ | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \ |
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+ | --x-includes=* | --x-libraries=* | --with-3psw=* \ |
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+ | --target=* | --with-runpath=* | --with-relative-runpath=* \ |
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+- | --no-create | --no-recursion) |
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++ | --help | --no-create | --no-recursion) |
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+ ;; |
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+ |
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+ * ) |
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+@@ -560,6 +576,8 @@ |
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+ ;; |
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+ esac |
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+ done |
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++m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD]) |
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++AC_DIVERT_POP |
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+ |
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+ |
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+ if test "$with_gbench" = "yes" ; then |
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+@@ -604,6 +622,13 @@ |
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+ : ${with_optimization=no} |
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+ fi |
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+ |
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++if test "$with_openmp" = yes; then |
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++ if test "$with_mt" = no; then |
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++ AC_MSG_ERROR([incompatible options: --without-mt but --with-openmp]) |
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++ fi |
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++ : ${with_mt=yes} |
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++fi |
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++ |
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+ #### Check for special options |
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+ if test "$with_extra_action" = "yes" ; then |
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+ AC_MSG_ERROR([--with-extra-action must have a value after =]) |
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+@@ -649,15 +674,10 @@ |
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+ *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; |
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+ esac |
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+ fi |
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+-if test -n "$with_projects"; then |
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+- case "$with_projects" in |
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+- /* ) abs_projects=$with_projects ;; |
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+- yes) abs_projects=$srcdir/projects ;; |
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+- * ) abs_projects=$srcdir/$with_projects ;; |
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+- esac |
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+- test -r "$abs_projects" || \ |
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+- AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) |
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+-fi |
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++# Generally save any originally specified flags. |
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++USER_CFLAGS=$CFLAGS |
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++USER_CXXFLAGS=$CXXFLAGS |
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++USER_LDFLAGS=$LDFLAGS |
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+ |
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+ #### Always define this |
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+ AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) |
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+@@ -675,6 +695,23 @@ |
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+ #### Make some provisions for traditional operation |
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+ AC_PROG_INSTALL |
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+ |
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++#### Point ICC at a suitable GCC version ASAP. |
202 |
++case "/$CXX" in |
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++ */icpc ) |
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++ if test -d /usr/local/gcc; then |
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++ case "`$CXX -dumpversion`:$host_cpu" in |
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++ *:i?86) v=4.4.5 ;; |
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++ ?.* | 1[[01]].* ) v=4.0.1 ;; |
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++ *) v=4.4.2 ;; |
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++ esac |
210 |
++ gcc=/usr/local/gcc/$v/bin/gcc |
211 |
++ if test -x $gcc; then |
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++ CC="$CC -gcc-name=$gcc" |
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++ CXX="$CXX -gcc-name=$gcc" |
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++ fi |
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++ fi |
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++ ;; |
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++esac |
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+ |
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+ #### C and C++ compilers |
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+ AC_LANG(C++) |
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+@@ -987,6 +1024,30 @@ |
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+ ;; |
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+ * ) NCBIATOMIC_LIB=xncbi ;; |
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+ esac |
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++ case "$compiler" in |
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++ GCC ) |
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++ if $CC -v | grep clang >/dev/null; then |
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++ : |
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++ # Will allegedly support -openmp at some point, but as of 3.4, |
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++ # just parses it as specifying an output filename: -o penmp. |
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++ else |
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++ case "$compiler_version" in |
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++ [[123]]?? | 4[[01]]? ) ;; |
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++ * ) : ${OPENMP_FLAGS=-fopenmp} ;; |
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++ esac |
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++ fi |
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++ ;; |
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++ ICC ) |
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++ : ${OPENMP_FLAGS=-openmp} |
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++ ;; |
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++ WorkShop* ) |
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++ : ${OPENMP_FLAGS=-xopenmp=parallel} |
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++ ;; |
244 |
++ esac |
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++ if test "$with_openmp" = yes; then |
246 |
++ MT_FLAG="$MT_FLAG $OPENMP_FLAGS" |
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++ OPENMP_FLAGS= |
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++ fi |
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+ mt_sfx="MT" |
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+ NCBI_FEATURE(MT) |
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+ else |
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+@@ -994,6 +1055,7 @@ |
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+ MT_FLAG= |
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+ THREAD_LIBS= |
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+ NCBIATOMIC_LIB= |
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++ OPENMP_FLAGS= |
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+ mt_sfx="" |
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+ fi |
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+ MT_SFX="${mt_sfx}" |
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+@@ -1006,6 +1068,9 @@ |
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+ APP_LDFLAGS= |
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+ DLL_LDFLAGS= |
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+ |
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++### Should go before any test compiler runs |
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++AC_GNU_SOURCE |
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++ |
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+ case "$host_os:$compiler" in |
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+ darwin*:GCC ) |
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+ AC_CACHE_CHECK([whether $CC supports -Wl,-rpath], |
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+@@ -1047,6 +1112,47 @@ |
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+ ;; |
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+ esac |
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+ |
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++case "$compiler:$compiler_version" in |
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++ GCC:4[[0-6]]? | ICC:1[[01]]?? ) |
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++ ncbi_cv_prog_cxx_11=no |
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++ ncbi_cv_prog_c_99=no |
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++ ;; |
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++ ICC:* ) |
280 |
++ ncbi_cv_prog_c_99='-std=gnu99 -fgnu89-inline' |
281 |
++ ;; |
282 |
++esac |
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++ |
284 |
++AC_CACHE_CHECK([how to enable C++ '11 features in $CXX], |
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++ ncbi_cv_prog_cxx_11, |
286 |
++ [orig_CXX=$CXX |
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++ ncbi_cv_prog_cxx_11=no |
288 |
++ for x in -std=gnu++11 -std=gnu++0x; do |
289 |
++ CXX="$orig_CXX $x" |
290 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])], |
291 |
++ [ncbi_cv_prog_cxx_11=$x]) |
292 |
++ test "x$ncbi_cv_prog_cxx_11" = "xno" || break |
293 |
++ done |
294 |
++ CXX=$orig_CXX]) |
295 |
++test "$ncbi_cv_prog_cxx_11" = no || CXX="$CXX $ncbi_cv_prog_cxx_11" |
296 |
++ |
297 |
++AC_LANG_PUSH(C) |
298 |
++AC_CACHE_CHECK([how to enable C '11 or at least '99 features in $CC], |
299 |
++ ncbi_cv_prog_c_99, |
300 |
++ [orig_CC=$CC |
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++ ncbi_cv_prog_c_99=no |
302 |
++ for x in -xc99=all "-std=gnu11 -fgnu89-inline" \ |
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++ "-std=gnu1x -fgnu89-inline" \ |
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++ "-std=gnu99 -fgnu89-inline" \ |
305 |
++ "-std=gnu9x -fgnu89-inline"; do |
306 |
++ CC="$orig_CC $x" |
307 |
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])], |
308 |
++ [ncbi_cv_prog_c_99=$x]) |
309 |
++ test "x$ncbi_cv_prog_c_99" = "xno" || break |
310 |
++ done |
311 |
++ CC=$orig_CC]) |
312 |
++AC_LANG_POP(C) |
313 |
++test "$ncbi_cv_prog_c_99" = no || CC="$CC $ncbi_cv_prog_c_99" |
314 |
++ |
315 |
+ #### Provide default environment setup for known platforms/compilers |
316 |
+ DEPFLAGS="-M" |
317 |
+ DEPFLAGS_POST="" # Needed for VisualAge |
318 |
+@@ -1059,7 +1165,15 @@ |
319 |
+ ;; |
320 |
+ |
321 |
+ solaris*:GCC ) |
322 |
+- CPPFLAGS="-D_XOPEN_SOURCE=500 $CPPFLAGS" |
323 |
++ # On Solaris, GCC defaults to setting _XOPEN_SOURCE (to 500) only |
324 |
++ # in C++ mode. Set it for C code as well to ensure consistent |
325 |
++ # header behavior, taking care to match the C standard version |
326 |
++ # (as enforced by <sys/feature_tests.h>). |
327 |
++ case "$ncbi_cv_prog_c_99" in |
328 |
++ no) CC="$CC -D_XOPEN_SOURCE=500" ;; |
329 |
++ *) CC="$CC -D_XOPEN_SOURCE=600" ;; |
330 |
++ esac |
331 |
++ |
332 |
+ STRIP="@:" |
333 |
+ ;; |
334 |
+ |
335 |
+@@ -1202,11 +1316,19 @@ |
336 |
+ LDFLAGS="-flat_namespace $LDFLAGS" |
337 |
+ |
338 |
+ if test "$with_ncbi_public" = yes; then |
339 |
++ sdks='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' |
340 |
++ case "$host_os" in |
341 |
++ darwin?.* | darwin10.* ) # Mac OS X 10.6.x or older |
342 |
+ TARGET='-mmacosx-version-min=10.5' |
343 |
+- sdks='/Developer/SDKs/MacOSX10.6.sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.6.sdk' |
344 |
++ sdks="/Developer/SDKs/MacOSX10.6.sdk" |
345 |
+ if test "$with_64:${with_universal-no}" != "yes:no"; then |
346 |
+ sdks="/Developer/SDKs/MacOSX10.5.sdk $sdks" |
347 |
+ fi |
348 |
++ ;; |
349 |
++ * ) |
350 |
++ TARGET='-mmacosx-version-min=10.7' |
351 |
++ ;; |
352 |
++ esac |
353 |
+ for sdk in $sdks; do |
354 |
+ if test -d "$sdk"; then |
355 |
+ TARGET="-isysroot $sdk $TARGET" |
356 |
+@@ -1487,8 +1609,8 @@ |
357 |
+ ;; |
358 |
+ GCC:* ) |
359 |
+ DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing" |
360 |
+- case "$host_os" in |
361 |
+- freebsd* ) ;; |
362 |
++ case "$host_os:$host_cpu:$compiler_version" in |
363 |
++ freebsd* | solaris*:*86*:* | *:4[[5-9]]? | *:[[5-9]]?? ) ;; |
364 |
+ * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;; |
365 |
+ esac |
366 |
+ if test "$with_profiling" != "yes"; then |
367 |
+@@ -1587,13 +1709,9 @@ |
368 |
+ solaris* ) |
369 |
+ CONF_f_runpath="-R" |
370 |
+ ;; |
371 |
+- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC ) |
372 |
++ linux*:[[GI]]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC ) |
373 |
+ CONF_f_runpath="-Wl,-rpath," |
374 |
+ ;; |
375 |
+- linux*:ICC ) |
376 |
+- # trying to use "-Wl,-rpath," here sends "ld" to endless 100% CPU loop |
377 |
+- CONF_f_runpath="-Xlinker -rpath -Xlinker " |
378 |
+- ;; |
379 |
+ irix*:* | linux*:KCC | *:Compaq ) |
380 |
+ CONF_f_runpath="-rpath " |
381 |
+ ;; |
382 |
+@@ -1697,8 +1815,11 @@ |
383 |
+ LINK="$LINK -Kc++" |
384 |
+ ;; |
385 |
+ ICC:1???:* ) |
386 |
+- APP_LDFLAGS="-static-intel $APP_LDFLAGS" |
387 |
+- DLL_LDFLAGS="-static-intel -nodefaultlibs $DLL_LDFLAGS" |
388 |
++ # Suppress "warning #10237: -lcilkrts linked in dynamically, static |
389 |
++ # library not available" which is not a problem in practice due to |
390 |
++ # as-needed linkage. |
391 |
++ APP_LDFLAGS="-static-intel -diag-disable 10237 $APP_LDFLAGS" |
392 |
++ DLL_LDFLAGS="-static-intel -diag-disable 10237 -nodefaultlibs $DLL_LDFLAGS" |
393 |
+ # Redundant for apps, but necessary for plugins to be adequately |
394 |
+ # self-contained, at least on 32-bit Linux. |
395 |
+ LIBS="$LIBS -lstdc++" |
396 |
+@@ -1817,18 +1938,6 @@ |
397 |
+ |
398 |
+ #### Intel compiler:: common flags and definitions |
399 |
+ if test "$compiler" = "ICC" ; then |
400 |
+- if test -d /usr/local/gcc; then |
401 |
+- case "$compiler_version:$HOST_CPU" in |
402 |
+- *:i?86) v=4.4.5 ;; |
403 |
+- ???:* | 1[[01]]??:* ) v=4.0.1 ;; |
404 |
+- *) v=4.4.2 ;; |
405 |
+- esac |
406 |
+- gcc=/usr/local/gcc/$v/bin/gcc |
407 |
+- if test -x $gcc; then |
408 |
+- CC="$CC -gcc-name=$gcc" |
409 |
+- CXX="$CXX -gcc-name=$gcc" |
410 |
+- fi |
411 |
+- fi |
412 |
+ if test -n "$icc_license" ; then |
413 |
+ icc_CC="$CC" |
414 |
+ icc_CXX="$CXX" |
415 |
+@@ -2073,6 +2182,7 @@ |
416 |
+ fi |
417 |
+ |
418 |
+ AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH) |
419 |
++dnl AC_PATH_PROG(GREP, grep) |
420 |
+ AC_PROG_EGREP |
421 |
+ AC_MSG_CHECKING([how to run $EGREP quietly]) |
422 |
+ if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then |
423 |
+@@ -2086,6 +2196,16 @@ |
424 |
+ |
425 |
+ AC_CHECK_PROG(VALGRIND_PATH, valgrind, valgrind) |
426 |
+ |
427 |
++AC_PATH_PROG(LDD, ldd) |
428 |
++if test -n "$LDD"; then |
429 |
++ AC_MSG_CHECKING([whether $LDD accepts -r]) |
430 |
++ if $LDD -r /bin/ls >/dev/null 2>&1; then |
431 |
++ AC_MSG_RESULT(yes) |
432 |
++ LDD_R="$LDD -r" |
433 |
++ else |
434 |
++ AC_MSG_RESULT(no) |
435 |
++ fi |
436 |
++fi |
437 |
+ |
438 |
+ #### Check if "${build_root}" is defined; provide a default one |
439 |
+ if test -n "${with_build_root}" ; then |
440 |
+@@ -2170,9 +2290,6 @@ |
441 |
+ fi |
442 |
+ |
443 |
+ |
444 |
+-### Should go before any test compiler runs |
445 |
+-AC_GNU_SOURCE |
446 |
+- |
447 |
+ #### Determine whether this is implicitly a 64-bit platform |
448 |
+ AC_TYPE_SIZE_T |
449 |
+ if test "${with_universal-no}" = "no"; then |
450 |
+@@ -2342,7 +2459,7 @@ |
451 |
+ fi |
452 |
+ ;; |
453 |
+ *:ICC ) |
454 |
+- runpath="$runpath -Xlinker -rpath-link -Xlinker \$(libdir)" |
455 |
++ runpath="$runpath -Wl,-rpath-link,\$(libdir)" |
456 |
+ ;; |
457 |
+ esac |
458 |
+ elif test "$with_runpath" = "yes" -o "$with_dll" != "no" ; then |
459 |
+@@ -2658,15 +2775,30 @@ |
460 |
+ dbgrx1="$wsrx-g[^cx$wschars]*$wsrx" |
461 |
+ dbgrx2="$wsrx-gx*coff[0-9+]*$wsrx" |
462 |
+ optrx="$wsrx-x*O[0-9s]*$wsrx" |
463 |
++ NDEB_CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` |
464 |
++ NDEB_CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` |
465 |
++ NDEB_LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` |
466 |
+ if test "$with_symbols" = "no" ; then |
467 |
+- CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` |
468 |
+- CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` |
469 |
+- LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"` |
470 |
++ CFLAGS=$NDEB_CFLAGS |
471 |
++ CXXFLAGS=$NDEB_CXXFLAGS |
472 |
++ LDFLAGS=$NDEB_LDFLAGS |
473 |
+ else |
474 |
+ echo " $CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || CFLAGS="$CFLAGS -g" |
475 |
+ echo " $CXXFLAGS "| $EGREP_Q "$dbgrx1|$dbgrx2" || CXXFLAGS="$CXXFLAGS -g" |
476 |
+ echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g" |
477 |
+ STRIP="@:" |
478 |
++ case "$compiler:$compiler_version" in |
479 |
++ GCC:4[89]? | GCC:[5-9]? | GCC:???? ) |
480 |
++ # GCC 4.8 defaults to DWARF 4, which Totalview for one |
481 |
++ # can't handle; roll back to version 3 by default. |
482 |
++ echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \ |
483 |
++ CFLAGS="$NDEB_CFLAGS -gdwarf-3" |
484 |
++ echo " $USER_CXXFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \ |
485 |
++ CXXFLAGS="$NDEB_CXXFLAGS -gdwarf-3" |
486 |
++ echo " $USER_LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \ |
487 |
++ LDFLAGS="$NDEB_LDFLAGS -gdwarf-3" |
488 |
++ ;; |
489 |
++ esac |
490 |
+ fi |
491 |
+ |
492 |
+ NOPT_CFLAGS=` echo " $CFLAGS " | sed "s/$optrx/ /g"` |
493 |
+@@ -3024,9 +3156,9 @@ |
494 |
+ ### Check for other standard library functions |
495 |
+ |
496 |
+ AC_FUNC_VPRINTF |
497 |
+-AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getpagesize \ |
498 |
+- getpass getpassphrase getpwuid getrusage gettimeofday \ |
499 |
+- getuid memrchr readpassphrase readv usleep \ |
500 |
++AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getgrouplist \ |
501 |
++ getpagesize getpass getpassphrase getpwuid getrusage \ |
502 |
++ gettimeofday getuid memrchr readpassphrase readv usleep \ |
503 |
+ asprintf vasprintf vsnprintf select statfs statvfs \ |
504 |
+ strcasecmp strlcat strlcpy strdup strndup strtok_r \ |
505 |
+ sysmp timegm utimes lutimes writev) |
506 |
+@@ -3253,17 +3385,6 @@ |
507 |
+ fi |
508 |
+ |
509 |
+ |
510 |
+-AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted, |
511 |
+- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM( |
512 |
+- [[#include <algorithm>]], |
513 |
+- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])], |
514 |
+- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])]) |
515 |
+-if test "$ncbi_cv_func_is_sorted" = yes; then |
516 |
+- AC_DEFINE(HAVE_IS_SORTED, 1, |
517 |
+- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.]) |
518 |
+-fi |
519 |
+- |
520 |
+- |
521 |
+ |
522 |
+ AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores, |
523 |
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h> |
524 |
+@@ -3400,7 +3521,7 @@ |
525 |
+ AC_CACHE_CHECK([whether the C compiler supports C99 restrict], |
526 |
+ ncbi_cv_c_restrict, |
527 |
+ [ncbi_cv_c_restrict=no |
528 |
+- for restrict in restrict __restrict__ __restrict; do |
529 |
++ for restrict in __restrict__ __restrict restrict; do |
530 |
+ test "$ncbi_cv_c_restrict" = "no" || break |
531 |
+ AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], |
532 |
+ [ncbi_cv_c_restrict=$restrict], []) |
533 |
+@@ -3420,7 +3541,7 @@ |
534 |
+ AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict], |
535 |
+ ncbi_cv_cxx_restrict, |
536 |
+ [ncbi_cv_cxx_restrict=no |
537 |
+- for restrict in restrict __restrict__ __restrict; do |
538 |
++ for restrict in __restrict__ __restrict restrict; do |
539 |
+ test "$ncbi_cv_cxx_restrict" = "no" || break |
540 |
+ AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], |
541 |
+ [ncbi_cv_cxx_restrict=$restrict], []) |
542 |
+@@ -3525,14 +3646,6 @@ |
543 |
+ unaligned addresses.]) |
544 |
+ fi |
545 |
+ |
546 |
+-AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr, |
547 |
+- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])], |
548 |
+- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])]) |
549 |
+-if test "$ncbi_cv_cxx_nullptr" = yes; then |
550 |
+- AC_DEFINE(HAVE_NULLPTR, 1, |
551 |
+- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.]) |
552 |
+-fi |
553 |
+- |
554 |
+ ### Check for the availability of other packages |
555 |
+ ### -------------------------------------------- |
556 |
+ |
557 |
+@@ -3630,7 +3743,16 @@ |
558 |
+ dnl NCBI_CHECK_LIBS(FUSE, fuse, fuse_loop) |
559 |
+ AC_SEARCH_LIBS(fuse_loop, fuse, [NCBI_PACKAGE(FUSE)]) |
560 |
+ LIBS=$orig_LIBS |
561 |
++# Temporarily drop OpenMP flags for this test, as some toolchains count |
562 |
++# its support library's indirect use of librt when building applications |
563 |
++# but not when building shared libraries with --no-undefined. |
564 |
++orig_CXXFLAGS=$CXXFLAGS |
565 |
++orig_LDFLAGS=$LDFLAGS |
566 |
++CXXFLAGS=`echo $CXXFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'` |
567 |
++LDFLAGS=`echo $LDFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'` |
568 |
+ NCBI_CHECK_LIBS(RT, rt posix4, clock_gettime) |
569 |
++CXXFLAGS=$orig_CXXFLAGS |
570 |
++LDFLAGS=$orig_LDFLAGS |
571 |
+ NCBI_CHECK_LIBS(DEMANGLE, demangle, cplus_demangle) |
572 |
+ # Add to (orig_)LIBS if present for the sake of corelib and the |
573 |
+ # following call to AC_CHECK_FUNCS. |
574 |
+@@ -3734,7 +3856,6 @@ |
575 |
+ NCBI_PACKAGE(LocalBZ2) |
576 |
+ fi |
577 |
+ |
578 |
+-: ${LZO_PATH=$NCBI/lzo2} |
579 |
+ if test -d "$LZO_PATH"; then |
580 |
+ NCBI_FIX_DIR(LZO_PATH) |
581 |
+ fi |
582 |
+@@ -3767,7 +3888,7 @@ |
583 |
+ ## SSL/TLS libraries |
584 |
+ case "$with_gcrypt" in |
585 |
+ no ) ac_cv_path_LIBGCRYPT_CONFIG=no ;; |
586 |
+- yes | '' ) : ${GCRYPT_PATH=$NCBI/gcrypt} ;; |
587 |
++ yes | '' ) ;; |
588 |
+ * ) GCRYPT_PATH=$with_gcrypt ;; |
589 |
+ esac |
590 |
+ if test -d "$GCRYPT_PATH"; then |
591 |
+@@ -3802,13 +3923,16 @@ |
592 |
+ |
593 |
+ case "$with_gnutls" in |
594 |
+ no ) ac_cv_path_LIBGNUTLS_CONFIG=no ;; |
595 |
+- yes | '' ) : ${GNUTLS_PATH=$NCBI/gnutls} ;; |
596 |
++ yes | '' ) ;; |
597 |
+ * ) GNUTLS_PATH=$with_gnutls ;; |
598 |
+ esac |
599 |
+ if test -d "$GNUTLS_PATH"; then |
600 |
+ NCBI_FIX_DIR(GNUTLS_PATH) |
601 |
++ gnutls_config_path=${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin |
602 |
++else |
603 |
++ gnutls_config_path=$PATH |
604 |
+ fi |
605 |
+-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]) |
606 |
++AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [$gnutls_config_path]) |
607 |
+ |
608 |
+ if test "x$with_gnutls" != xno; then |
609 |
+ if test -x "$LIBGNUTLS_CONFIG"; then |
610 |
+@@ -3817,7 +3941,7 @@ |
611 |
+ test "x$p" = "x/usr" || GNUTLS_PATH=$p |
612 |
+ fi |
613 |
+ else |
614 |
+- LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls" |
615 |
++ LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static" |
616 |
+ $LIBGNUTLS_CONFIG --exists >/dev/null 2>&1 || LIBGNUTLS_CONFIG=no |
617 |
+ fi |
618 |
+ case "$LIBGNUTLS_CONFIG" in |
619 |
+@@ -3846,6 +3970,10 @@ |
620 |
+ $GNUTLS_CONFIG_LIBS $GCRYPT_LIBS) |
621 |
+ if test "x$with_gnutls" != xno -a -n "$GNUTLS_CONFIG_LIBS"; then |
622 |
+ NCBI_RPATHIFY_OUTPUT(GNUTLS_LIBS, [echo $GNUTLS_CONFIG_LIBS], [$no_usr_lib]) |
623 |
++ # Conservatively build against gcrypt if available even when gnutls |
624 |
++ # uses nettle instead, because gcrypt needs explicit initialization |
625 |
++ # to be thread-safe, but gnutls's headers don't indicate which |
626 |
++ # underlying crypto library it's actually using. |
627 |
+ case "$GNUTLS_INCLUDE" in |
628 |
+ *$GCRYPT_INCLUDE* ) ;; |
629 |
+ * ) GNUTLS_INCLUDE="$GNUTLS_INCLUDE $GCRYPT_INCLUDE" ;; |
630 |
+@@ -4108,7 +4236,8 @@ |
631 |
+ SYBASE_DBLIBS="$SYBASE_LPATH $SYBASE_DBLIBS" |
632 |
+ SYBASE_DLLS="$SYBASE_DLLLIST" |
633 |
+ |
634 |
+- AC_CACHE_CHECK([for Sybase in $SYBASE_PATH], ncbi_cv_lib_sybase, |
635 |
++ AC_CACHE_CHECK([for Sybase${SYBASE_PATH:+ in $SYBASE_PATH}], |
636 |
++ ncbi_cv_lib_sybase, |
637 |
+ [CPPFLAGS="$SYBASE_INCLUDE $orig_CPPFLAGS" |
638 |
+ LIBS="$SYBASE_LIBS $SYBASE_DLLS $SYBASE_NETWORK_LIBS $DL_LIBS $orig_LIBS" |
639 |
+ AC_LINK_IFELSE([AC_LANG_PROGRAM( |
640 |
+@@ -4216,7 +4345,8 @@ |
641 |
+ AC_MSG_NOTICE([Using bundled FreeTDS (version $ftds_ver) from $FTDS_PATH]) |
642 |
+ else |
643 |
+ FTDS_LIBS="$FTDS_CTLIBS" |
644 |
+- AC_CACHE_CHECK([for FreeTDS in $FTDS_PATH], ncbi_cv_lib_freetds, |
645 |
++ AC_CACHE_CHECK([for FreeTDS${FTDS_PATH:+ in $FTDS_PATH}], |
646 |
++ ncbi_cv_lib_freetds, |
647 |
+ [CPPFLAGS="$FTDS_INCLUDE $orig_CPPFLAGS" |
648 |
+ LIBS="$FTDS_LIBS $NETWORK_LIBS $orig_LIBS" |
649 |
+ AC_LINK_IFELSE([AC_LANG_PROGRAM( |
650 |
+@@ -4281,7 +4411,7 @@ |
651 |
+ # Kill off single quotes, due to later requoting |
652 |
+ : ${MYSQL_INCLUDE=`$mysql_config --include | tr -d \'`} |
653 |
+ NCBI_RPATHIFY_OUTPUT_COND(MYSQL_LIBS, $mysql_config --libs${mt_sfx:+_r}, |
654 |
+- [s/'//g; ]) |
655 |
++ [s/'//g; $no_usr_lib]) |
656 |
+ AC_CACHE_CHECK([whether MySQL works], ncbi_cv_lib_mysql, |
657 |
+ [CPPFLAGS="$MYSQL_INCLUDE $orig_CPPFLAGS" |
658 |
+ LIBS="$MYSQL_LIBS $orig_LIBS" |
659 |
+@@ -4310,7 +4440,6 @@ |
660 |
+ if test "$with_bdb" != "no" ; then |
661 |
+ case "$with_bdb" in |
662 |
+ yes | "" ) |
663 |
+- : ${BERKELEYDB_PATH:="$NCBI/BerkeleyDB"} |
664 |
+ ;; |
665 |
+ */*) |
666 |
+ BERKELEYDB_PATH=$with_bdb |
667 |
+@@ -4351,7 +4480,8 @@ |
668 |
+ else |
669 |
+ BERKELEYDB_STATIC_LIBS=${BERKELEYDB_LIBS} |
670 |
+ fi |
671 |
+- AC_CACHE_CHECK([for Berkeley DB libraries in $BERKELEYDB_PATH], |
672 |
++ AC_CACHE_CHECK( |
673 |
++ [for Berkeley DB libraries${BERKELEYDB_PATH:+ in $BERKELEYDB_PATH}], |
674 |
+ ncbi_cv_lib_berkeley_db, |
675 |
+ [CPPFLAGS="$BERKELEYDB_INCLUDE $orig_CPPFLAGS" |
676 |
+ LIBS="$BERKELEYDB_LIBS $orig_LIBS" |
677 |
+@@ -4450,7 +4580,8 @@ |
678 |
+ NCBI_RPATHIFY(ODBC_LIBS, ${ODBC_LIBPATH}, [ -lodbc -lodbcinst]) |
679 |
+ CPPFLAGS="$ODBC_INCLUDE $orig_CPPFLAGS" |
680 |
+ LIBS="$ODBC_LIBS $orig_LIBS" |
681 |
+- AC_CACHE_CHECK([for ODBC libraries in $ODBC_PATH], ncbi_cv_lib_odbc, |
682 |
++ AC_CACHE_CHECK([for ODBC libraries${ODBC_PATH:+ in $ODBC_PATH}], |
683 |
++ ncbi_cv_lib_odbc, |
684 |
+ [AC_LINK_IFELSE([AC_LANG_PROGRAM( |
685 |
+ [[#include <sql.h>]], |
686 |
+ [[SQLHDBC hdbc; SQLCHAR* cp = (SQLCHAR*) "x"; |
687 |
+@@ -4542,7 +4673,7 @@ |
688 |
+ AC_PATH_PROG(PERL, perl, [], [$PERL_PATH/bin:$PATH]) |
689 |
+ if test -x "$PERL"; then |
690 |
+ PERL_ARCHLIB=`$PERL -MConfig -e 'print \$Config{archlibexp};'` |
691 |
+- PERL_FLAGS=`$PERL -MConfig -e 'print \$Config{cppflags};'` |
692 |
++ PERL_FLAGS=`$PERL -MConfig -e 'print join " ", grep /^-[[DI]]/, split /\\s+/, \$Config{cppflags};'` |
693 |
+ PERL_INCLUDE="-I$PERL_ARCHLIB/CORE $PERL_FLAGS" |
694 |
+ PERL_DEPS=`$PERL -MConfig -e 'print \$Config{libs};'` |
695 |
+ NCBI_RPATHIFY(PERL_LIBS, $PERL_ARCHLIB/CORE, [ -lperl $PERL_DEPS]) |
696 |
+@@ -4603,9 +4734,7 @@ |
697 |
+ |
698 |
+ ## Boost |
699 |
+ if test "$with_boost" != "no"; then |
700 |
+- if test "${with_boost-yes}" = yes; then |
701 |
+- : ${BOOST_PATH=$NCBI/boost} |
702 |
+- else |
703 |
++ if test "${with_boost-yes}" != yes; then |
704 |
+ BOOST_PATH=$with_boost |
705 |
+ fi |
706 |
+ if test -d "$BOOST_PATH"; then |
707 |
+@@ -4644,17 +4773,22 @@ |
708 |
+ if test -d `echo $BOOST_INCLUDE | sed -e 's/^-I//'`/boost-${ncbi_cv_lib_boost_version}/boost; then |
709 |
+ BOOST_INCLUDE=$BOOST_INCLUDE/boost-${ncbi_cv_lib_boost_version} |
710 |
+ fi |
711 |
+- case "$ncbi_compiler" in |
712 |
+- MIPSPRO) |
713 |
++ case "$compiler:$ncbi_compiler_ver" in |
714 |
++ MIPSpro*) |
715 |
+ BOOST_INCLUDE="$BOOST_INCLUDE $BOOST_INCLUDE/boost/compatibility/cpp_c_headers" |
716 |
+ ;; |
717 |
+- WORKSHOP) |
718 |
++ WorkShop*) |
719 |
+ # Boost.Test's macros yield a *lot* of spurious "should not initialize |
720 |
+ # a non-const reference with a temporary" warnings, to the point of |
721 |
+ # overwhelming the compiler in some cases; turn them off altogether |
722 |
+ # when using Boost at all. |
723 |
+ BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp" |
724 |
+ ;; |
725 |
++ GCC*:4[[7-9]]* | GCC*:5*) |
726 |
++ # Some portions of Boost also have a lot of "unused" typedefs |
727 |
++ # from concept checking. |
728 |
++ BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs" |
729 |
++ ;; |
730 |
+ esac |
731 |
+ case "$ncbi_cv_lib_boost_version" in |
732 |
+ 0_* | 1_[[0-9]] | 1_[[0-9]]_* | 1_[[0-2]][[0-9]] | 1_[[0-2]][[0-9]]_* ) ;; |
733 |
+@@ -4666,7 +4800,7 @@ |
734 |
+ fi |
735 |
+ with_boost=no |
736 |
+ ;; |
737 |
+- 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-2]] | 1_5[[0-2]]_* ) ;; |
738 |
++ 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-3]] | 1_5[[0-3]]_* ) ;; |
739 |
+ '' ) with_boost=no ;; |
740 |
+ * ) |
741 |
+ AC_MSG_WARN( |
742 |
+@@ -4751,7 +4885,9 @@ |
743 |
+ BOOST_REGEX_STATIC_LIBS=$BOOST_REGEX_LIBS |
744 |
+ fi |
745 |
+ |
746 |
+- AC_CACHE_CHECK([for Boost.Regex in $BOOST_PATH], ncbi_cv_lib_boost_regex, |
747 |
++ in_path=${BOOST_PATH:+ in $BOOST_PATH} |
748 |
++ |
749 |
++ AC_CACHE_CHECK([for Boost.Regex$in_path], ncbi_cv_lib_boost_regex, |
750 |
+ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" |
751 |
+ LIBS="$BOOST_LIBPATH $BOOST_REGEX_LIBS $RT_LIBS $orig_LIBS" |
752 |
+ [AC_LINK_IFELSE( |
753 |
+@@ -4759,7 +4895,7 @@ |
754 |
+ [[throw boost::regex_error(boost::regex_constants::error_stack);]])], |
755 |
+ [ncbi_cv_lib_boost_regex=yes], [ncbi_cv_lib_boost_regex=no])]) |
756 |
+ |
757 |
+- AC_CACHE_CHECK([for Boost.Spirit in $BOOST_PATH], ncbi_cv_lib_boost_spirit, |
758 |
++ AC_CACHE_CHECK([for Boost.Spirit$in_path], ncbi_cv_lib_boost_spirit, |
759 |
+ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" |
760 |
+ LIBS="$RT_LIBS $orig_LIBS" |
761 |
+ [AC_LINK_IFELSE( |
762 |
+@@ -4774,7 +4910,7 @@ |
763 |
+ BOOST_SYSTEM_STATIC_LIBS=$BOOST_SYSTEM_LIBS |
764 |
+ fi |
765 |
+ |
766 |
+- AC_CACHE_CHECK([for Boost.System in $BOOST_PATH], ncbi_cv_lib_boost_system, |
767 |
++ AC_CACHE_CHECK([for Boost.System$in_path], ncbi_cv_lib_boost_system, |
768 |
+ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" |
769 |
+ LIBS="$BOOST_LIBPATH $BOOST_SYSTEM_LIBS $RT_LIBS $orig_LIBS" |
770 |
+ [AC_LINK_IFELSE( |
771 |
+@@ -4785,6 +4921,24 @@ |
772 |
+ BOOST_SYSTEM_LIBS= |
773 |
+ BOOST_SYSTEM_STATIC_LIBS=])]) |
774 |
+ |
775 |
++ boost_fs_lib=-lboost_filesystem${BOOST_TAG} |
776 |
++ if test -f "$BOOST_LIBPATH_/libboost_filesystem${BOOST_TAG}-static.a"; then |
777 |
++ boost_fs_static_lib=-lboost_filesystem${BOOST_TAG}-static |
778 |
++ else |
779 |
++ boost_fs_static_lib=$boost_fs_lib |
780 |
++ fi |
781 |
++ BOOST_FILESYSTEM_LIBS="$boost_fs_lib $BOOST_SYSTEM_LIBS" |
782 |
++ BOOST_FILESYSTEM_STATIC_LIBS="$boost_fs_static_lib $BOOST_SYSTEM_STATIC_LIBS" |
783 |
++ |
784 |
++ AC_CACHE_CHECK([for Boost.Filesystem$in_path], ncbi_cv_lib_boost_filesystem, |
785 |
++ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" |
786 |
++ LIBS="$BOOST_LIBPATH $BOOST_FILESYSTEM_LIBS $RT_LIBS $orig_LIBS" |
787 |
++ [AC_LINK_IFELSE( |
788 |
++ [AC_LANG_PROGRAM([[#include <boost/filesystem.hpp>]], |
789 |
++ [[return boost::filesystem::portable_name("foo");]])], |
790 |
++ [ncbi_cv_lib_boost_filesystem=yes], |
791 |
++ [ncbi_cv_lib_boost_filesystem=no])]) |
792 |
++ |
793 |
+ BOOST_TEST_PEM_LIBS=-lboost_prg_exec_monitor${BOOST_TAG} |
794 |
+ if test -f "$BOOST_LIBPATH_/libboost_prg_exec_monitor${BOOST_TAG}-static.a"; then |
795 |
+ BOOST_TEST_PEM_STATIC_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}-static |
796 |
+@@ -4813,7 +4967,7 @@ |
797 |
+ BOOST_TEST_TEM_LIBS=$BOOST_TEST_TEM_STATIC_LIBS |
798 |
+ BOOST_TEST_UTF_LIBS=$BOOST_TEST_UTF_STATIC_LIBS |
799 |
+ |
800 |
+- AC_CACHE_CHECK([for Boost.Test in $BOOST_PATH], ncbi_cv_lib_boost_test, |
801 |
++ AC_CACHE_CHECK([for Boost.Test$in_path], ncbi_cv_lib_boost_test, |
802 |
+ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" |
803 |
+ LIBS="$RT_LIBS $orig_LIBS" |
804 |
+ found= |
805 |
+@@ -4853,7 +5007,7 @@ |
806 |
+ BOOST_THREAD_STATIC_LIBS=$BOOST_THREAD_LIBS |
807 |
+ fi |
808 |
+ |
809 |
+- AC_CACHE_CHECK([for Boost.Threads in $BOOST_PATH], ncbi_cv_lib_boost_thread, |
810 |
++ AC_CACHE_CHECK([for Boost.Threads$in_path], ncbi_cv_lib_boost_thread, |
811 |
+ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS" |
812 |
+ LIBS="$BOOST_LIBPATH $BOOST_THREAD_LIBS $RT_LIBS $orig_LIBS" |
813 |
+ [AC_LINK_IFELSE( |
814 |
+@@ -4864,12 +5018,25 @@ |
815 |
+ BOOST_INCLUDE= |
816 |
+ BOOST_LIBPATH= |
817 |
+ BOOST_TAG= |
818 |
++ ncbi_cv_lib_boost_filesystem=no |
819 |
+ ncbi_cv_lib_boost_regex=no |
820 |
+ ncbi_cv_lib_boost_spirit=no |
821 |
++ ncbi_cv_lib_boost_system=no |
822 |
+ ncbi_cv_lib_boost_test=no |
823 |
+ ncbi_cv_lib_boost_thread=no |
824 |
+ fi |
825 |
+ |
826 |
++if test "$ncbi_cv_lib_boost_filesystem" != "no"; then |
827 |
++ dnl AC_DEFINE(HAVE_BOOST_FILESYSTEM, 1, |
828 |
++ dnl [Define to 1 if the `Boost.Filesystem' library is available.]) |
829 |
++ NCBI_PACKAGE(Boost.Filesystem) |
830 |
++else |
831 |
++ boost_fs_lib= |
832 |
++ boost_fs_static_lib= |
833 |
++ BOOST_FILESYSTEM_LIBS= |
834 |
++ BOOST_FILESYSTEM_STATIC_LIBS= |
835 |
++fi |
836 |
++ |
837 |
+ if test "$ncbi_cv_lib_boost_regex" != "no"; then |
838 |
+ AC_DEFINE(HAVE_BOOST_REGEX, 1, |
839 |
+ [Define to 1 if the `Boost.Regex' library is available.]) |
840 |
+@@ -4927,7 +5094,10 @@ |
841 |
+ |
842 |
+ ## NCBI C Toolkit |
843 |
+ if test "$with_ncbi_c" != "no" ; then |
844 |
+- NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"} |
845 |
++ if test "${with_ncbi_c-yes}" != yes; then |
846 |
++ NCBI_C_PATH=$with_ncbi_c |
847 |
++ fi |
848 |
++ : ${NCBI_C_PATH="$NCBI"} |
849 |
+ if test "$ncbi_compiler" = ICC -a -d "$NCBI_C_PATH/ncbi_icc"; then |
850 |
+ NCBI_C_PATH=$NCBI_C_PATH/ncbi_icc |
851 |
+ fi |
852 |
+@@ -4949,7 +5119,8 @@ |
853 |
+ NCBI_C_ncbi="-lncbi" |
854 |
+ fi |
855 |
+ NCBI_C_LIBPATH="-L$NCBI_C_LIBPATH" |
856 |
+- AC_CACHE_CHECK([for the NCBI C toolkit in $NCBI_C_PATH], ncbi_cv_lib_ctools, |
857 |
++ AC_CACHE_CHECK([for the NCBI C toolkit${NCBI_C_PATH:+ in $NCBI_C_PATH}], |
858 |
++ ncbi_cv_lib_ctools, |
859 |
+ [CPPFLAGS="$NCBI_C_INCLUDE $orig_CPPFLAGS" |
860 |
+ LIBS="$NCBI_C_LIBPATH $NCBI_C_ncbi $NETWORK_LIBS $orig_LIBS" |
861 |
+ AC_LINK_IFELSE([AC_LANG_PROGRAM( |
862 |
+@@ -5000,11 +5171,7 @@ |
863 |
+ |
864 |
+ ## OpenGL |
865 |
+ if test "$with_opengl" != "no"; then |
866 |
+- if test "${with_opengl-yes}" = yes; then |
867 |
+- if test -d $NCBI/MesaGL; then |
868 |
+- : ${OPENGL_PATH=$NCBI/MesaGL} |
869 |
+- fi |
870 |
+- else |
871 |
++ if test "${with_opengl-yes}" != yes; then |
872 |
+ OPENGL_PATH=$with_opengl |
873 |
+ fi |
874 |
+ if test -d "$OPENGL_PATH"; then |
875 |
+@@ -5101,7 +5268,6 @@ |
876 |
+ else |
877 |
+ OSMESA_STATIC_LIBS=$OSMESA_LIBS |
878 |
+ fi |
879 |
+- : ${GLUT_PATH=$NCBI/glut} |
880 |
+ if test "$with_glut" != "no"; then |
881 |
+ if test "${with_glut-yes}" != "yes"; then |
882 |
+ GLUT_PATH=$with_glut |
883 |
+@@ -5121,7 +5287,6 @@ |
884 |
+ NCBI_MISSING_PACKAGE(glut) |
885 |
+ fi |
886 |
+ fi |
887 |
+- : ${GLEW_PATH=$NCBI/glew} |
888 |
+ if test "$with_glew" != "no"; then |
889 |
+ if test "${with_glew-yes}" != "yes"; then |
890 |
+ GLEW_PATH=$with_glew |
891 |
+@@ -5214,7 +5379,7 @@ |
892 |
+ : ${with_wxwidgets_ucs=no} |
893 |
+ if test "$with_wxwidgets" != "no" ; then |
894 |
+ case "$with_wxwidgets" in |
895 |
+- yes | "" ) : ${WXWIDGETS_PATH=$NCBI/wxwidgets} ;; |
896 |
++ yes | "" ) ;; |
897 |
+ * ) WXWIDGETS_PATH=$with_wxwidgets ;; |
898 |
+ esac |
899 |
+ if test -d "$WXWIDGETS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \ |
900 |
+@@ -5283,12 +5448,13 @@ |
901 |
+ libsed=$basesed |
902 |
+ ;; |
903 |
+ esac |
904 |
+- AC_CACHE_CHECK([for wxWidgets in $WXWIDGETS_ARCH_PATH], |
905 |
++ AC_CACHE_CHECK( |
906 |
++ [for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}], |
907 |
+ ncbi_cv_lib_wxwidgets, |
908 |
+ [if test -x "$wxconf" ; then |
909 |
+ WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`" |
910 |
+ NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, ["$wxconf" $wxcfflags --libs], |
911 |
+- [$libsed; ]) |
912 |
++ [$libsed; s/ -lm / /g;]) |
913 |
+ |
914 |
+ CPPFLAGS="$WXWIDGETS_INCLUDE $orig_CPPFLAGS" |
915 |
+ LIBS="$WXWIDGETS_LIBS $orig_LIBS" |
916 |
+@@ -5315,12 +5481,12 @@ |
917 |
+ else |
918 |
+ NCBI_PACKAGE(wxWidgets) |
919 |
+ case "`"$wxconf" $wxcfflags --version`" in |
920 |
+- 2.[[89]].* | 2.[[0-9]][[0-9]]* ) |
921 |
+- NCBI_PACKAGE(wx2.8) |
922 |
+- wxlibs=std,richtext,aui |
923 |
++ 1.* | 2.[[0-7]].*) |
924 |
++ wxlibs=std |
925 |
+ ;; |
926 |
+ *) |
927 |
+- wxlibs=std |
928 |
++ NCBI_PACKAGE(wx2.8) |
929 |
++ wxlibs=std,richtext,aui,propgrid |
930 |
+ ;; |
931 |
+ esac |
932 |
+ # The "yes" may have been cached; get the actual settings again if needed |
933 |
+@@ -5328,9 +5494,9 @@ |
934 |
+ WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`" |
935 |
+ fi |
936 |
+ NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, [$wxconf $wxcfflags --libs $wxlibs], |
937 |
+- [$libsed; ]) |
938 |
++ [$libsed; s/ -lm / /g;]) |
939 |
+ WXWIDGETS_STATIC_LIBS=`"$wxconf" $wxcfflags --libs --static $wxlibs \ |
940 |
+- 2>/dev/null | sed -e "$basesed"` |
941 |
++ 2>/dev/null | sed -e "$basesed; s/ -lm / /g;"` |
942 |
+ if test -n "$WXWIDGETS_STATIC_LIBS"; then |
943 |
+ # Allow direct use of underlying libraries with strict linkers |
944 |
+ WXWIDGETS_LIBS="$WXWIDGETS_LIBS `echo $WXWIDGETS_STATIC_LIBS | sed -e 's/.*\.a *//'`" |
945 |
+@@ -5350,7 +5516,7 @@ |
946 |
+ ## In-house Fast-CGI library |
947 |
+ if test "$with_fastcgi" != "no" ; then |
948 |
+ case "$with_fastcgi" in |
949 |
+- yes | "" ) : ${FASTCGI_PATH:="$NCBI/fcgi-current"} ;; |
950 |
++ yes | "" ) ;; |
951 |
+ */* ) FASTCGI_PATH=$with_fastcgi ;; |
952 |
+ * ) FASTCGI_PATH=$NCBI/fcgi-${with_fastcgi} ;; |
953 |
+ esac |
954 |
+@@ -5366,7 +5532,8 @@ |
955 |
+ NCBI_RPATHIFY(FASTCGI_LIBS, $FASTCGI_LIBDIR, [ -lfcgi $NETWORK_LIBS]) |
956 |
+ FASTCGI_OBJS="fcgibuf" |
957 |
+ LIBS="$FASTCGI_LIBS $orig_LIBS" |
958 |
+- AC_CACHE_CHECK([for FastCGI libraries in $FASTCGI_PATH], ncbi_cv_lib_fcgi, |
959 |
++ AC_CACHE_CHECK([for FastCGI libraries${FASTCGI_PATH:+ in $FASTCGI_PATH}], |
960 |
++ ncbi_cv_lib_fcgi, |
961 |
+ [CPPFLAGS="$FASTCGI_INCLUDE $orig_CPPFLAGS" |
962 |
+ AC_LINK_IFELSE([AC_LANG_PROGRAM( |
963 |
+ [[#include <fcgiapp.h>]], |
964 |
+@@ -5416,7 +5583,11 @@ |
965 |
+ else |
966 |
+ with_included_sss=no |
967 |
+ fi |
968 |
++ if test "${with_sss-yes}" = yes; then |
969 |
+ NCBI_SSS_PATH=${NCBI_SSS_PATH:="$NCBI/sss/BUILD"} |
970 |
++ else |
971 |
++ NCBI_SSS_PATH=$with_sss |
972 |
++ fi |
973 |
+ NCBI_SSS_INCLUDE=${NCBI_SSS_INCLUDE:="$NCBI_SSS_PATH/include"} |
974 |
+ if test -z "$NCBI_SSS_LIBPATH" ; then |
975 |
+ NCBI_SSS_LIBPATH="${NCBI_SSS_PATH}/lib/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}" |
976 |
+@@ -5424,7 +5595,8 @@ |
977 |
+ NCBI_SSS_LIBPATH="${NCBI_SSS_LIBPATH}mt" |
978 |
+ fi |
979 |
+ fi |
980 |
+- AC_MSG_CHECKING([for NCBI SSS directories in $NCBI_SSS_PATH]) |
981 |
++ AC_MSG_CHECKING( |
982 |
++ [for NCBI SSS directories${NCBI_SSS_PATH:+ in $NCBI_SSS_PATH}]) |
983 |
+ if test "$with_included_sss" = "yes"; then |
984 |
+ AC_MSG_RESULT([yes]) # duh |
985 |
+ elif test ! -d "${NCBI_SSS_LIBPATH}" -o ! -d "${NCBI_SSS_INCLUDE}" ; then |
986 |
+@@ -5510,7 +5682,6 @@ |
987 |
+ |
988 |
+ # SP |
989 |
+ if test "$with_sp" != "no" ; then |
990 |
+- SP_PATH=${SP_PATH:="$NCBI/SP"} |
991 |
+ if test -n "$SP_INCLUDE"; then |
992 |
+ SP_GENERIC="$SP_INCLUDE/../generic" |
993 |
+ else |
994 |
+@@ -5520,7 +5691,7 @@ |
995 |
+ if test -z "$SP_LIBPATH" ; then |
996 |
+ SP_LIBPATH="${SP_PATH}/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}" |
997 |
+ fi |
998 |
+- AC_MSG_CHECKING([for SP directories in $SP_PATH]) |
999 |
++ AC_MSG_CHECKING([for SP directories${SP_PATH:+ in $SP_PATH}]) |
1000 |
+ if test ! -d "${SP_LIBPATH}" -o ! -d "${SP_INCLUDE}" ; then |
1001 |
+ AC_MSG_RESULT([no]) |
1002 |
+ NCBI_MISSING_PACKAGE(sp) |
1003 |
+@@ -5558,19 +5729,13 @@ |
1004 |
+ |
1005 |
+ |
1006 |
+ ## ORBacus CORBA |
1007 |
+-if test "${with_orbacus:-yes}" = yes; then |
1008 |
+- if test -d $NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT; then |
1009 |
+- : ${ORBACUS_PATH=$NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT} |
1010 |
+- else |
1011 |
+- : ${ORBACUS_PATH=$NCBI/corba/OB-4.0.1} |
1012 |
+- fi |
1013 |
+-elif test "$with_orbacus" != no; then |
1014 |
++if test "$with_orbacus" != no; then |
1015 |
++ if test "$with_orbacus" != yes; then |
1016 |
+ ORBACUS_PATH=$with_orbacus |
1017 |
+ fi |
1018 |
+ if test -d "$ORBACUS_PATH"; then |
1019 |
+ NCBI_FIX_DIR(ORBACUS_PATH) |
1020 |
+ fi |
1021 |
+-if test "$with_orbacus" != no; then |
1022 |
+ fullpath=${ORBACUS_PATH}/${DEBUG_SFX}${mt_sfx}${bit64_sfx} |
1023 |
+ if test -f ${fullpath}/inc/OB/Config.h ; then |
1024 |
+ : ${ORBACUS_INCLUDE="-I$ORBACUS_PATH/include -I$fullpath/inc"} |
1025 |
+@@ -5594,7 +5759,8 @@ |
1026 |
+ LIBIMR= |
1027 |
+ ;; |
1028 |
+ esac |
1029 |
+- AC_CACHE_CHECK([for ORBacus in $ORBACUS_PATH], ncbi_cv_lib_orbacus, |
1030 |
++ AC_CACHE_CHECK([for ORBacus${ORBACUS_PATH:+ in $ORBACUS_PATH}], |
1031 |
++ ncbi_cv_lib_orbacus, |
1032 |
+ [CPPFLAGS="$ORBACUS_INCLUDE $orig_CPPFLAGS" |
1033 |
+ LIBS="$ORBACUS_LIBPATH $LIBOB $NETWORK_LIBS $DL_LIBS $orig_LIBS" |
1034 |
+ AC_LINK_IFELSE([AC_LANG_PROGRAM( |
1035 |
+@@ -5633,7 +5799,7 @@ |
1036 |
+ |
1037 |
+ if test "$with_icu" != "no" ; then |
1038 |
+ case "$with_icu" in |
1039 |
+- yes | "" ) : ${ICU_PATH=$NCBI/icu} ;; |
1040 |
++ yes | "" ) ;; |
1041 |
+ * ) ICU_PATH=$with_icu ;; |
1042 |
+ esac |
1043 |
+ if test -d "$ICU_PATH/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}${mt_sfx}/lib" \ |
1044 |
+@@ -5648,7 +5814,8 @@ |
1045 |
+ ICU_BINPATH=${ICU_BINPATH:="$ICU_ARCH_PATH/bin"} |
1046 |
+ ICU_LIBPATH=${ICU_LIBPATH:="$ICU_ARCH_PATH/lib"} |
1047 |
+ ICU_INCLUDE= |
1048 |
+- AC_CACHE_CHECK([for ICU in $ICU_ARCH_PATH], ncbi_cv_lib_icu, |
1049 |
++ AC_CACHE_CHECK([for ICU${ICU_ARCH_PATH:+ in $ICU_ARCH_PATH}], |
1050 |
++ ncbi_cv_lib_icu, |
1051 |
+ [ICU_CONFIG=`$ICU_BINPATH/icu-config --bindir 2>/dev/null`/icu-config |
1052 |
+ if test -x "$ICU_CONFIG" ; then |
1053 |
+ ICU_INCLUDE=`$ICU_CONFIG --cppflags-searchpath` |
1054 |
+@@ -5690,9 +5857,6 @@ |
1055 |
+ |
1056 |
+ |
1057 |
+ ### XML/XSL libraries |
1058 |
+-if test -d "$NCBI/expat/include"; then |
1059 |
+- : ${EXPAT_PATH=$NCBI/expat} |
1060 |
+-fi |
1061 |
+ NCBI_CHECK_THIRD_PARTY_LIB(expat, |
1062 |
+ AC_LANG_PROGRAM([#include <expat.h>], |
1063 |
+ [XML_Parser parser = XML_ParserCreate("utf-8");])) |
1064 |
+@@ -5701,7 +5865,6 @@ |
1065 |
+ else |
1066 |
+ EXPAT_STATIC_LIBS=${EXPAT_LIBS} |
1067 |
+ fi |
1068 |
+-: ${SABLOT_PATH=$NCBI/Sablot} |
1069 |
+ vpath="$SABLOT_PATH/${compiler_vpfx}build" |
1070 |
+ test -d "$vpath" && SABLOT_PATH=$vpath |
1071 |
+ if test -d "$SABLOT_PATH"; then |
1072 |
+@@ -5718,7 +5881,6 @@ |
1073 |
+ SABLOT_STATIC_LIBS=${SABLOT_LIBS} |
1074 |
+ fi |
1075 |
+ |
1076 |
+-: ${LIBXML_PATH=$NCBI/libxml} |
1077 |
+ # test -d "$LIBXML_PATH" || LIBXML_PATH=`xml2-config --prefix 2>/dev/null` |
1078 |
+ if test "$with_libxml" != "no"; then |
1079 |
+ case "$with_libxml" in |
1080 |
+@@ -5813,7 +5975,6 @@ |
1081 |
+ LIBEXSLT_STATIC_LIBS=${LIBEXSLT_LIBS} |
1082 |
+ fi |
1083 |
+ |
1084 |
+-: ${XERCES_PATH=$NCBI/xerces} |
1085 |
+ if test "$with_xerces" != no; then |
1086 |
+ if test "${with_xerces-yes}" != yes; then |
1087 |
+ XERCES_PATH=$with_xerces |
1088 |
+@@ -5838,7 +5999,7 @@ |
1089 |
+ NCBI_FIX_DIR(XERCES_LIBPATH) |
1090 |
+ fi |
1091 |
+ fi |
1092 |
+- if test -d $XERCES_PATH; then |
1093 |
++ if test -d "$XERCES_PATH"; then |
1094 |
+ in_path=" in $XERCES_PATH" |
1095 |
+ : ${XERCES_INCLUDE=-I$XERCES_PATH/include} |
1096 |
+ : ${XERCES_LIBPATH=$XERCES_PATH/lib} |
1097 |
+@@ -5875,7 +6036,6 @@ |
1098 |
+ XERCES_STATIC_LIBS= |
1099 |
+ fi |
1100 |
+ |
1101 |
+-: ${XALAN_PATH=$NCBI/xalan} |
1102 |
+ if test "$with_xalan" != no; then |
1103 |
+ if test "${with_xalan-yes}" != yes; then |
1104 |
+ XALAN_PATH=$with_xalan |
1105 |
+@@ -5900,7 +6060,7 @@ |
1106 |
+ NCBI_FIX_DIR(XALAN_LIBPATH) |
1107 |
+ fi |
1108 |
+ fi |
1109 |
+- if test -d $XALAN_PATH; then |
1110 |
++ if test -d "$XALAN_PATH"; then |
1111 |
+ in_path=" in $XALAN_PATH" |
1112 |
+ : ${XALAN_INCLUDE=-I$XALAN_PATH/include} |
1113 |
+ : ${XALAN_LIBPATH=$XALAN_PATH/lib} |
1114 |
+@@ -5937,7 +6097,6 @@ |
1115 |
+ |
1116 |
+ test -d SunWS_cache && rm -r SunWS_cache |
1117 |
+ |
1118 |
+-: ${ZORBA_PATH=$NCBI/zorba} |
1119 |
+ if test "$with_zorba" != no; then |
1120 |
+ if test "${with_zorba-yes}" != yes; then |
1121 |
+ ZORBA_PATH=$with_zorba |
1122 |
+@@ -5967,7 +6126,7 @@ |
1123 |
+ ZORBA_PATH=`$ZORBA_CONFIG --prefix` |
1124 |
+ : ${ZORBA_INCLUDE=`$ZORBA_CONFIG --cppflags`} |
1125 |
+ fi |
1126 |
+- if test -d $ZORBA_PATH; then |
1127 |
++ if test -d "$ZORBA_PATH"; then |
1128 |
+ in_path=" in $ZORBA_PATH" |
1129 |
+ : ${ZORBA_INCLUDE=-I$ZORBA_PATH/include} |
1130 |
+ : ${ZORBA_LIBPATH=$ZORBA_PATH/lib} |
1131 |
+@@ -6010,7 +6169,7 @@ |
1132 |
+ |
1133 |
+ ### SQLite |
1134 |
+ case "$with_sqlite3" in |
1135 |
+- yes | '' ) : ${SQLITE3_PATH=$NCBI/sqlite3} ;; |
1136 |
++ yes | '' ) ;; |
1137 |
+ * ) SQLITE3_PATH=$with_sqlite3 ;; |
1138 |
+ esac |
1139 |
+ |
1140 |
+@@ -6048,7 +6207,6 @@ |
1141 |
+ ### OEChem |
1142 |
+ # somewhat kludgish, as we now wanto to add in oeiupac and oedepict, |
1143 |
+ # which depend on oechem.... |
1144 |
+-: ${OECHEM_PATH=$NCBI/oechem} |
1145 |
+ NCBI_CHECK_THIRD_PARTY_LIB(oechem, |
1146 |
+ AC_LANG_PROGRAM([#include <oechem.h>], |
1147 |
+ [OEChem::OEMol mol; OEChem::OEConfBase* c = mol.GetActive();]), |
1148 |
+@@ -6091,7 +6249,7 @@ |
1149 |
+ |
1150 |
+ ### muParser |
1151 |
+ case "$with_muparser" in |
1152 |
+- yes | '' ) : ${MUPARSER_PATH=$NCBI/muParser} ;; |
1153 |
++ yes | '' ) ;; |
1154 |
+ * ) MUPARSER_PATH=$with_muparser ;; |
1155 |
+ esac |
1156 |
+ |
1157 |
+@@ -6111,7 +6269,7 @@ |
1158 |
+ |
1159 |
+ ### hdf5 |
1160 |
+ case "$with_hdf5" in |
1161 |
+- yes | '' ) : ${HDF5_PATH=$NCBI/hdf5} ;; |
1162 |
++ yes | '' ) ;; |
1163 |
+ * ) HDF5_PATH=$with_hdf5 ;; |
1164 |
+ esac |
1165 |
+ |
1166 |
+@@ -6176,7 +6334,7 @@ |
1167 |
+ GIF_LIBS=$UNGIF_LIBS |
1168 |
+ fi |
1169 |
+ |
1170 |
+-test -n "$x_libraries" && : ${XPM_PATH=`dirname "$x_libraries"`} |
1171 |
++case "$x_libraries" in */*) : ${XPM_PATH=`dirname "$x_libraries"`} ;; esac |
1172 |
+ NCBI_CHECK_THIRD_PARTY_LIB(Xpm, |
1173 |
+ AC_LANG_PROGRAM([#include <X11/xpm.h>], |
1174 |
+ [XpmImage image; XpmInfo info; |
1175 |
+@@ -6241,7 +6399,7 @@ |
1176 |
+ fi |
1177 |
+ |
1178 |
+ case "$with_ftgl" in |
1179 |
+- yes | '' ) : ${FTGL_PATH=$NCBI/ftgl} ;; |
1180 |
++ yes | '' ) ;; |
1181 |
+ * ) FTGL_PATH=$with_ftgl ;; |
1182 |
+ esac |
1183 |
+ |
1184 |
+@@ -6268,7 +6426,7 @@ |
1185 |
+ |
1186 |
+ # Mimetic |
1187 |
+ case "$with_mimetic" in |
1188 |
+- yes | '' ) : ${MIMETIC_PATH=$NCBI/mimetic} ;; |
1189 |
++ yes | '' ) ;; |
1190 |
+ * ) MIMETIC_PATH=$with_mimetic ;; |
1191 |
+ esac |
1192 |
+ if test -d "$MIMETIC_PATH"; then |
1193 |
+@@ -6293,6 +6451,88 @@ |
1194 |
+ [mimetic::MimeEntity me;])]) |
1195 |
+ |
1196 |
+ |
1197 |
++# gSOAP++ |
1198 |
++case "$with_gsoap" in |
1199 |
++ yes | '' ) ;; |
1200 |
++ * ) GSOAP_PATH=$with_gsoap ;; |
1201 |
++esac |
1202 |
++if test -d "$GSOAP_PATH"; then |
1203 |
++ NCBI_FIX_DIR(GSOAP_PATH) |
1204 |
++fi |
1205 |
++for d in "$GSOAP_LIBDIR" \ |
1206 |
++ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \ |
1207 |
++ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \ |
1208 |
++ "$GSOAP_PATH/lib${bit64_sfx}" \ |
1209 |
++ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}/lib" \ |
1210 |
++ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}/lib" \ |
1211 |
++ "$GSOAP_PATH/lib"; do |
1212 |
++ if test -d "$d"; then |
1213 |
++ GSOAP_LIBDIR=$d |
1214 |
++ NCBI_FIX_DIR(GSOAP_LIBDIR) |
1215 |
++ break |
1216 |
++ fi |
1217 |
++done |
1218 |
++NCBI_RPATHIFY(GSOAP_LIBPATH, $GSOAP_LIBDIR) |
1219 |
++ |
1220 |
++: ${GSOAP_BINDIR=`dirname "$GSOAP_LIBDIR"`/bin} |
1221 |
++AC_PATH_PROG(GSOAP_SOAPCPP2, soapcpp2, [], $GSOAP_BINDIR:$PATH) |
1222 |
++AC_PATH_PROG(GSOAP_WSDL2H, wsdl2h, [], $GSOAP_BINDIR:$PATH) |
1223 |
++ |
1224 |
++NCBI_CHECK_THIRD_PARTY_LIB_EX(gsoap, GSOAP, gsoapssl++, |
1225 |
++ [AC_LANG_PROGRAM([#include <stdsoap2.h> |
1226 |
++ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultcode(struct soap*) |
1227 |
++ { return NULL; } |
1228 |
++ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultsubcode(struct soap*) |
1229 |
++ { return NULL; } |
1230 |
++ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultstring(struct soap*) |
1231 |
++ { return NULL; } |
1232 |
++ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultdetail(struct soap*) |
1233 |
++ { return NULL; } |
1234 |
++ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultsubcode(struct soap*) |
1235 |
++ { return NULL; } |
1236 |
++ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultdetail(struct soap*) |
1237 |
++ { return NULL; } |
1238 |
++ SOAP_FMAC3 void SOAP_FMAC4 soap_serializeheader(struct soap*) { } |
1239 |
++ SOAP_FMAC3 int SOAP_FMAC4 soap_putheader(struct soap*) { return 0; } |
1240 |
++ SOAP_FMAC3 int SOAP_FMAC4 soap_getheader(struct soap*) { return 0; } |
1241 |
++ SOAP_FMAC3 void SOAP_FMAC4 soap_serializefault(struct soap*) { } |
1242 |
++ SOAP_FMAC3 int SOAP_FMAC4 soap_putfault(struct soap*) { return 0; } |
1243 |
++ SOAP_FMAC3 int SOAP_FMAC4 soap_getfault(struct soap*) { return 0; }], |
1244 |
++ [soap s;])], |
1245 |
++ $OPENSSL_LIBS $Z_LIBS) |
1246 |
++ |
1247 |
++case "$with_sqlite3" in |
1248 |
++ yes | '' ) ;; |
1249 |
++ * ) SQLITE3_PATH=$with_sqlite3 ;; |
1250 |
++esac |
1251 |
++ |
1252 |
++ |
1253 |
++# MongoDB |
1254 |
++if test -d "$MONGODB_PATH"; then |
1255 |
++ NCBI_FIX_DIR(MONGODB_PATH) |
1256 |
++fi |
1257 |
++if test -d $MONGODB_PATH/lib${bit64_sfx}; then |
1258 |
++ MONGODB_LIBDIR=$MONGODB_PATH/lib${bit64_sfx} |
1259 |
++else |
1260 |
++ MONGODB_LIBDIR=$MONGODB_PATH/lib |
1261 |
++fi |
1262 |
++# need Boost rpath |
1263 |
++NCBI_RPATHIFY(MONGODB_LIBPATH, $MONGODB_LIBDIR) |
1264 |
++NCBI_CHECK_THIRD_PARTY_LIB_EX(mongodb, MONGODB, mongoclient, |
1265 |
++ [AC_LANG_PROGRAM([#include <mongo/client/dbclient.h>], |
1266 |
++ [std::vector<mongo::HostAndPort> v; |
1267 |
++ mongo::DBClientReplicaSet client("foo", v); |
1268 |
++ client.connect();])], |
1269 |
++ [$BOOST_LIBPATH $boost_fs_lib $BOOST_THREAD_LIBS], [], |
1270 |
++ [$BOOST_INCLUDE]) |
1271 |
++# MongoDB's own library is normally static, but its supporting Boost |
1272 |
++# libraries might not be by default. |
1273 |
++if test -n "$MONGODB_LIBS"; then |
1274 |
++ MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongodb $BOOST_LIBPATH $boost_fs_static_lib $BOOST_THREAD_STATIC_LIBS" |
1275 |
++else |
1276 |
++ MONGODB_STATIC_LIBS= |
1277 |
++fi |
1278 |
++ |
1279 |
+ ### Restore original compiler/linker flags |
1280 |
+ LIBS="$orig_LIBS" |
1281 |
+ CPPFLAGS="$orig_CPPFLAGS" |
1282 |
+@@ -6499,16 +6739,6 @@ |
1283 |
+ fi |
1284 |
+ |
1285 |
+ |
1286 |
+-## Sequence Read Archive SDK, which may be attached on either the |
1287 |
+-## public or the internal side |
1288 |
+- |
1289 |
+-if test -f "${real_srcdir}/src/sra/sdk/Makefile.sra_macros.mk"; then |
1290 |
+- sra=sra |
1291 |
+-else |
1292 |
+- sra= |
1293 |
+-fi |
1294 |
+- |
1295 |
+- |
1296 |
+ ## `internal' project cluster |
1297 |
+ |
1298 |
+ if test "$with_internal" = "no" \ |
1299 |
+@@ -6781,6 +7011,7 @@ |
1300 |
+ AC_SUBST(C_LINK) |
1301 |
+ AC_SUBST(TAIL_N) |
1302 |
+ AC_SUBST(EGREP_Q) |
1303 |
++AC_SUBST(LDD_R) |
1304 |
+ |
1305 |
+ AC_SUBST(CFLAGS) |
1306 |
+ AC_SUBST(FAST_CFLAGS) |
1307 |
+@@ -6829,7 +7060,6 @@ |
1308 |
+ AC_SUBST(algo) |
1309 |
+ AC_SUBST(app) |
1310 |
+ AC_SUBST(internal) |
1311 |
+-AC_SUBST(sra) |
1312 |
+ |
1313 |
+ AC_SUBST(check) |
1314 |
+ AC_SUBST(CHECK_ARG) |
1315 |
+@@ -6865,6 +7095,7 @@ |
1316 |
+ |
1317 |
+ AC_SUBST(THREAD_LIBS) |
1318 |
+ AC_SUBST(NCBIATOMIC_LIB) |
1319 |
++AC_SUBST(OPENMP_FLAGS) |
1320 |
+ AC_SUBST(NETWORK_LIBS) |
1321 |
+ AC_SUBST(NETWORK_PURE_LIBS) |
1322 |
+ AC_SUBST(RESOLVER_LIBS) |
1323 |
+@@ -6902,6 +7133,8 @@ |
1324 |
+ AC_SUBST(BOOST_INCLUDE) |
1325 |
+ AC_SUBST(BOOST_LIBPATH) |
1326 |
+ AC_SUBST(BOOST_TAG) |
1327 |
++AC_SUBST(BOOST_FILESYSTEM_LIBS) |
1328 |
++AC_SUBST(BOOST_FILESYSTEM_STATIC_LIBS) |
1329 |
+ AC_SUBST(BOOST_REGEX_LIBS) |
1330 |
+ AC_SUBST(BOOST_REGEX_STATIC_LIBS) |
1331 |
+ AC_SUBST(BOOST_SYSTEM_LIBS) |
1332 |
+@@ -6968,6 +7201,8 @@ |
1333 |
+ AC_SUBST(SQLITE3_STATIC_LIBS) |
1334 |
+ AC_SUBST(FREETYPE_INCLUDE) |
1335 |
+ AC_SUBST(FREETYPE_LIBS) |
1336 |
++AC_SUBST(GSOAP_PATH) |
1337 |
++AC_SUBST(MONGODB_STATIC_LIBS) |
1338 |
+ AC_SUBST(ncbi_xreader_pubseqos) |
1339 |
+ AC_SUBST(ncbi_xreader_pubseqos2) |
1340 |
+ AC_SUBST(UNLESS_PUBSEQOS) |
1341 |
+@@ -7194,7 +7429,9 @@ |
1342 |
+ |
1343 |
+ cat << EOCONF |
1344 |
+ =============================================================================== |
1345 |
+-NCBI C++ Toolkit documentation: doc/index.html, doc/config.html#ref_Running |
1346 |
++NCBI C++ Toolkit documentation: |
1347 |
++ Online: http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ |
1348 |
++ Local: ./doc/public/index.html |
1349 |
+ For the available configuration flags run: ./configure --help |
1350 |
+ |
1351 |
+ CFLAGS = $CFLAGS |
1352 |
+--- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014-06-23 17:36:18.000000000 +0200 |
1353 |
++++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014-06-23 17:36:59.000000000 +0200 |
1354 |
+@@ -1,126 +1,45 @@ |
1355 |
+-# Hacked up in various ways, since Autoconf's version doesn't quite |
1356 |
+-# suit our (unusual) conventions. (Originally from status.m4) |
1357 |
+-m4_define([_AC_SRCPATHS], |
1358 |
+-[#ac_builddir=. # Useless! |
1359 |
+-ac_builddir=$builddir |
1360 |
+-dnl Base source directories on path to *input* file. |
1361 |
+-if test -n "$ac_file_in"; then |
1362 |
+- ac_dir_in=`AS_DIRNAME(["$ac_file_in"])` |
1363 |
++# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS) |
1364 |
++# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly. |
1365 |
++m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS]) |
1366 |
++m4_define([_AC_SRCDIRS], |
1367 |
++[# Base source directories on path to *input* file. |
1368 |
++if test -n "$ac_f"; then |
1369 |
++ ac_dir_in=`AS_DIRNAME(["$ac_f"])` |
1370 |
+ else |
1371 |
+ ac_dir_in=$1 |
1372 |
+ fi |
1373 |
+ |
1374 |
+-if test $ac_dir_in != .; then |
1375 |
+- ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'` |
1376 |
+- # A "../" for each directory in $ac_dir_suffix. |
1377 |
+- ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'` |
1378 |
+-else |
1379 |
+- ac_dir_suffix= ac_top_builddir= |
1380 |
+-fi |
1381 |
++NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"]) |
1382 |
+ |
1383 |
+-case $srcdir in |
1384 |
+- .) # No --srcdir option. We are building in place. |
1385 |
+- ac_srcdir=. |
1386 |
+- if test -z "$ac_top_builddir"; then |
1387 |
+- ac_top_srcdir=. |
1388 |
+- else |
1389 |
+- ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'` |
1390 |
+- fi ;; |
1391 |
+- [[\\/]]* | ?:[[\\/]]* ) # Absolute path. |
1392 |
+- ac_srcdir=$srcdir/$ac_dir_suffix; |
1393 |
+- ac_top_srcdir=$srcdir ;; |
1394 |
+- *) # Relative path. |
1395 |
+- ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix |
1396 |
+- ac_top_srcdir=$ac_top_builddir$srcdir ;; |
1397 |
+-esac |
1398 |
+-# Do not use `cd foo && pwd` to compute absolute paths, because |
1399 |
+-# the directories may not exist. |
1400 |
+-AS_SET_CATFILE([ac_abs_builddir], [$builddir], [$1]) |
1401 |
+-AS_SET_CATFILE([ac_abs_top_builddir], |
1402 |
+- [$ac_abs_builddir], [${ac_top_builddir}.]) |
1403 |
+ AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir]) |
1404 |
+-AS_SET_CATFILE([ac_abs_srcdir], [$ac_abs_top_srcdir], [$ac_dir_suffix]) |
1405 |
+-])# _AC_SRCPATHS |
1406 |
+- |
1407 |
++ac_builddir=$builddir |
1408 |
++]) |
1409 |
+ |
1410 |
+-# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a |
1411 |
+-# last resort due to issues with sourcing .bashrc. |
1412 |
+-m4_define([_AS_LINENO_PREPARE], |
1413 |
+-[_AS_LINENO_WORKS || { |
1414 |
+- # Find who we are. Look in the path if we contain no path at all |
1415 |
+- # relative or not. |
1416 |
+- case $[0] in |
1417 |
+- *[[\\/]]* ) as_myself=$[0] ;; |
1418 |
+- *) _AS_PATH_WALK([], |
1419 |
+- [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break]) |
1420 |
+- ;; |
1421 |
+- esac |
1422 |
+- # We did not find ourselves, most probably we were run as `sh COMMAND' |
1423 |
+- # in which case we are not to be found in the path. |
1424 |
+- if test "x$as_myself" = x; then |
1425 |
+- as_myself=$[0] |
1426 |
+- fi |
1427 |
+- if test ! -f "$as_myself"; then |
1428 |
+- AS_ERROR([cannot find myself; rerun with an absolute path]) |
1429 |
+- fi |
1430 |
+- case $CONFIG_SHELL in |
1431 |
+- '') |
1432 |
+- AS_UNSET(ZSH_VERSION) |
1433 |
+- for as_base in sh ksh sh5 bash; do |
1434 |
+- _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH], |
1435 |
+- [case $as_dir in |
1436 |
+- /*) |
1437 |
+- if ("$as_dir/$as_base" -c \ |
1438 |
+- 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null |
1439 |
+- then |
1440 |
+- AS_UNSET(BASH_ENV) |
1441 |
+- AS_UNSET(ENV) |
1442 |
+- CONFIG_SHELL=$as_dir/$as_base |
1443 |
+- export CONFIG_SHELL |
1444 |
+- exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"} |
1445 |
+- fi;; |
1446 |
+- esac |
1447 |
+- done]);; |
1448 |
+- esac |
1449 |
+ |
1450 |
+- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO |
1451 |
+- # uniformly replaced by the line number. The first 'sed' inserts a |
1452 |
+- # line-number line before each line; the second 'sed' does the real |
1453 |
+- # work. The second script uses 'N' to pair each line-number line |
1454 |
+- # with the numbered line, and appends trailing '-' during |
1455 |
+- # substitution so that $LINENO is not a special case at line end. |
1456 |
+- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the |
1457 |
+- # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) |
1458 |
+- sed '=' <$as_myself | |
1459 |
+- sed ' |
1460 |
+- N |
1461 |
+- s,$,-, |
1462 |
+- : loop |
1463 |
+- s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3, |
1464 |
+- t loop |
1465 |
+- s,-$,, |
1466 |
+- s,^[['$as_cr_digits']]*\n,, |
1467 |
+- ' >$as_me.lineno && |
1468 |
+- chmod +x $as_me.lineno || |
1469 |
+- AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell]) |
1470 |
+- |
1471 |
+- # Don't try to exec as it changes $[0], causing all sort of problems |
1472 |
+- # (the dirname of $[0] is not the place where we might find the |
1473 |
+- # original and so on. Autoconf is especially sensible to this). |
1474 |
+- . ./$as_me.lineno |
1475 |
+- # Exit status is that of the last command. |
1476 |
+- exit |
1477 |
+-} |
1478 |
+-])# _AS_LINENO_PREPARE |
1479 |
++# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both |
1480 |
++# historically part of _AS_LINENO_PREPARE) also need tweaking, to make |
1481 |
++# bash a last resort due to issues with sourcing .bashrc while entirely |
1482 |
++# avoiding zsh, which passes itself off as ksh on some systems but runs |
1483 |
++# parent shells' exit handlers from subshells, resulting in premature |
1484 |
++# cleanup of temporary files (notably confdefs.h). |
1485 |
++m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL]) |
1486 |
++m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN]) |
1487 |
++ |
1488 |
++m4_define([_AS_DETECT_BETTER_SHELL], |
1489 |
++ [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]), |
1490 |
++ [sh bash ksh sh5], [sh ksh sh5 bash])]) |
1491 |
++m4_define([_AS_RUN], |
1492 |
++[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl |
1493 |
++NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])]) |
1494 |
+ |
1495 |
+ |
1496 |
+ # One more hack: suppress PACKAGE_*, as we don't use them and some |
1497 |
+ # third-party libraries expose their corresponding settings, leading |
1498 |
+ # to preprocessor warnings. |
1499 |
+-m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED])) |
1500 |
++m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED]) |
1501 |
+ m4_define([AC_DEFINE_UNQUOTED], |
1502 |
+ [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [], |
1503 |
+- [NCBI_ORIG_ACDU($@)])]) |
1504 |
++ [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])]) |
1505 |
+ |
1506 |
+ |
1507 |
+ AC_DEFUN(NCBI_FIX_DIR, |
1508 |
+@@ -158,7 +77,7 @@ |
1509 |
+ AC_MSG_WARN([Proceeding without questions per --without-caution]) ;; |
1510 |
+ * ) |
1511 |
+ echo "$1 [[y/N]]" |
1512 |
+- read answer |
1513 |
++ read answer <& AS_ORIGINAL_STDIN_FD |
1514 |
+ case "$answer" in |
1515 |
+ [[Yy]]* ) AC_MSG_WARN([Proceeding at your own risk...]) ;; |
1516 |
+ * ) AC_MSG_ERROR([Configuration has been canceled by user.]) ;; |
1517 |
+--- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014-06-23 17:38:56.000000000 +0200 |
1518 |
++++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014-06-23 17:39:04.000000000 +0200 |
1519 |
+@@ -98,6 +98,9 @@ |
1520 |
+ /* Define to 1 if you have the `getaddrinfo' function. */ |
1521 |
+ #undef HAVE_GETADDRINFO |
1522 |
+ |
1523 |
++/* Define to 1 if you have the `getgrouplist' function. */ |
1524 |
++#undef HAVE_GETGROUPLIST |
1525 |
++ |
1526 |
+ /* If you have the `gethostbyaddr_r' function, define to the number of |
1527 |
+ arguments it takes (normally 7 or 8). */ |
1528 |
+ #undef HAVE_GETHOSTBYADDR_R |
1529 |
+@@ -176,9 +179,6 @@ |
1530 |
+ /* Define to 1 if you have `ios(_base)::register_callback'. */ |
1531 |
+ #undef HAVE_IOS_REGISTER_CALLBACK |
1532 |
+ |
1533 |
+-/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ |
1534 |
+-#undef HAVE_IS_SORTED |
1535 |
+- |
1536 |
+ /* Define to 1 if you have the `lchown' function. */ |
1537 |
+ #undef HAVE_LCHOWN |
1538 |
+ |
1539 |
+@@ -234,6 +234,9 @@ |
1540 |
+ /* Define to 1 if libgnutls is available. */ |
1541 |
+ #undef HAVE_LIBGNUTLS |
1542 |
+ |
1543 |
++/* Define to 1 if libgsoapssl++ is available. */ |
1544 |
++#undef HAVE_LIBGSOAP |
1545 |
++ |
1546 |
+ /* Define to 1 if libhdf5_cpp is available. */ |
1547 |
+ #undef HAVE_LIBHDF5 |
1548 |
+ |
1549 |
+@@ -260,6 +263,9 @@ |
1550 |
+ /* Define to 1 if libmimetic is available. */ |
1551 |
+ #undef HAVE_LIBMIMETIC |
1552 |
+ |
1553 |
++/* Define to 1 if libmongoclient is available. */ |
1554 |
++#undef HAVE_LIBMONGODB |
1555 |
++ |
1556 |
+ /* Define to 1 if libmuparser is available. */ |
1557 |
+ #undef HAVE_LIBMUPARSER |
1558 |
+ |
1559 |
+@@ -382,9 +388,6 @@ |
1560 |
+ /* Define to 1 if `min'/`max' templates are not implemented. */ |
1561 |
+ #undef HAVE_NO_MINMAX_TEMPLATE |
1562 |
+ |
1563 |
+-/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */ |
1564 |
+-#undef HAVE_NULLPTR |
1565 |
+- |
1566 |
+ /* Define to 1 if ODBC libraries are available. */ |
1567 |
+ #undef HAVE_ODBC |
1568 |
+ |
1569 |
+@@ -799,37 +802,37 @@ |
1570 |
+ by a signal. */ |
1571 |
+ #undef SELECT_UPDATES_TIMEOUT |
1572 |
+ |
1573 |
+-/* The size of a `char', as computed by sizeof. */ |
1574 |
++/* The size of `char', as computed by sizeof. */ |
1575 |
+ #undef SIZEOF_CHAR |
1576 |
+ |
1577 |
+-/* The size of a `double', as computed by sizeof. */ |
1578 |
++/* The size of `double', as computed by sizeof. */ |
1579 |
+ #undef SIZEOF_DOUBLE |
1580 |
+ |
1581 |
+-/* The size of a `float', as computed by sizeof. */ |
1582 |
++/* The size of `float', as computed by sizeof. */ |
1583 |
+ #undef SIZEOF_FLOAT |
1584 |
+ |
1585 |
+-/* The size of a `int', as computed by sizeof. */ |
1586 |
++/* The size of `int', as computed by sizeof. */ |
1587 |
+ #undef SIZEOF_INT |
1588 |
+ |
1589 |
+-/* The size of a `long', as computed by sizeof. */ |
1590 |
++/* The size of `long', as computed by sizeof. */ |
1591 |
+ #undef SIZEOF_LONG |
1592 |
+ |
1593 |
+-/* The size of a `long double', as computed by sizeof. */ |
1594 |
++/* The size of `long double', as computed by sizeof. */ |
1595 |
+ #undef SIZEOF_LONG_DOUBLE |
1596 |
+ |
1597 |
+-/* The size of a `long long', as computed by sizeof. */ |
1598 |
++/* The size of `long long', as computed by sizeof. */ |
1599 |
+ #undef SIZEOF_LONG_LONG |
1600 |
+ |
1601 |
+-/* The size of a `short', as computed by sizeof. */ |
1602 |
++/* The size of `short', as computed by sizeof. */ |
1603 |
+ #undef SIZEOF_SHORT |
1604 |
+ |
1605 |
+-/* The size of a `size_t', as computed by sizeof. */ |
1606 |
++/* The size of `size_t', as computed by sizeof. */ |
1607 |
+ #undef SIZEOF_SIZE_T |
1608 |
+ |
1609 |
+-/* The size of a `void*', as computed by sizeof. */ |
1610 |
++/* The size of `void*', as computed by sizeof. */ |
1611 |
+ #undef SIZEOF_VOIDP |
1612 |
+ |
1613 |
+-/* The size of a `__int64', as computed by sizeof. */ |
1614 |
++/* The size of `__int64', as computed by sizeof. */ |
1615 |
+ #undef SIZEOF___INT64 |
1616 |
+ |
1617 |
+ /* Define to 1 if the stack grows down. */ |
1618 |
+@@ -870,5 +873,5 @@ |
1619 |
+ /* Define to empty if `const' does not conform to ANSI C. */ |
1620 |
+ #undef const |
1621 |
+ |
1622 |
+-/* Define to `unsigned' if <sys/types.h> does not define. */ |
1623 |
++/* Define to `unsigned int' if <sys/types.h> does not define. */ |
1624 |
+ #undef size_t |
1625 |
+--- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014-06-23 17:40:40.000000000 +0200 |
1626 |
++++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014-06-23 17:40:57.000000000 +0200 |
1627 |
+@@ -1,4 +1,4 @@ |
1628 |
+-/* $Id: ncbiconf_xcode.h 361821 2012-05-04 14:28:13Z ucko $ |
1629 |
++/* $Id$ |
1630 |
+ * By Vlad Lebedev, NCBI (lebedev@××××××××××××.gov) |
1631 |
+ * |
1632 |
+ * Mac OS X - xCode Build |
1633 |
+@@ -258,9 +258,6 @@ |
1634 |
+ /* Define to 1 if you have `ios(_base)::register_callback'. */ |
1635 |
+ #define HAVE_IOS_REGISTER_CALLBACK 1 |
1636 |
+ |
1637 |
+-/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ |
1638 |
+-/* #undef HAVE_IS_SORTED */ |
1639 |
+- |
1640 |
+ /* Define to 1 if you have the `lchown' function. */ |
1641 |
+ /* #undef HAVE_LCHOWN */ |
1642 |
+ |
1643 |
+@@ -358,6 +355,9 @@ |
1644 |
+ /* Define to 1 if you have the `lutimes' function. */ |
1645 |
+ /* #undef HAVE_LUTIMES */ |
1646 |
+ |
1647 |
++/* Define to 1 if you have the `madvise' function. */ |
1648 |
++#define HAVE_MADVISE 1 |
1649 |
++ |
1650 |
+ /* Define to 1 if you have the <malloc.h> header file. */ |
1651 |
+ /* #undef HAVE_MALLOC_H */ |
1652 |
+ |
1653 |
+@@ -589,15 +589,15 @@ |
1654 |
+ /* Define to 1 if you have the <windows.h> header file. */ |
1655 |
+ /* #undef HAVE_WINDOWS_H */ |
1656 |
+ |
1657 |
++/* Define to 1 if you have the `writev' function. */ |
1658 |
++#define HAVE_WRITEV 1 |
1659 |
++ |
1660 |
+ /* Define to 1 if the system has the type `wstring'. */ |
1661 |
+ #define HAVE_WSTRING 1 |
1662 |
+ |
1663 |
+ /* Define to 1 if wxWidgets is available. */ |
1664 |
+ /* #undef HAVE_WXWIDGETS */ |
1665 |
+ |
1666 |
+-/* Define to 1 if nullptr keyword is available. */ |
1667 |
+-/* #undef HAVE_NULLPTR */ |
1668 |
+- |
1669 |
+ /* Define as const if the declaration of iconv() needs const. */ |
1670 |
+ #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */ |
1671 |
+ # define ICONV_CONST |
1672 |
+@@ -694,7 +694,7 @@ |
1673 |
+ /* Define to empty if `const' does not conform to ANSI C. */ |
1674 |
+ /* #undef const */ |
1675 |
+ |
1676 |
+-/* Define to `unsigned' if <sys/types.h> does not define. */ |
1677 |
++/* Define to `unsigned int' if <sys/types.h> does not define. */ |
1678 |
+ /* #undef size_t */ |
1679 |
+ |
1680 |
+ /* |
1681 |
|
1682 |
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild |
1683 |
index 3b19a93..64e8c23 100644 |
1684 |
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild |
1685 |
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild |
1686 |
@@ -26,12 +26,14 @@ IUSE=" |
1687 |
debug static-libs static threads pch |
1688 |
test wxwidgets odbc |
1689 |
berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif |
1690 |
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python |
1691 |
+ glut hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python |
1692 |
sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X" |
1693 |
+# removed IUSE=gnutls due to Gentoo bug #421777 |
1694 |
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
1695 |
KEYWORDS="" |
1696 |
|
1697 |
# sys-libs/db should be compiled with USE=cxx |
1698 |
+# dropped 'gnutls? ( net-libs/gnutls[lzo] )' from DEPEND due to Gentoo bug #421777 |
1699 |
DEPEND=" |
1700 |
berkdb? ( sys-libs/db:4.3[cxx] ) |
1701 |
ftds? ( dev-db/freetds ) |
1702 |
@@ -40,7 +42,6 @@ DEPEND=" |
1703 |
sqlite? ( dev-db/sqlite ) |
1704 |
sqlite3? ( dev-db/sqlite:3 ) |
1705 |
mysql? ( virtual/mysql ) |
1706 |
- gnutls? ( net-libs/gnutls[lzo] ) |
1707 |
ssl? ( dev-libs/openssl ) |
1708 |
fltk? ( x11-libs/fltk ) |
1709 |
opengl? ( virtual/opengl ) |
1710 |
@@ -112,6 +113,7 @@ src_prepare() { |
1711 |
"${FILESDIR}"/${P}-fix-creaders-linking.patch |
1712 |
"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch |
1713 |
"${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch |
1714 |
+ "${FILESDIR}"/${P}-support-autoconf-2.60.patch |
1715 |
) |
1716 |
epatch ${PATCHES[@]} |
1717 |
|
1718 |
@@ -120,8 +122,10 @@ src_prepare() { |
1719 |
cd src/build-system || die |
1720 |
# eautoreconf |
1721 |
eautoconf |
1722 |
+ # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support |
1723 |
} |
1724 |
|
1725 |
+# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site |
1726 |
src_configure() { |
1727 |
local myconf=() |
1728 |
#--without-optimization turn off optimization flags in non-debug mode |
1729 |
@@ -214,7 +218,7 @@ src_configure() { |
1730 |
$(use_with pch) |
1731 |
$(use_with lzo lzo "${EPREFIX}/usr") |
1732 |
$(use_with pcre pcre "${EPREFIX}/usr") |
1733 |
- $(use_with gnutls gnutls "${EPREFIX}/usr") |
1734 |
+# $(use_with gnutls gnutls "${EPREFIX}/usr") |
1735 |
$(use_with ssl openssl "${EPREFIX}/usr") |
1736 |
$(use_with ftds ftds "${EPREFIX}/usr") |
1737 |
$(use_with mysql mysql "${EPREFIX}/usr") |