Gentoo Archives: gentoo-commits

From: Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/
Date: Wed, 25 Jun 2014 23:27:22
Message-Id: 1403738699.88e4dd4274fab0bd7e7a26ad618d34de95489656.mmokrejs@gentoo
1 commit: 88e4dd4274fab0bd7e7a26ad618d34de95489656
2 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Wed Jun 25 23:24:59 2014 +0000
4 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5 CommitDate: Wed Jun 25 23:24:59 2014 +0000
6 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=88e4dd42
7
8 sci-biology/ncbi-tools++-12.0.0: dropped unneeded patch
9
10 ---
11 ...-tools++-12.0.0-support-autoconf-2.60.patch.bad | 1660 --------------------
12 1 file changed, 1660 deletions(-)
13
14 diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch.bad b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch.bad
15 deleted file mode 100644
16 index 80b23e9..0000000
17 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch.bad
18 +++ /dev/null
19 @@ -1,1660 +0,0 @@
20 ---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014-06-23 17:35:47.000000000 +0200
21 -+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014-06-23 17:36:41.000000000 +0200
22 -@@ -1,5 +1,5 @@
23 - #############################################################################
24 --# $Id: configure.ac 398256 2013-05-03 19:14:07Z rafanovi $
25 -+# $Id$
26 - # Derived from configure.in version 1.173.
27 - # ==========================================================================
28 - #
29 -@@ -38,7 +38,7 @@
30 - #
31 - #############################################################################
32 -
33 --AC_PREREQ(2.59)
34 -+AC_PREREQ(2.60)
35 -
36 - dnl Early setup, most crucially for locking. The diversion magic lets
37 - dnl this occur before AC_INIT, which already interferes with other
38 -@@ -71,7 +71,7 @@
39 - python, perl, jni, sqlite3, mimetic, sge, icu, sp, expat,
40 - sablot, libxml, libxslt, libexslt, xerces, xalan, zorba,
41 - oechem, muparser, hdf5, gif, jpeg, png, tiff, xpm,
42 -- magic, curl],
43 -+ magic, curl, gsoap, mongodb],
44 - [if test "${[with_]X-no}" != "no"; then
45 - AC_MSG_ERROR([incompatible options: --with-]X[ but --without-3psw])
46 - else
47 -@@ -143,6 +143,8 @@
48 - [ --with-bin-release build executables suitable for public release])
49 - AC_ARG_WITH(mt,
50 - [ --with-mt compile in a MultiThread-safe manner])
51 -+AC_ARG_WITH(openmp,
52 -+ [ --with-openmp enable OpenMP extensions for all projects])
53 - AC_ARG_WITH(64,
54 - [ --with-64 compile to 64-bit code])
55 - AC_ARG_WITH(universal,
56 -@@ -220,11 +222,15 @@
57 -
58 - ## NCBI packages
59 - AC_ARG_WITH(ncbi-c,
60 -+ [ --with-ncbi-c=DIR use NCBI C Toolkit installation in DIR])
61 -+AC_ARG_WITH(ncbi-c2,
62 - [ --without-ncbi-c do not use NCBI C Toolkit])
63 - AC_ARG_WITH(sss,
64 -+ [ --with-sss=DIR use NCBI SSS installation in DIR])
65 -+AC_ARG_WITH(sss2,
66 - [ --without-sss do not use NCBI SSS libraries])
67 - AC_ARG_WITH(sssutils,
68 -- [ --without-sssutils do not use NCBI SSS UTIL library])
69 -+ [ --without-utils do not use NCBI SSS UTIL library])
70 - AC_ARG_WITH(sssdb,
71 - [ --without-sssdb do not use NCBI SSS DB library])
72 - AC_ARG_WITH(included-sss,
73 -@@ -439,6 +445,14 @@
74 - [ --with-mimetic=DIR use libmimetic installation in DIR])
75 - AC_ARG_WITH(mimetic2,
76 - [ --without-mimetic do not use libmimetic])
77 -+AC_ARG_WITH(gsoap,
78 -+ [ --with-gsoap=DIR use gSOAP++ installation in DIR])
79 -+AC_ARG_WITH(gsoap2,
80 -+ [ --without-gsoap do not use gSOAP++])
81 -+AC_ARG_WITH(mongodb,
82 -+ [ --with-mongodb=DIR use MongoDB installation in DIR])
83 -+AC_ARG_WITH(mongodb2,
84 -+ [ --without-mongodb do not use MongoDB])
85 - AC_ARG_WITH(3psw,
86 - [ --with-3psw=std:netopt favor standard (system) builds of the above pkgs.])
87 - AC_ARG_WITH(3psw2,
88 -@@ -479,24 +493,28 @@
89 - [***** See also HTML documentation in ./doc/index.html *****])
90 -
91 -
92 -+AC_DIVERT_PUSH(PARSE_ARGS)
93 -+dnl As of Autoconf 2.60, this needs to run too early for config.log,
94 -+dnl to which AC_MSG_ERROR normally copies its output, to be available.
95 -+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD])
96 - #### Check the passed arguments against the list of available ones
97 - x_with_list="\
98 - debug max-debug symbols optimization profiling tcheck dll static static-exe \
99 - plugin-auto-load bundles bin-release mt 64 universal exe runpath hard-runpath \
100 --lfs limited-linker \
101 -+lfs limited-linker openmp \
102 - autodep suffix hostspec version execopy bincopy lib-rebuilds lib-rebuilds=ask \
103 - deactivation makefile-auto-update projects flat-makefile configure-dialog \
104 - check ncbi-public strip pch caution ccache distcc \
105 - ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \
106 - geo included-geo \
107 - z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \
108 --ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \
109 -+ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \
110 - bdb python perl jni sqlite3 icu boost boost-tag \
111 - sp expat sablot libxml libxslt libexslt xerces xalan zorba \
112 - oechem sge muparser hdf5 \
113 --gif jpeg tiff png xpm magic curl mimetic 3psw \
114 -+gif jpeg tiff png xpm magic curl mimetic gsoap mongodb 3psw \
115 - local-lbsm ncbi-crypt connext \
116 --serial objects dbapi app ctools gui algo internal gbench x"
117 -+serial objects dbapi app ctools gui algo internal gbench"
118 -
119 - changequote(, )dnl
120 - x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'`
121 -@@ -522,7 +540,6 @@
122 - case "$x_arg" in
123 - --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \
124 - | --cache-file= | --build= | --host= | --target= | --with-runpath= \
125 -- | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \
126 - | --with-relative-runpath= | --x-includes= | --x-libraries= )
127 - AC_MSG_ERROR([$x_arg: requires value; use --help to show usage])
128 - ;;
129 -@@ -533,12 +550,11 @@
130 - | --with-universal=* | --with-tcheck=* \
131 - | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
132 - | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
133 -- | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \
134 - | [[A-Z]*=*] \
135 - | --with-z=* | --with-bz2=* | --with-lzo=* \
136 -- | --with-pcre=* \
137 -+ | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \
138 - | --with-gcrypt=* | --with-gnutls=* | --with-openssl=* \
139 -- | --with-krb5=* | --with-curl=* \
140 -+ | --with-krb5=* | --with-curl=* | --with-gsoap=* | --with-mongodb=* \
141 - | --with-sybase-local=* | --with-wxwidgets=* | --with-mimetic=* \
142 - | --with-ftds=* | --with-mysql=* | --with-fastcgi=* \
143 - | --with-sqlite3=* | --with-expat=* | --with-sablot=* \
144 -@@ -552,7 +568,7 @@
145 - | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
146 - | --x-includes=* | --x-libraries=* | --with-3psw=* \
147 - | --target=* | --with-runpath=* | --with-relative-runpath=* \
148 -- | --no-create | --no-recursion)
149 -+ | --help | --no-create | --no-recursion)
150 - ;;
151 -
152 - * )
153 -@@ -560,6 +576,8 @@
154 - ;;
155 - esac
156 - done
157 -+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD])
158 -+AC_DIVERT_POP
159 -
160 -
161 - if test "$with_gbench" = "yes" ; then
162 -@@ -604,6 +622,13 @@
163 - : ${with_optimization=no}
164 - fi
165 -
166 -+if test "$with_openmp" = yes; then
167 -+ if test "$with_mt" = no; then
168 -+ AC_MSG_ERROR([incompatible options: --without-mt but --with-openmp])
169 -+ fi
170 -+ : ${with_mt=yes}
171 -+fi
172 -+
173 - #### Check for special options
174 - if test "$with_extra_action" = "yes" ; then
175 - AC_MSG_ERROR([--with-extra-action must have a value after =])
176 -@@ -649,15 +674,10 @@
177 - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
178 - esac
179 - fi
180 --if test -n "$with_projects"; then
181 -- case "$with_projects" in
182 -- /* ) abs_projects=$with_projects ;;
183 -- yes) abs_projects=$srcdir/projects ;;
184 -- * ) abs_projects=$srcdir/$with_projects ;;
185 -- esac
186 -- test -r "$abs_projects" || \
187 -- AC_MSG_ERROR([unable to read requested projects file "$abs_projects".])
188 --fi
189 -+# Generally save any originally specified flags.
190 -+USER_CFLAGS=$CFLAGS
191 -+USER_CXXFLAGS=$CXXFLAGS
192 -+USER_LDFLAGS=$LDFLAGS
193 -
194 - #### Always define this
195 - AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.])
196 -@@ -675,6 +695,23 @@
197 - #### Make some provisions for traditional operation
198 - AC_PROG_INSTALL
199 -
200 -+#### Point ICC at a suitable GCC version ASAP.
201 -+case "/$CXX" in
202 -+ */icpc )
203 -+ if test -d /usr/local/gcc; then
204 -+ case "`$CXX -dumpversion`:$host_cpu" in
205 -+ *:i?86) v=4.4.5 ;;
206 -+ ?.* | 1[[01]].* ) v=4.0.1 ;;
207 -+ *) v=4.4.2 ;;
208 -+ esac
209 -+ gcc=/usr/local/gcc/$v/bin/gcc
210 -+ if test -x $gcc; then
211 -+ CC="$CC -gcc-name=$gcc"
212 -+ CXX="$CXX -gcc-name=$gcc"
213 -+ fi
214 -+ fi
215 -+ ;;
216 -+esac
217 -
218 - #### C and C++ compilers
219 - AC_LANG(C++)
220 -@@ -987,6 +1024,30 @@
221 - ;;
222 - * ) NCBIATOMIC_LIB=xncbi ;;
223 - esac
224 -+ case "$compiler" in
225 -+ GCC )
226 -+ if $CC -v | grep clang >/dev/null; then
227 -+ :
228 -+ # Will allegedly support -openmp at some point, but as of 3.4,
229 -+ # just parses it as specifying an output filename: -o penmp.
230 -+ else
231 -+ case "$compiler_version" in
232 -+ [[123]]?? | 4[[01]]? ) ;;
233 -+ * ) : ${OPENMP_FLAGS=-fopenmp} ;;
234 -+ esac
235 -+ fi
236 -+ ;;
237 -+ ICC )
238 -+ : ${OPENMP_FLAGS=-openmp}
239 -+ ;;
240 -+ WorkShop* )
241 -+ : ${OPENMP_FLAGS=-xopenmp=parallel}
242 -+ ;;
243 -+ esac
244 -+ if test "$with_openmp" = yes; then
245 -+ MT_FLAG="$MT_FLAG $OPENMP_FLAGS"
246 -+ OPENMP_FLAGS=
247 -+ fi
248 - mt_sfx="MT"
249 - NCBI_FEATURE(MT)
250 - else
251 -@@ -994,6 +1055,7 @@
252 - MT_FLAG=
253 - THREAD_LIBS=
254 - NCBIATOMIC_LIB=
255 -+ OPENMP_FLAGS=
256 - mt_sfx=""
257 - fi
258 - MT_SFX="${mt_sfx}"
259 -@@ -1006,6 +1068,9 @@
260 - APP_LDFLAGS=
261 - DLL_LDFLAGS=
262 -
263 -+### Should go before any test compiler runs
264 -+AC_GNU_SOURCE
265 -+
266 - case "$host_os:$compiler" in
267 - darwin*:GCC )
268 - AC_CACHE_CHECK([whether $CC supports -Wl,-rpath],
269 -@@ -1047,6 +1112,47 @@
270 - ;;
271 - esac
272 -
273 -+case "$compiler:$compiler_version" in
274 -+ GCC:4[[0-6]]? | ICC:1[[01]]?? )
275 -+ ncbi_cv_prog_cxx_11=no
276 -+ ncbi_cv_prog_c_99=no
277 -+ ;;
278 -+ ICC:* )
279 -+ ncbi_cv_prog_c_99='-std=gnu99 -fgnu89-inline'
280 -+ ;;
281 -+esac
282 -+
283 -+AC_CACHE_CHECK([how to enable C++ '11 features in $CXX],
284 -+ ncbi_cv_prog_cxx_11,
285 -+ [orig_CXX=$CXX
286 -+ ncbi_cv_prog_cxx_11=no
287 -+ for x in -std=gnu++11 -std=gnu++0x; do
288 -+ CXX="$orig_CXX $x"
289 -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
290 -+ [ncbi_cv_prog_cxx_11=$x])
291 -+ test "x$ncbi_cv_prog_cxx_11" = "xno" || break
292 -+ done
293 -+ CXX=$orig_CXX])
294 -+test "$ncbi_cv_prog_cxx_11" = no || CXX="$CXX $ncbi_cv_prog_cxx_11"
295 -+
296 -+AC_LANG_PUSH(C)
297 -+AC_CACHE_CHECK([how to enable C '11 or at least '99 features in $CC],
298 -+ ncbi_cv_prog_c_99,
299 -+ [orig_CC=$CC
300 -+ ncbi_cv_prog_c_99=no
301 -+ for x in -xc99=all "-std=gnu11 -fgnu89-inline" \
302 -+ "-std=gnu1x -fgnu89-inline" \
303 -+ "-std=gnu99 -fgnu89-inline" \
304 -+ "-std=gnu9x -fgnu89-inline"; do
305 -+ CC="$orig_CC $x"
306 -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([], [])],
307 -+ [ncbi_cv_prog_c_99=$x])
308 -+ test "x$ncbi_cv_prog_c_99" = "xno" || break
309 -+ done
310 -+ CC=$orig_CC])
311 -+AC_LANG_POP(C)
312 -+test "$ncbi_cv_prog_c_99" = no || CC="$CC $ncbi_cv_prog_c_99"
313 -+
314 - #### Provide default environment setup for known platforms/compilers
315 - DEPFLAGS="-M"
316 - DEPFLAGS_POST="" # Needed for VisualAge
317 -@@ -1059,7 +1165,15 @@
318 - ;;
319 -
320 - solaris*:GCC )
321 -- CPPFLAGS="-D_XOPEN_SOURCE=500 $CPPFLAGS"
322 -+ # On Solaris, GCC defaults to setting _XOPEN_SOURCE (to 500) only
323 -+ # in C++ mode. Set it for C code as well to ensure consistent
324 -+ # header behavior, taking care to match the C standard version
325 -+ # (as enforced by <sys/feature_tests.h>).
326 -+ case "$ncbi_cv_prog_c_99" in
327 -+ no) CC="$CC -D_XOPEN_SOURCE=500" ;;
328 -+ *) CC="$CC -D_XOPEN_SOURCE=600" ;;
329 -+ esac
330 -+
331 - STRIP="@:"
332 - ;;
333 -
334 -@@ -1202,11 +1316,19 @@
335 - LDFLAGS="-flat_namespace $LDFLAGS"
336 -
337 - if test "$with_ncbi_public" = yes; then
338 -+ sdks='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk'
339 -+ case "$host_os" in
340 -+ darwin?.* | darwin10.* ) # Mac OS X 10.6.x or older
341 - TARGET='-mmacosx-version-min=10.5'
342 -- sdks='/Developer/SDKs/MacOSX10.6.sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.6.sdk'
343 -+ sdks="/Developer/SDKs/MacOSX10.6.sdk"
344 - if test "$with_64:${with_universal-no}" != "yes:no"; then
345 - sdks="/Developer/SDKs/MacOSX10.5.sdk $sdks"
346 - fi
347 -+ ;;
348 -+ * )
349 -+ TARGET='-mmacosx-version-min=10.7'
350 -+ ;;
351 -+ esac
352 - for sdk in $sdks; do
353 - if test -d "$sdk"; then
354 - TARGET="-isysroot $sdk $TARGET"
355 -@@ -1487,8 +1609,8 @@
356 - ;;
357 - GCC:* )
358 - DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing"
359 -- case "$host_os" in
360 -- freebsd* ) ;;
361 -+ case "$host_os:$host_cpu:$compiler_version" in
362 -+ freebsd* | solaris*:*86*:* | *:4[[5-9]]? | *:[[5-9]]?? ) ;;
363 - * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;
364 - esac
365 - if test "$with_profiling" != "yes"; then
366 -@@ -1587,13 +1709,9 @@
367 - solaris* )
368 - CONF_f_runpath="-R"
369 - ;;
370 -- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
371 -+ linux*:[[GI]]CC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
372 - CONF_f_runpath="-Wl,-rpath,"
373 - ;;
374 -- linux*:ICC )
375 -- # trying to use "-Wl,-rpath," here sends "ld" to endless 100% CPU loop
376 -- CONF_f_runpath="-Xlinker -rpath -Xlinker "
377 -- ;;
378 - irix*:* | linux*:KCC | *:Compaq )
379 - CONF_f_runpath="-rpath "
380 - ;;
381 -@@ -1697,8 +1815,11 @@
382 - LINK="$LINK -Kc++"
383 - ;;
384 - ICC:1???:* )
385 -- APP_LDFLAGS="-static-intel $APP_LDFLAGS"
386 -- DLL_LDFLAGS="-static-intel -nodefaultlibs $DLL_LDFLAGS"
387 -+ # Suppress "warning #10237: -lcilkrts linked in dynamically, static
388 -+ # library not available" which is not a problem in practice due to
389 -+ # as-needed linkage.
390 -+ APP_LDFLAGS="-static-intel -diag-disable 10237 $APP_LDFLAGS"
391 -+ DLL_LDFLAGS="-static-intel -diag-disable 10237 -nodefaultlibs $DLL_LDFLAGS"
392 - # Redundant for apps, but necessary for plugins to be adequately
393 - # self-contained, at least on 32-bit Linux.
394 - LIBS="$LIBS -lstdc++"
395 -@@ -1817,18 +1938,6 @@
396 -
397 - #### Intel compiler:: common flags and definitions
398 - if test "$compiler" = "ICC" ; then
399 -- if test -d /usr/local/gcc; then
400 -- case "$compiler_version:$HOST_CPU" in
401 -- *:i?86) v=4.4.5 ;;
402 -- ???:* | 1[[01]]??:* ) v=4.0.1 ;;
403 -- *) v=4.4.2 ;;
404 -- esac
405 -- gcc=/usr/local/gcc/$v/bin/gcc
406 -- if test -x $gcc; then
407 -- CC="$CC -gcc-name=$gcc"
408 -- CXX="$CXX -gcc-name=$gcc"
409 -- fi
410 -- fi
411 - if test -n "$icc_license" ; then
412 - icc_CC="$CC"
413 - icc_CXX="$CXX"
414 -@@ -2073,6 +2182,7 @@
415 - fi
416 -
417 - AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
418 -+dnl AC_PATH_PROG(GREP, grep)
419 - AC_PROG_EGREP
420 - AC_MSG_CHECKING([how to run $EGREP quietly])
421 - if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
422 -@@ -2086,6 +2196,16 @@
423 -
424 - AC_CHECK_PROG(VALGRIND_PATH, valgrind, valgrind)
425 -
426 -+AC_PATH_PROG(LDD, ldd)
427 -+if test -n "$LDD"; then
428 -+ AC_MSG_CHECKING([whether $LDD accepts -r])
429 -+ if $LDD -r /bin/ls >/dev/null 2>&1; then
430 -+ AC_MSG_RESULT(yes)
431 -+ LDD_R="$LDD -r"
432 -+ else
433 -+ AC_MSG_RESULT(no)
434 -+ fi
435 -+fi
436 -
437 - #### Check if "${build_root}" is defined; provide a default one
438 - if test -n "${with_build_root}" ; then
439 -@@ -2170,9 +2290,6 @@
440 - fi
441 -
442 -
443 --### Should go before any test compiler runs
444 --AC_GNU_SOURCE
445 --
446 - #### Determine whether this is implicitly a 64-bit platform
447 - AC_TYPE_SIZE_T
448 - if test "${with_universal-no}" = "no"; then
449 -@@ -2342,7 +2459,7 @@
450 - fi
451 - ;;
452 - *:ICC )
453 -- runpath="$runpath -Xlinker -rpath-link -Xlinker \$(libdir)"
454 -+ runpath="$runpath -Wl,-rpath-link,\$(libdir)"
455 - ;;
456 - esac
457 - elif test "$with_runpath" = "yes" -o "$with_dll" != "no" ; then
458 -@@ -2658,15 +2775,30 @@
459 - dbgrx1="$wsrx-g[^cx$wschars]*$wsrx"
460 - dbgrx2="$wsrx-gx*coff[0-9+]*$wsrx"
461 - optrx="$wsrx-x*O[0-9s]*$wsrx"
462 -+ NDEB_CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
463 -+ NDEB_CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
464 -+ NDEB_LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
465 - if test "$with_symbols" = "no" ; then
466 -- CFLAGS=` echo " $CFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
467 -- CXXFLAGS=`echo " $CXXFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
468 -- LDFLAGS=` echo " $LDFLAGS " | sed "s/$dbgrx1/ /g; s/$dbgrx2/ /g"`
469 -+ CFLAGS=$NDEB_CFLAGS
470 -+ CXXFLAGS=$NDEB_CXXFLAGS
471 -+ LDFLAGS=$NDEB_LDFLAGS
472 - else
473 - echo " $CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || CFLAGS="$CFLAGS -g"
474 - echo " $CXXFLAGS "| $EGREP_Q "$dbgrx1|$dbgrx2" || CXXFLAGS="$CXXFLAGS -g"
475 - echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g"
476 - STRIP="@:"
477 -+ case "$compiler:$compiler_version" in
478 -+ GCC:4[89]? | GCC:[5-9]? | GCC:???? )
479 -+ # GCC 4.8 defaults to DWARF 4, which Totalview for one
480 -+ # can't handle; roll back to version 3 by default.
481 -+ echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
482 -+ CFLAGS="$NDEB_CFLAGS -gdwarf-3"
483 -+ echo " $USER_CXXFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
484 -+ CXXFLAGS="$NDEB_CXXFLAGS -gdwarf-3"
485 -+ echo " $USER_LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
486 -+ LDFLAGS="$NDEB_LDFLAGS -gdwarf-3"
487 -+ ;;
488 -+ esac
489 - fi
490 -
491 - NOPT_CFLAGS=` echo " $CFLAGS " | sed "s/$optrx/ /g"`
492 -@@ -3024,9 +3156,9 @@
493 - ### Check for other standard library functions
494 -
495 - AC_FUNC_VPRINTF
496 --AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getpagesize \
497 -- getpass getpassphrase getpwuid getrusage gettimeofday \
498 -- getuid memrchr readpassphrase readv usleep \
499 -+AC_CHECK_FUNCS(euidaccess atoll basename lchown fseeko getgrouplist \
500 -+ getpagesize getpass getpassphrase getpwuid getrusage \
501 -+ gettimeofday getuid memrchr readpassphrase readv usleep \
502 - asprintf vasprintf vsnprintf select statfs statvfs \
503 - strcasecmp strlcat strlcpy strdup strndup strtok_r \
504 - sysmp timegm utimes lutimes writev)
505 -@@ -3253,17 +3385,6 @@
506 - fi
507 -
508 -
509 --AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted,
510 -- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
511 -- [[#include <algorithm>]],
512 -- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])],
513 -- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])])
514 --if test "$ncbi_cv_func_is_sorted" = yes; then
515 -- AC_DEFINE(HAVE_IS_SORTED, 1,
516 -- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.])
517 --fi
518 --
519 --
520 -
521 - AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores,
522 - AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h>
523 -@@ -3400,7 +3521,7 @@
524 - AC_CACHE_CHECK([whether the C compiler supports C99 restrict],
525 - ncbi_cv_c_restrict,
526 - [ncbi_cv_c_restrict=no
527 -- for restrict in restrict __restrict__ __restrict; do
528 -+ for restrict in __restrict__ __restrict restrict; do
529 - test "$ncbi_cv_c_restrict" = "no" || break
530 - AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
531 - [ncbi_cv_c_restrict=$restrict], [])
532 -@@ -3420,7 +3541,7 @@
533 - AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict],
534 - ncbi_cv_cxx_restrict,
535 - [ncbi_cv_cxx_restrict=no
536 -- for restrict in restrict __restrict__ __restrict; do
537 -+ for restrict in __restrict__ __restrict restrict; do
538 - test "$ncbi_cv_cxx_restrict" = "no" || break
539 - AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])],
540 - [ncbi_cv_cxx_restrict=$restrict], [])
541 -@@ -3525,14 +3646,6 @@
542 - unaligned addresses.])
543 - fi
544 -
545 --AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr,
546 -- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])],
547 -- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])])
548 --if test "$ncbi_cv_cxx_nullptr" = yes; then
549 -- AC_DEFINE(HAVE_NULLPTR, 1,
550 -- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.])
551 --fi
552 --
553 - ### Check for the availability of other packages
554 - ### --------------------------------------------
555 -
556 -@@ -3630,7 +3743,16 @@
557 - dnl NCBI_CHECK_LIBS(FUSE, fuse, fuse_loop)
558 - AC_SEARCH_LIBS(fuse_loop, fuse, [NCBI_PACKAGE(FUSE)])
559 - LIBS=$orig_LIBS
560 -+# Temporarily drop OpenMP flags for this test, as some toolchains count
561 -+# its support library's indirect use of librt when building applications
562 -+# but not when building shared libraries with --no-undefined.
563 -+orig_CXXFLAGS=$CXXFLAGS
564 -+orig_LDFLAGS=$LDFLAGS
565 -+CXXFLAGS=`echo $CXXFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
566 -+LDFLAGS=`echo $LDFLAGS | sed -e 's/[[^ ]]*openmp[[^ ]]*//g'`
567 - NCBI_CHECK_LIBS(RT, rt posix4, clock_gettime)
568 -+CXXFLAGS=$orig_CXXFLAGS
569 -+LDFLAGS=$orig_LDFLAGS
570 - NCBI_CHECK_LIBS(DEMANGLE, demangle, cplus_demangle)
571 - # Add to (orig_)LIBS if present for the sake of corelib and the
572 - # following call to AC_CHECK_FUNCS.
573 -@@ -3734,7 +3856,6 @@
574 - NCBI_PACKAGE(LocalBZ2)
575 - fi
576 -
577 --: ${LZO_PATH=$NCBI/lzo2}
578 - if test -d "$LZO_PATH"; then
579 - NCBI_FIX_DIR(LZO_PATH)
580 - fi
581 -@@ -3767,7 +3888,7 @@
582 - ## SSL/TLS libraries
583 - case "$with_gcrypt" in
584 - no ) ac_cv_path_LIBGCRYPT_CONFIG=no ;;
585 -- yes | '' ) : ${GCRYPT_PATH=$NCBI/gcrypt} ;;
586 -+ yes | '' ) ;;
587 - * ) GCRYPT_PATH=$with_gcrypt ;;
588 - esac
589 - if test -d "$GCRYPT_PATH"; then
590 -@@ -3802,13 +3923,16 @@
591 -
592 - case "$with_gnutls" in
593 - no ) ac_cv_path_LIBGNUTLS_CONFIG=no ;;
594 -- yes | '' ) : ${GNUTLS_PATH=$NCBI/gnutls} ;;
595 -+ yes | '' ) ;;
596 - * ) GNUTLS_PATH=$with_gnutls ;;
597 - esac
598 - if test -d "$GNUTLS_PATH"; then
599 - NCBI_FIX_DIR(GNUTLS_PATH)
600 -+ gnutls_config_path=${GNUTLS_BIN-$GNUTLS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/bin}:$GNUTLS_PATH/bin${bit64_sfx}:$GNUTLS_PATH/bin
601 -+else
602 -+ gnutls_config_path=$PATH
603 - fi
604 --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])
605 -+AC_PATH_PROG(LIBGNUTLS_CONFIG, libgnutls-config, [], [$gnutls_config_path])
606 -
607 - if test "x$with_gnutls" != xno; then
608 - if test -x "$LIBGNUTLS_CONFIG"; then
609 -@@ -3817,7 +3941,7 @@
610 - test "x$p" = "x/usr" || GNUTLS_PATH=$p
611 - fi
612 - else
613 -- LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls"
614 -+ LIBGNUTLS_CONFIG="eval PKG_CONFIG_PATH=\"$GNUTLS_PATH/lib/pkgconfig\" pkg-config gnutls --static"
615 - $LIBGNUTLS_CONFIG --exists >/dev/null 2>&1 || LIBGNUTLS_CONFIG=no
616 - fi
617 - case "$LIBGNUTLS_CONFIG" in
618 -@@ -3846,6 +3970,10 @@
619 - $GNUTLS_CONFIG_LIBS $GCRYPT_LIBS)
620 - if test "x$with_gnutls" != xno -a -n "$GNUTLS_CONFIG_LIBS"; then
621 - NCBI_RPATHIFY_OUTPUT(GNUTLS_LIBS, [echo $GNUTLS_CONFIG_LIBS], [$no_usr_lib])
622 -+ # Conservatively build against gcrypt if available even when gnutls
623 -+ # uses nettle instead, because gcrypt needs explicit initialization
624 -+ # to be thread-safe, but gnutls's headers don't indicate which
625 -+ # underlying crypto library it's actually using.
626 - case "$GNUTLS_INCLUDE" in
627 - *$GCRYPT_INCLUDE* ) ;;
628 - * ) GNUTLS_INCLUDE="$GNUTLS_INCLUDE $GCRYPT_INCLUDE" ;;
629 -@@ -4108,7 +4236,8 @@
630 - SYBASE_DBLIBS="$SYBASE_LPATH $SYBASE_DBLIBS"
631 - SYBASE_DLLS="$SYBASE_DLLLIST"
632 -
633 -- AC_CACHE_CHECK([for Sybase in $SYBASE_PATH], ncbi_cv_lib_sybase,
634 -+ AC_CACHE_CHECK([for Sybase${SYBASE_PATH:+ in $SYBASE_PATH}],
635 -+ ncbi_cv_lib_sybase,
636 - [CPPFLAGS="$SYBASE_INCLUDE $orig_CPPFLAGS"
637 - LIBS="$SYBASE_LIBS $SYBASE_DLLS $SYBASE_NETWORK_LIBS $DL_LIBS $orig_LIBS"
638 - AC_LINK_IFELSE([AC_LANG_PROGRAM(
639 -@@ -4216,7 +4345,8 @@
640 - AC_MSG_NOTICE([Using bundled FreeTDS (version $ftds_ver) from $FTDS_PATH])
641 - else
642 - FTDS_LIBS="$FTDS_CTLIBS"
643 -- AC_CACHE_CHECK([for FreeTDS in $FTDS_PATH], ncbi_cv_lib_freetds,
644 -+ AC_CACHE_CHECK([for FreeTDS${FTDS_PATH:+ in $FTDS_PATH}],
645 -+ ncbi_cv_lib_freetds,
646 - [CPPFLAGS="$FTDS_INCLUDE $orig_CPPFLAGS"
647 - LIBS="$FTDS_LIBS $NETWORK_LIBS $orig_LIBS"
648 - AC_LINK_IFELSE([AC_LANG_PROGRAM(
649 -@@ -4281,7 +4411,7 @@
650 - # Kill off single quotes, due to later requoting
651 - : ${MYSQL_INCLUDE=`$mysql_config --include | tr -d \'`}
652 - NCBI_RPATHIFY_OUTPUT_COND(MYSQL_LIBS, $mysql_config --libs${mt_sfx:+_r},
653 -- [s/'//g; ])
654 -+ [s/'//g; $no_usr_lib])
655 - AC_CACHE_CHECK([whether MySQL works], ncbi_cv_lib_mysql,
656 - [CPPFLAGS="$MYSQL_INCLUDE $orig_CPPFLAGS"
657 - LIBS="$MYSQL_LIBS $orig_LIBS"
658 -@@ -4310,7 +4440,6 @@
659 - if test "$with_bdb" != "no" ; then
660 - case "$with_bdb" in
661 - yes | "" )
662 -- : ${BERKELEYDB_PATH:="$NCBI/BerkeleyDB"}
663 - ;;
664 - */*)
665 - BERKELEYDB_PATH=$with_bdb
666 -@@ -4351,7 +4480,8 @@
667 - else
668 - BERKELEYDB_STATIC_LIBS=${BERKELEYDB_LIBS}
669 - fi
670 -- AC_CACHE_CHECK([for Berkeley DB libraries in $BERKELEYDB_PATH],
671 -+ AC_CACHE_CHECK(
672 -+ [for Berkeley DB libraries${BERKELEYDB_PATH:+ in $BERKELEYDB_PATH}],
673 - ncbi_cv_lib_berkeley_db,
674 - [CPPFLAGS="$BERKELEYDB_INCLUDE $orig_CPPFLAGS"
675 - LIBS="$BERKELEYDB_LIBS $orig_LIBS"
676 -@@ -4450,7 +4580,8 @@
677 - NCBI_RPATHIFY(ODBC_LIBS, ${ODBC_LIBPATH}, [ -lodbc -lodbcinst])
678 - CPPFLAGS="$ODBC_INCLUDE $orig_CPPFLAGS"
679 - LIBS="$ODBC_LIBS $orig_LIBS"
680 -- AC_CACHE_CHECK([for ODBC libraries in $ODBC_PATH], ncbi_cv_lib_odbc,
681 -+ AC_CACHE_CHECK([for ODBC libraries${ODBC_PATH:+ in $ODBC_PATH}],
682 -+ ncbi_cv_lib_odbc,
683 - [AC_LINK_IFELSE([AC_LANG_PROGRAM(
684 - [[#include <sql.h>]],
685 - [[SQLHDBC hdbc; SQLCHAR* cp = (SQLCHAR*) "x";
686 -@@ -4542,7 +4673,7 @@
687 - AC_PATH_PROG(PERL, perl, [], [$PERL_PATH/bin:$PATH])
688 - if test -x "$PERL"; then
689 - PERL_ARCHLIB=`$PERL -MConfig -e 'print \$Config{archlibexp};'`
690 -- PERL_FLAGS=`$PERL -MConfig -e 'print \$Config{cppflags};'`
691 -+ PERL_FLAGS=`$PERL -MConfig -e 'print join " ", grep /^-[[DI]]/, split /\\s+/, \$Config{cppflags};'`
692 - PERL_INCLUDE="-I$PERL_ARCHLIB/CORE $PERL_FLAGS"
693 - PERL_DEPS=`$PERL -MConfig -e 'print \$Config{libs};'`
694 - NCBI_RPATHIFY(PERL_LIBS, $PERL_ARCHLIB/CORE, [ -lperl $PERL_DEPS])
695 -@@ -4603,9 +4734,7 @@
696 -
697 - ## Boost
698 - if test "$with_boost" != "no"; then
699 -- if test "${with_boost-yes}" = yes; then
700 -- : ${BOOST_PATH=$NCBI/boost}
701 -- else
702 -+ if test "${with_boost-yes}" != yes; then
703 - BOOST_PATH=$with_boost
704 - fi
705 - if test -d "$BOOST_PATH"; then
706 -@@ -4644,17 +4773,22 @@
707 - if test -d `echo $BOOST_INCLUDE | sed -e 's/^-I//'`/boost-${ncbi_cv_lib_boost_version}/boost; then
708 - BOOST_INCLUDE=$BOOST_INCLUDE/boost-${ncbi_cv_lib_boost_version}
709 - fi
710 -- case "$ncbi_compiler" in
711 -- MIPSPRO)
712 -+ case "$compiler:$ncbi_compiler_ver" in
713 -+ MIPSpro*)
714 - BOOST_INCLUDE="$BOOST_INCLUDE $BOOST_INCLUDE/boost/compatibility/cpp_c_headers"
715 - ;;
716 -- WORKSHOP)
717 -+ WorkShop*)
718 - # Boost.Test's macros yield a *lot* of spurious "should not initialize
719 - # a non-const reference with a temporary" warnings, to the point of
720 - # overwhelming the compiler in some cases; turn them off altogether
721 - # when using Boost at all.
722 - BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp"
723 - ;;
724 -+ GCC*:4[[7-9]]* | GCC*:5*)
725 -+ # Some portions of Boost also have a lot of "unused" typedefs
726 -+ # from concept checking.
727 -+ BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs"
728 -+ ;;
729 - esac
730 - case "$ncbi_cv_lib_boost_version" in
731 - 0_* | 1_[[0-9]] | 1_[[0-9]]_* | 1_[[0-2]][[0-9]] | 1_[[0-2]][[0-9]]_* ) ;;
732 -@@ -4666,7 +4800,7 @@
733 - fi
734 - with_boost=no
735 - ;;
736 -- 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-2]] | 1_5[[0-2]]_* ) ;;
737 -+ 1_3[[5-9]] | 1_3[[5-9]]_* | 1_4* | 1_5[[0-3]] | 1_5[[0-3]]_* ) ;;
738 - '' ) with_boost=no ;;
739 - * )
740 - AC_MSG_WARN(
741 -@@ -4751,7 +4885,9 @@
742 - BOOST_REGEX_STATIC_LIBS=$BOOST_REGEX_LIBS
743 - fi
744 -
745 -- AC_CACHE_CHECK([for Boost.Regex in $BOOST_PATH], ncbi_cv_lib_boost_regex,
746 -+ in_path=${BOOST_PATH:+ in $BOOST_PATH}
747 -+
748 -+ AC_CACHE_CHECK([for Boost.Regex$in_path], ncbi_cv_lib_boost_regex,
749 - CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
750 - LIBS="$BOOST_LIBPATH $BOOST_REGEX_LIBS $RT_LIBS $orig_LIBS"
751 - [AC_LINK_IFELSE(
752 -@@ -4759,7 +4895,7 @@
753 - [[throw boost::regex_error(boost::regex_constants::error_stack);]])],
754 - [ncbi_cv_lib_boost_regex=yes], [ncbi_cv_lib_boost_regex=no])])
755 -
756 -- AC_CACHE_CHECK([for Boost.Spirit in $BOOST_PATH], ncbi_cv_lib_boost_spirit,
757 -+ AC_CACHE_CHECK([for Boost.Spirit$in_path], ncbi_cv_lib_boost_spirit,
758 - CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
759 - LIBS="$RT_LIBS $orig_LIBS"
760 - [AC_LINK_IFELSE(
761 -@@ -4774,7 +4910,7 @@
762 - BOOST_SYSTEM_STATIC_LIBS=$BOOST_SYSTEM_LIBS
763 - fi
764 -
765 -- AC_CACHE_CHECK([for Boost.System in $BOOST_PATH], ncbi_cv_lib_boost_system,
766 -+ AC_CACHE_CHECK([for Boost.System$in_path], ncbi_cv_lib_boost_system,
767 - CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
768 - LIBS="$BOOST_LIBPATH $BOOST_SYSTEM_LIBS $RT_LIBS $orig_LIBS"
769 - [AC_LINK_IFELSE(
770 -@@ -4785,6 +4921,24 @@
771 - BOOST_SYSTEM_LIBS=
772 - BOOST_SYSTEM_STATIC_LIBS=])])
773 -
774 -+ boost_fs_lib=-lboost_filesystem${BOOST_TAG}
775 -+ if test -f "$BOOST_LIBPATH_/libboost_filesystem${BOOST_TAG}-static.a"; then
776 -+ boost_fs_static_lib=-lboost_filesystem${BOOST_TAG}-static
777 -+ else
778 -+ boost_fs_static_lib=$boost_fs_lib
779 -+ fi
780 -+ BOOST_FILESYSTEM_LIBS="$boost_fs_lib $BOOST_SYSTEM_LIBS"
781 -+ BOOST_FILESYSTEM_STATIC_LIBS="$boost_fs_static_lib $BOOST_SYSTEM_STATIC_LIBS"
782 -+
783 -+ AC_CACHE_CHECK([for Boost.Filesystem$in_path], ncbi_cv_lib_boost_filesystem,
784 -+ CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
785 -+ LIBS="$BOOST_LIBPATH $BOOST_FILESYSTEM_LIBS $RT_LIBS $orig_LIBS"
786 -+ [AC_LINK_IFELSE(
787 -+ [AC_LANG_PROGRAM([[#include <boost/filesystem.hpp>]],
788 -+ [[return boost::filesystem::portable_name("foo");]])],
789 -+ [ncbi_cv_lib_boost_filesystem=yes],
790 -+ [ncbi_cv_lib_boost_filesystem=no])])
791 -+
792 - BOOST_TEST_PEM_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}
793 - if test -f "$BOOST_LIBPATH_/libboost_prg_exec_monitor${BOOST_TAG}-static.a"; then
794 - BOOST_TEST_PEM_STATIC_LIBS=-lboost_prg_exec_monitor${BOOST_TAG}-static
795 -@@ -4813,7 +4967,7 @@
796 - BOOST_TEST_TEM_LIBS=$BOOST_TEST_TEM_STATIC_LIBS
797 - BOOST_TEST_UTF_LIBS=$BOOST_TEST_UTF_STATIC_LIBS
798 -
799 -- AC_CACHE_CHECK([for Boost.Test in $BOOST_PATH], ncbi_cv_lib_boost_test,
800 -+ AC_CACHE_CHECK([for Boost.Test$in_path], ncbi_cv_lib_boost_test,
801 - CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
802 - LIBS="$RT_LIBS $orig_LIBS"
803 - found=
804 -@@ -4853,7 +5007,7 @@
805 - BOOST_THREAD_STATIC_LIBS=$BOOST_THREAD_LIBS
806 - fi
807 -
808 -- AC_CACHE_CHECK([for Boost.Threads in $BOOST_PATH], ncbi_cv_lib_boost_thread,
809 -+ AC_CACHE_CHECK([for Boost.Threads$in_path], ncbi_cv_lib_boost_thread,
810 - CPPFLAGS="$BOOST_INCLUDE $orig_CPPFLAGS"
811 - LIBS="$BOOST_LIBPATH $BOOST_THREAD_LIBS $RT_LIBS $orig_LIBS"
812 - [AC_LINK_IFELSE(
813 -@@ -4864,12 +5018,25 @@
814 - BOOST_INCLUDE=
815 - BOOST_LIBPATH=
816 - BOOST_TAG=
817 -+ ncbi_cv_lib_boost_filesystem=no
818 - ncbi_cv_lib_boost_regex=no
819 - ncbi_cv_lib_boost_spirit=no
820 -+ ncbi_cv_lib_boost_system=no
821 - ncbi_cv_lib_boost_test=no
822 - ncbi_cv_lib_boost_thread=no
823 - fi
824 -
825 -+if test "$ncbi_cv_lib_boost_filesystem" != "no"; then
826 -+ dnl AC_DEFINE(HAVE_BOOST_FILESYSTEM, 1,
827 -+ dnl [Define to 1 if the `Boost.Filesystem' library is available.])
828 -+ NCBI_PACKAGE(Boost.Filesystem)
829 -+else
830 -+ boost_fs_lib=
831 -+ boost_fs_static_lib=
832 -+ BOOST_FILESYSTEM_LIBS=
833 -+ BOOST_FILESYSTEM_STATIC_LIBS=
834 -+fi
835 -+
836 - if test "$ncbi_cv_lib_boost_regex" != "no"; then
837 - AC_DEFINE(HAVE_BOOST_REGEX, 1,
838 - [Define to 1 if the `Boost.Regex' library is available.])
839 -@@ -4927,7 +5094,10 @@
840 -
841 - ## NCBI C Toolkit
842 - if test "$with_ncbi_c" != "no" ; then
843 -- NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"}
844 -+ if test "${with_ncbi_c-yes}" != yes; then
845 -+ NCBI_C_PATH=$with_ncbi_c
846 -+ fi
847 -+ : ${NCBI_C_PATH="$NCBI"}
848 - if test "$ncbi_compiler" = ICC -a -d "$NCBI_C_PATH/ncbi_icc"; then
849 - NCBI_C_PATH=$NCBI_C_PATH/ncbi_icc
850 - fi
851 -@@ -4949,7 +5119,8 @@
852 - NCBI_C_ncbi="-lncbi"
853 - fi
854 - NCBI_C_LIBPATH="-L$NCBI_C_LIBPATH"
855 -- AC_CACHE_CHECK([for the NCBI C toolkit in $NCBI_C_PATH], ncbi_cv_lib_ctools,
856 -+ AC_CACHE_CHECK([for the NCBI C toolkit${NCBI_C_PATH:+ in $NCBI_C_PATH}],
857 -+ ncbi_cv_lib_ctools,
858 - [CPPFLAGS="$NCBI_C_INCLUDE $orig_CPPFLAGS"
859 - LIBS="$NCBI_C_LIBPATH $NCBI_C_ncbi $NETWORK_LIBS $orig_LIBS"
860 - AC_LINK_IFELSE([AC_LANG_PROGRAM(
861 -@@ -5000,11 +5171,7 @@
862 -
863 - ## OpenGL
864 - if test "$with_opengl" != "no"; then
865 -- if test "${with_opengl-yes}" = yes; then
866 -- if test -d $NCBI/MesaGL; then
867 -- : ${OPENGL_PATH=$NCBI/MesaGL}
868 -- fi
869 -- else
870 -+ if test "${with_opengl-yes}" != yes; then
871 - OPENGL_PATH=$with_opengl
872 - fi
873 - if test -d "$OPENGL_PATH"; then
874 -@@ -5101,7 +5268,6 @@
875 - else
876 - OSMESA_STATIC_LIBS=$OSMESA_LIBS
877 - fi
878 -- : ${GLUT_PATH=$NCBI/glut}
879 - if test "$with_glut" != "no"; then
880 - if test "${with_glut-yes}" != "yes"; then
881 - GLUT_PATH=$with_glut
882 -@@ -5121,7 +5287,6 @@
883 - NCBI_MISSING_PACKAGE(glut)
884 - fi
885 - fi
886 -- : ${GLEW_PATH=$NCBI/glew}
887 - if test "$with_glew" != "no"; then
888 - if test "${with_glew-yes}" != "yes"; then
889 - GLEW_PATH=$with_glew
890 -@@ -5214,7 +5379,7 @@
891 - : ${with_wxwidgets_ucs=no}
892 - if test "$with_wxwidgets" != "no" ; then
893 - case "$with_wxwidgets" in
894 -- yes | "" ) : ${WXWIDGETS_PATH=$NCBI/wxwidgets} ;;
895 -+ yes | "" ) ;;
896 - * ) WXWIDGETS_PATH=$with_wxwidgets ;;
897 - esac
898 - if test -d "$WXWIDGETS_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
899 -@@ -5283,12 +5448,13 @@
900 - libsed=$basesed
901 - ;;
902 - esac
903 -- AC_CACHE_CHECK([for wxWidgets in $WXWIDGETS_ARCH_PATH],
904 -+ AC_CACHE_CHECK(
905 -+ [for wxWidgets${WXWIDGETS_ARCH_PATH:+ in $WXWIDGETS_ARCH_PATH}],
906 - ncbi_cv_lib_wxwidgets,
907 - [if test -x "$wxconf" ; then
908 - WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
909 - NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, ["$wxconf" $wxcfflags --libs],
910 -- [$libsed; ])
911 -+ [$libsed; s/ -lm / /g;])
912 -
913 - CPPFLAGS="$WXWIDGETS_INCLUDE $orig_CPPFLAGS"
914 - LIBS="$WXWIDGETS_LIBS $orig_LIBS"
915 -@@ -5315,12 +5481,12 @@
916 - else
917 - NCBI_PACKAGE(wxWidgets)
918 - case "`"$wxconf" $wxcfflags --version`" in
919 -- 2.[[89]].* | 2.[[0-9]][[0-9]]* )
920 -- NCBI_PACKAGE(wx2.8)
921 -- wxlibs=std,richtext,aui
922 -+ 1.* | 2.[[0-7]].*)
923 -+ wxlibs=std
924 - ;;
925 - *)
926 -- wxlibs=std
927 -+ NCBI_PACKAGE(wx2.8)
928 -+ wxlibs=std,richtext,aui,propgrid
929 - ;;
930 - esac
931 - # The "yes" may have been cached; get the actual settings again if needed
932 -@@ -5328,9 +5494,9 @@
933 - WXWIDGETS_INCLUDE="$baseflags `"$wxconf" $wxcfflags --cflags`"
934 - fi
935 - NCBI_RPATHIFY_OUTPUT(WXWIDGETS_LIBS, [$wxconf $wxcfflags --libs $wxlibs],
936 -- [$libsed; ])
937 -+ [$libsed; s/ -lm / /g;])
938 - WXWIDGETS_STATIC_LIBS=`"$wxconf" $wxcfflags --libs --static $wxlibs \
939 -- 2>/dev/null | sed -e "$basesed"`
940 -+ 2>/dev/null | sed -e "$basesed; s/ -lm / /g;"`
941 - if test -n "$WXWIDGETS_STATIC_LIBS"; then
942 - # Allow direct use of underlying libraries with strict linkers
943 - WXWIDGETS_LIBS="$WXWIDGETS_LIBS `echo $WXWIDGETS_STATIC_LIBS | sed -e 's/.*\.a *//'`"
944 -@@ -5350,7 +5516,7 @@
945 - ## In-house Fast-CGI library
946 - if test "$with_fastcgi" != "no" ; then
947 - case "$with_fastcgi" in
948 -- yes | "" ) : ${FASTCGI_PATH:="$NCBI/fcgi-current"} ;;
949 -+ yes | "" ) ;;
950 - */* ) FASTCGI_PATH=$with_fastcgi ;;
951 - * ) FASTCGI_PATH=$NCBI/fcgi-${with_fastcgi} ;;
952 - esac
953 -@@ -5366,7 +5532,8 @@
954 - NCBI_RPATHIFY(FASTCGI_LIBS, $FASTCGI_LIBDIR, [ -lfcgi $NETWORK_LIBS])
955 - FASTCGI_OBJS="fcgibuf"
956 - LIBS="$FASTCGI_LIBS $orig_LIBS"
957 -- AC_CACHE_CHECK([for FastCGI libraries in $FASTCGI_PATH], ncbi_cv_lib_fcgi,
958 -+ AC_CACHE_CHECK([for FastCGI libraries${FASTCGI_PATH:+ in $FASTCGI_PATH}],
959 -+ ncbi_cv_lib_fcgi,
960 - [CPPFLAGS="$FASTCGI_INCLUDE $orig_CPPFLAGS"
961 - AC_LINK_IFELSE([AC_LANG_PROGRAM(
962 - [[#include <fcgiapp.h>]],
963 -@@ -5416,7 +5583,11 @@
964 - else
965 - with_included_sss=no
966 - fi
967 -+ if test "${with_sss-yes}" = yes; then
968 - NCBI_SSS_PATH=${NCBI_SSS_PATH:="$NCBI/sss/BUILD"}
969 -+ else
970 -+ NCBI_SSS_PATH=$with_sss
971 -+ fi
972 - NCBI_SSS_INCLUDE=${NCBI_SSS_INCLUDE:="$NCBI_SSS_PATH/include"}
973 - if test -z "$NCBI_SSS_LIBPATH" ; then
974 - NCBI_SSS_LIBPATH="${NCBI_SSS_PATH}/lib/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}"
975 -@@ -5424,7 +5595,8 @@
976 - NCBI_SSS_LIBPATH="${NCBI_SSS_LIBPATH}mt"
977 - fi
978 - fi
979 -- AC_MSG_CHECKING([for NCBI SSS directories in $NCBI_SSS_PATH])
980 -+ AC_MSG_CHECKING(
981 -+ [for NCBI SSS directories${NCBI_SSS_PATH:+ in $NCBI_SSS_PATH}])
982 - if test "$with_included_sss" = "yes"; then
983 - AC_MSG_RESULT([yes]) # duh
984 - elif test ! -d "${NCBI_SSS_LIBPATH}" -o ! -d "${NCBI_SSS_INCLUDE}" ; then
985 -@@ -5510,7 +5682,6 @@
986 -
987 - # SP
988 - if test "$with_sp" != "no" ; then
989 -- SP_PATH=${SP_PATH:="$NCBI/SP"}
990 - if test -n "$SP_INCLUDE"; then
991 - SP_GENERIC="$SP_INCLUDE/../generic"
992 - else
993 -@@ -5520,7 +5691,7 @@
994 - if test -z "$SP_LIBPATH" ; then
995 - SP_LIBPATH="${SP_PATH}/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}"
996 - fi
997 -- AC_MSG_CHECKING([for SP directories in $SP_PATH])
998 -+ AC_MSG_CHECKING([for SP directories${SP_PATH:+ in $SP_PATH}])
999 - if test ! -d "${SP_LIBPATH}" -o ! -d "${SP_INCLUDE}" ; then
1000 - AC_MSG_RESULT([no])
1001 - NCBI_MISSING_PACKAGE(sp)
1002 -@@ -5558,19 +5729,13 @@
1003 -
1004 -
1005 - ## ORBacus CORBA
1006 --if test "${with_orbacus:-yes}" = yes; then
1007 -- if test -d $NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT; then
1008 -- : ${ORBACUS_PATH=$NCBI/corba/${compiler_vpfx}Release${bit64_sfx}MT}
1009 -- else
1010 -- : ${ORBACUS_PATH=$NCBI/corba/OB-4.0.1}
1011 -- fi
1012 --elif test "$with_orbacus" != no; then
1013 -+if test "$with_orbacus" != no; then
1014 -+ if test "$with_orbacus" != yes; then
1015 - ORBACUS_PATH=$with_orbacus
1016 - fi
1017 - if test -d "$ORBACUS_PATH"; then
1018 - NCBI_FIX_DIR(ORBACUS_PATH)
1019 - fi
1020 --if test "$with_orbacus" != no; then
1021 - fullpath=${ORBACUS_PATH}/${DEBUG_SFX}${mt_sfx}${bit64_sfx}
1022 - if test -f ${fullpath}/inc/OB/Config.h ; then
1023 - : ${ORBACUS_INCLUDE="-I$ORBACUS_PATH/include -I$fullpath/inc"}
1024 -@@ -5594,7 +5759,8 @@
1025 - LIBIMR=
1026 - ;;
1027 - esac
1028 -- AC_CACHE_CHECK([for ORBacus in $ORBACUS_PATH], ncbi_cv_lib_orbacus,
1029 -+ AC_CACHE_CHECK([for ORBacus${ORBACUS_PATH:+ in $ORBACUS_PATH}],
1030 -+ ncbi_cv_lib_orbacus,
1031 - [CPPFLAGS="$ORBACUS_INCLUDE $orig_CPPFLAGS"
1032 - LIBS="$ORBACUS_LIBPATH $LIBOB $NETWORK_LIBS $DL_LIBS $orig_LIBS"
1033 - AC_LINK_IFELSE([AC_LANG_PROGRAM(
1034 -@@ -5633,7 +5799,7 @@
1035 -
1036 - if test "$with_icu" != "no" ; then
1037 - case "$with_icu" in
1038 -- yes | "" ) : ${ICU_PATH=$NCBI/icu} ;;
1039 -+ yes | "" ) ;;
1040 - * ) ICU_PATH=$with_icu ;;
1041 - esac
1042 - if test -d "$ICU_PATH/${compiler_vpfx}${DEBUG_SFX}${bit64_sfx}${mt_sfx}/lib" \
1043 -@@ -5648,7 +5814,8 @@
1044 - ICU_BINPATH=${ICU_BINPATH:="$ICU_ARCH_PATH/bin"}
1045 - ICU_LIBPATH=${ICU_LIBPATH:="$ICU_ARCH_PATH/lib"}
1046 - ICU_INCLUDE=
1047 -- AC_CACHE_CHECK([for ICU in $ICU_ARCH_PATH], ncbi_cv_lib_icu,
1048 -+ AC_CACHE_CHECK([for ICU${ICU_ARCH_PATH:+ in $ICU_ARCH_PATH}],
1049 -+ ncbi_cv_lib_icu,
1050 - [ICU_CONFIG=`$ICU_BINPATH/icu-config --bindir 2>/dev/null`/icu-config
1051 - if test -x "$ICU_CONFIG" ; then
1052 - ICU_INCLUDE=`$ICU_CONFIG --cppflags-searchpath`
1053 -@@ -5690,9 +5857,6 @@
1054 -
1055 -
1056 - ### XML/XSL libraries
1057 --if test -d "$NCBI/expat/include"; then
1058 -- : ${EXPAT_PATH=$NCBI/expat}
1059 --fi
1060 - NCBI_CHECK_THIRD_PARTY_LIB(expat,
1061 - AC_LANG_PROGRAM([#include <expat.h>],
1062 - [XML_Parser parser = XML_ParserCreate("utf-8");]))
1063 -@@ -5701,7 +5865,6 @@
1064 - else
1065 - EXPAT_STATIC_LIBS=${EXPAT_LIBS}
1066 - fi
1067 --: ${SABLOT_PATH=$NCBI/Sablot}
1068 - vpath="$SABLOT_PATH/${compiler_vpfx}build"
1069 - test -d "$vpath" && SABLOT_PATH=$vpath
1070 - if test -d "$SABLOT_PATH"; then
1071 -@@ -5718,7 +5881,6 @@
1072 - SABLOT_STATIC_LIBS=${SABLOT_LIBS}
1073 - fi
1074 -
1075 --: ${LIBXML_PATH=$NCBI/libxml}
1076 - # test -d "$LIBXML_PATH" || LIBXML_PATH=`xml2-config --prefix 2>/dev/null`
1077 - if test "$with_libxml" != "no"; then
1078 - case "$with_libxml" in
1079 -@@ -5813,7 +5975,6 @@
1080 - LIBEXSLT_STATIC_LIBS=${LIBEXSLT_LIBS}
1081 - fi
1082 -
1083 --: ${XERCES_PATH=$NCBI/xerces}
1084 - if test "$with_xerces" != no; then
1085 - if test "${with_xerces-yes}" != yes; then
1086 - XERCES_PATH=$with_xerces
1087 -@@ -5838,7 +5999,7 @@
1088 - NCBI_FIX_DIR(XERCES_LIBPATH)
1089 - fi
1090 - fi
1091 -- if test -d $XERCES_PATH; then
1092 -+ if test -d "$XERCES_PATH"; then
1093 - in_path=" in $XERCES_PATH"
1094 - : ${XERCES_INCLUDE=-I$XERCES_PATH/include}
1095 - : ${XERCES_LIBPATH=$XERCES_PATH/lib}
1096 -@@ -5875,7 +6036,6 @@
1097 - XERCES_STATIC_LIBS=
1098 - fi
1099 -
1100 --: ${XALAN_PATH=$NCBI/xalan}
1101 - if test "$with_xalan" != no; then
1102 - if test "${with_xalan-yes}" != yes; then
1103 - XALAN_PATH=$with_xalan
1104 -@@ -5900,7 +6060,7 @@
1105 - NCBI_FIX_DIR(XALAN_LIBPATH)
1106 - fi
1107 - fi
1108 -- if test -d $XALAN_PATH; then
1109 -+ if test -d "$XALAN_PATH"; then
1110 - in_path=" in $XALAN_PATH"
1111 - : ${XALAN_INCLUDE=-I$XALAN_PATH/include}
1112 - : ${XALAN_LIBPATH=$XALAN_PATH/lib}
1113 -@@ -5937,7 +6097,6 @@
1114 -
1115 - test -d SunWS_cache && rm -r SunWS_cache
1116 -
1117 --: ${ZORBA_PATH=$NCBI/zorba}
1118 - if test "$with_zorba" != no; then
1119 - if test "${with_zorba-yes}" != yes; then
1120 - ZORBA_PATH=$with_zorba
1121 -@@ -5967,7 +6126,7 @@
1122 - ZORBA_PATH=`$ZORBA_CONFIG --prefix`
1123 - : ${ZORBA_INCLUDE=`$ZORBA_CONFIG --cppflags`}
1124 - fi
1125 -- if test -d $ZORBA_PATH; then
1126 -+ if test -d "$ZORBA_PATH"; then
1127 - in_path=" in $ZORBA_PATH"
1128 - : ${ZORBA_INCLUDE=-I$ZORBA_PATH/include}
1129 - : ${ZORBA_LIBPATH=$ZORBA_PATH/lib}
1130 -@@ -6010,7 +6169,7 @@
1131 -
1132 - ### SQLite
1133 - case "$with_sqlite3" in
1134 -- yes | '' ) : ${SQLITE3_PATH=$NCBI/sqlite3} ;;
1135 -+ yes | '' ) ;;
1136 - * ) SQLITE3_PATH=$with_sqlite3 ;;
1137 - esac
1138 -
1139 -@@ -6048,7 +6207,6 @@
1140 - ### OEChem
1141 - # somewhat kludgish, as we now wanto to add in oeiupac and oedepict,
1142 - # which depend on oechem....
1143 --: ${OECHEM_PATH=$NCBI/oechem}
1144 - NCBI_CHECK_THIRD_PARTY_LIB(oechem,
1145 - AC_LANG_PROGRAM([#include <oechem.h>],
1146 - [OEChem::OEMol mol; OEChem::OEConfBase* c = mol.GetActive();]),
1147 -@@ -6091,7 +6249,7 @@
1148 -
1149 - ### muParser
1150 - case "$with_muparser" in
1151 -- yes | '' ) : ${MUPARSER_PATH=$NCBI/muParser} ;;
1152 -+ yes | '' ) ;;
1153 - * ) MUPARSER_PATH=$with_muparser ;;
1154 - esac
1155 -
1156 -@@ -6111,7 +6269,7 @@
1157 -
1158 - ### hdf5
1159 - case "$with_hdf5" in
1160 -- yes | '' ) : ${HDF5_PATH=$NCBI/hdf5} ;;
1161 -+ yes | '' ) ;;
1162 - * ) HDF5_PATH=$with_hdf5 ;;
1163 - esac
1164 -
1165 -@@ -6176,7 +6334,7 @@
1166 - GIF_LIBS=$UNGIF_LIBS
1167 - fi
1168 -
1169 --test -n "$x_libraries" && : ${XPM_PATH=`dirname "$x_libraries"`}
1170 -+case "$x_libraries" in */*) : ${XPM_PATH=`dirname "$x_libraries"`} ;; esac
1171 - NCBI_CHECK_THIRD_PARTY_LIB(Xpm,
1172 - AC_LANG_PROGRAM([#include <X11/xpm.h>],
1173 - [XpmImage image; XpmInfo info;
1174 -@@ -6241,7 +6399,7 @@
1175 - fi
1176 -
1177 - case "$with_ftgl" in
1178 -- yes | '' ) : ${FTGL_PATH=$NCBI/ftgl} ;;
1179 -+ yes | '' ) ;;
1180 - * ) FTGL_PATH=$with_ftgl ;;
1181 - esac
1182 -
1183 -@@ -6268,7 +6426,7 @@
1184 -
1185 - # Mimetic
1186 - case "$with_mimetic" in
1187 -- yes | '' ) : ${MIMETIC_PATH=$NCBI/mimetic} ;;
1188 -+ yes | '' ) ;;
1189 - * ) MIMETIC_PATH=$with_mimetic ;;
1190 - esac
1191 - if test -d "$MIMETIC_PATH"; then
1192 -@@ -6293,6 +6451,88 @@
1193 - [mimetic::MimeEntity me;])])
1194 -
1195 -
1196 -+# gSOAP++
1197 -+case "$with_gsoap" in
1198 -+ yes | '' ) ;;
1199 -+ * ) GSOAP_PATH=$with_gsoap ;;
1200 -+esac
1201 -+if test -d "$GSOAP_PATH"; then
1202 -+ NCBI_FIX_DIR(GSOAP_PATH)
1203 -+fi
1204 -+for d in "$GSOAP_LIBDIR" \
1205 -+ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
1206 -+ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}${bit64_sfx}/lib" \
1207 -+ "$GSOAP_PATH/lib${bit64_sfx}" \
1208 -+ "$GSOAP_PATH/${compiler_vpfx}${DEBUG_SFX}${mt_sfx}/lib" \
1209 -+ "$GSOAP_PATH/${compiler_pfx}${DEBUG_SFX}${mt_sfx}/lib" \
1210 -+ "$GSOAP_PATH/lib"; do
1211 -+ if test -d "$d"; then
1212 -+ GSOAP_LIBDIR=$d
1213 -+ NCBI_FIX_DIR(GSOAP_LIBDIR)
1214 -+ break
1215 -+ fi
1216 -+done
1217 -+NCBI_RPATHIFY(GSOAP_LIBPATH, $GSOAP_LIBDIR)
1218 -+
1219 -+: ${GSOAP_BINDIR=`dirname "$GSOAP_LIBDIR"`/bin}
1220 -+AC_PATH_PROG(GSOAP_SOAPCPP2, soapcpp2, [], $GSOAP_BINDIR:$PATH)
1221 -+AC_PATH_PROG(GSOAP_WSDL2H, wsdl2h, [], $GSOAP_BINDIR:$PATH)
1222 -+
1223 -+NCBI_CHECK_THIRD_PARTY_LIB_EX(gsoap, GSOAP, gsoapssl++,
1224 -+ [AC_LANG_PROGRAM([#include <stdsoap2.h>
1225 -+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultcode(struct soap*)
1226 -+ { return NULL; }
1227 -+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultsubcode(struct soap*)
1228 -+ { return NULL; }
1229 -+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultstring(struct soap*)
1230 -+ { return NULL; }
1231 -+ SOAP_FMAC3 const char** SOAP_FMAC4 soap_faultdetail(struct soap*)
1232 -+ { return NULL; }
1233 -+ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultsubcode(struct soap*)
1234 -+ { return NULL; }
1235 -+ SOAP_FMAC3 const char* SOAP_FMAC4 soap_check_faultdetail(struct soap*)
1236 -+ { return NULL; }
1237 -+ SOAP_FMAC3 void SOAP_FMAC4 soap_serializeheader(struct soap*) { }
1238 -+ SOAP_FMAC3 int SOAP_FMAC4 soap_putheader(struct soap*) { return 0; }
1239 -+ SOAP_FMAC3 int SOAP_FMAC4 soap_getheader(struct soap*) { return 0; }
1240 -+ SOAP_FMAC3 void SOAP_FMAC4 soap_serializefault(struct soap*) { }
1241 -+ SOAP_FMAC3 int SOAP_FMAC4 soap_putfault(struct soap*) { return 0; }
1242 -+ SOAP_FMAC3 int SOAP_FMAC4 soap_getfault(struct soap*) { return 0; }],
1243 -+ [soap s;])],
1244 -+ $OPENSSL_LIBS $Z_LIBS)
1245 -+
1246 -+case "$with_sqlite3" in
1247 -+ yes | '' ) ;;
1248 -+ * ) SQLITE3_PATH=$with_sqlite3 ;;
1249 -+esac
1250 -+
1251 -+
1252 -+# MongoDB
1253 -+if test -d "$MONGODB_PATH"; then
1254 -+ NCBI_FIX_DIR(MONGODB_PATH)
1255 -+fi
1256 -+if test -d $MONGODB_PATH/lib${bit64_sfx}; then
1257 -+ MONGODB_LIBDIR=$MONGODB_PATH/lib${bit64_sfx}
1258 -+else
1259 -+ MONGODB_LIBDIR=$MONGODB_PATH/lib
1260 -+fi
1261 -+# need Boost rpath
1262 -+NCBI_RPATHIFY(MONGODB_LIBPATH, $MONGODB_LIBDIR)
1263 -+NCBI_CHECK_THIRD_PARTY_LIB_EX(mongodb, MONGODB, mongoclient,
1264 -+ [AC_LANG_PROGRAM([#include <mongo/client/dbclient.h>],
1265 -+ [std::vector<mongo::HostAndPort> v;
1266 -+ mongo::DBClientReplicaSet client("foo", v);
1267 -+ client.connect();])],
1268 -+ [$BOOST_LIBPATH $boost_fs_lib $BOOST_THREAD_LIBS], [],
1269 -+ [$BOOST_INCLUDE])
1270 -+# MongoDB's own library is normally static, but its supporting Boost
1271 -+# libraries might not be by default.
1272 -+if test -n "$MONGODB_LIBS"; then
1273 -+ MONGODB_STATIC_LIBS="$MONGODB_LIBPATH -lmongodb $BOOST_LIBPATH $boost_fs_static_lib $BOOST_THREAD_STATIC_LIBS"
1274 -+else
1275 -+ MONGODB_STATIC_LIBS=
1276 -+fi
1277 -+
1278 - ### Restore original compiler/linker flags
1279 - LIBS="$orig_LIBS"
1280 - CPPFLAGS="$orig_CPPFLAGS"
1281 -@@ -6499,16 +6739,6 @@
1282 - fi
1283 -
1284 -
1285 --## Sequence Read Archive SDK, which may be attached on either the
1286 --## public or the internal side
1287 --
1288 --if test -f "${real_srcdir}/src/sra/sdk/Makefile.sra_macros.mk"; then
1289 -- sra=sra
1290 --else
1291 -- sra=
1292 --fi
1293 --
1294 --
1295 - ## `internal' project cluster
1296 -
1297 - if test "$with_internal" = "no" \
1298 -@@ -6781,6 +7011,7 @@
1299 - AC_SUBST(C_LINK)
1300 - AC_SUBST(TAIL_N)
1301 - AC_SUBST(EGREP_Q)
1302 -+AC_SUBST(LDD_R)
1303 -
1304 - AC_SUBST(CFLAGS)
1305 - AC_SUBST(FAST_CFLAGS)
1306 -@@ -6829,7 +7060,6 @@
1307 - AC_SUBST(algo)
1308 - AC_SUBST(app)
1309 - AC_SUBST(internal)
1310 --AC_SUBST(sra)
1311 -
1312 - AC_SUBST(check)
1313 - AC_SUBST(CHECK_ARG)
1314 -@@ -6865,6 +7095,7 @@
1315 -
1316 - AC_SUBST(THREAD_LIBS)
1317 - AC_SUBST(NCBIATOMIC_LIB)
1318 -+AC_SUBST(OPENMP_FLAGS)
1319 - AC_SUBST(NETWORK_LIBS)
1320 - AC_SUBST(NETWORK_PURE_LIBS)
1321 - AC_SUBST(RESOLVER_LIBS)
1322 -@@ -6902,6 +7133,8 @@
1323 - AC_SUBST(BOOST_INCLUDE)
1324 - AC_SUBST(BOOST_LIBPATH)
1325 - AC_SUBST(BOOST_TAG)
1326 -+AC_SUBST(BOOST_FILESYSTEM_LIBS)
1327 -+AC_SUBST(BOOST_FILESYSTEM_STATIC_LIBS)
1328 - AC_SUBST(BOOST_REGEX_LIBS)
1329 - AC_SUBST(BOOST_REGEX_STATIC_LIBS)
1330 - AC_SUBST(BOOST_SYSTEM_LIBS)
1331 -@@ -6968,6 +7201,8 @@
1332 - AC_SUBST(SQLITE3_STATIC_LIBS)
1333 - AC_SUBST(FREETYPE_INCLUDE)
1334 - AC_SUBST(FREETYPE_LIBS)
1335 -+AC_SUBST(GSOAP_PATH)
1336 -+AC_SUBST(MONGODB_STATIC_LIBS)
1337 - AC_SUBST(ncbi_xreader_pubseqos)
1338 - AC_SUBST(ncbi_xreader_pubseqos2)
1339 - AC_SUBST(UNLESS_PUBSEQOS)
1340 -@@ -7194,7 +7429,9 @@
1341 -
1342 - cat << EOCONF
1343 - ===============================================================================
1344 --NCBI C++ Toolkit documentation: doc/index.html, doc/config.html#ref_Running
1345 -+NCBI C++ Toolkit documentation:
1346 -+ Online: http://www.ncbi.nlm.nih.gov/toolkit/doc/book/
1347 -+ Local: ./doc/public/index.html
1348 - For the available configuration flags run: ./configure --help
1349 -
1350 - CFLAGS = $CFLAGS
1351 ---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014-06-23 17:36:18.000000000 +0200
1352 -+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014-06-23 17:36:59.000000000 +0200
1353 -@@ -1,126 +1,45 @@
1354 --# Hacked up in various ways, since Autoconf's version doesn't quite
1355 --# suit our (unusual) conventions. (Originally from status.m4)
1356 --m4_define([_AC_SRCPATHS],
1357 --[#ac_builddir=. # Useless!
1358 --ac_builddir=$builddir
1359 --dnl Base source directories on path to *input* file.
1360 --if test -n "$ac_file_in"; then
1361 -- ac_dir_in=`AS_DIRNAME(["$ac_file_in"])`
1362 -+# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS)
1363 -+# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly.
1364 -+m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS])
1365 -+m4_define([_AC_SRCDIRS],
1366 -+[# Base source directories on path to *input* file.
1367 -+if test -n "$ac_f"; then
1368 -+ ac_dir_in=`AS_DIRNAME(["$ac_f"])`
1369 - else
1370 - ac_dir_in=$1
1371 - fi
1372 -
1373 --if test $ac_dir_in != .; then
1374 -- ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'`
1375 -- # A "../" for each directory in $ac_dir_suffix.
1376 -- ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'`
1377 --else
1378 -- ac_dir_suffix= ac_top_builddir=
1379 --fi
1380 -+NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"])
1381 -
1382 --case $srcdir in
1383 -- .) # No --srcdir option. We are building in place.
1384 -- ac_srcdir=.
1385 -- if test -z "$ac_top_builddir"; then
1386 -- ac_top_srcdir=.
1387 -- else
1388 -- ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
1389 -- fi ;;
1390 -- [[\\/]]* | ?:[[\\/]]* ) # Absolute path.
1391 -- ac_srcdir=$srcdir/$ac_dir_suffix;
1392 -- ac_top_srcdir=$srcdir ;;
1393 -- *) # Relative path.
1394 -- ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix
1395 -- ac_top_srcdir=$ac_top_builddir$srcdir ;;
1396 --esac
1397 --# Do not use `cd foo && pwd` to compute absolute paths, because
1398 --# the directories may not exist.
1399 --AS_SET_CATFILE([ac_abs_builddir], [$builddir], [$1])
1400 --AS_SET_CATFILE([ac_abs_top_builddir],
1401 -- [$ac_abs_builddir], [${ac_top_builddir}.])
1402 - AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir])
1403 --AS_SET_CATFILE([ac_abs_srcdir], [$ac_abs_top_srcdir], [$ac_dir_suffix])
1404 --])# _AC_SRCPATHS
1405 --
1406 -+ac_builddir=$builddir
1407 -+])
1408 -
1409 --# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a
1410 --# last resort due to issues with sourcing .bashrc.
1411 --m4_define([_AS_LINENO_PREPARE],
1412 --[_AS_LINENO_WORKS || {
1413 -- # Find who we are. Look in the path if we contain no path at all
1414 -- # relative or not.
1415 -- case $[0] in
1416 -- *[[\\/]]* ) as_myself=$[0] ;;
1417 -- *) _AS_PATH_WALK([],
1418 -- [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break])
1419 -- ;;
1420 -- esac
1421 -- # We did not find ourselves, most probably we were run as `sh COMMAND'
1422 -- # in which case we are not to be found in the path.
1423 -- if test "x$as_myself" = x; then
1424 -- as_myself=$[0]
1425 -- fi
1426 -- if test ! -f "$as_myself"; then
1427 -- AS_ERROR([cannot find myself; rerun with an absolute path])
1428 -- fi
1429 -- case $CONFIG_SHELL in
1430 -- '')
1431 -- AS_UNSET(ZSH_VERSION)
1432 -- for as_base in sh ksh sh5 bash; do
1433 -- _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH],
1434 -- [case $as_dir in
1435 -- /*)
1436 -- if ("$as_dir/$as_base" -c \
1437 -- 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null
1438 -- then
1439 -- AS_UNSET(BASH_ENV)
1440 -- AS_UNSET(ENV)
1441 -- CONFIG_SHELL=$as_dir/$as_base
1442 -- export CONFIG_SHELL
1443 -- exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"}
1444 -- fi;;
1445 -- esac
1446 -- done]);;
1447 -- esac
1448 -
1449 -- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
1450 -- # uniformly replaced by the line number. The first 'sed' inserts a
1451 -- # line-number line before each line; the second 'sed' does the real
1452 -- # work. The second script uses 'N' to pair each line-number line
1453 -- # with the numbered line, and appends trailing '-' during
1454 -- # substitution so that $LINENO is not a special case at line end.
1455 -- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
1456 -- # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-)
1457 -- sed '=' <$as_myself |
1458 -- sed '
1459 -- N
1460 -- s,$,-,
1461 -- : loop
1462 -- s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3,
1463 -- t loop
1464 -- s,-$,,
1465 -- s,^[['$as_cr_digits']]*\n,,
1466 -- ' >$as_me.lineno &&
1467 -- chmod +x $as_me.lineno ||
1468 -- AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell])
1469 --
1470 -- # Don't try to exec as it changes $[0], causing all sort of problems
1471 -- # (the dirname of $[0] is not the place where we might find the
1472 -- # original and so on. Autoconf is especially sensible to this).
1473 -- . ./$as_me.lineno
1474 -- # Exit status is that of the last command.
1475 -- exit
1476 --}
1477 --])# _AS_LINENO_PREPARE
1478 -+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both
1479 -+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make
1480 -+# bash a last resort due to issues with sourcing .bashrc while entirely
1481 -+# avoiding zsh, which passes itself off as ksh on some systems but runs
1482 -+# parent shells' exit handlers from subshells, resulting in premature
1483 -+# cleanup of temporary files (notably confdefs.h).
1484 -+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL])
1485 -+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN])
1486 -+
1487 -+m4_define([_AS_DETECT_BETTER_SHELL],
1488 -+ [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]),
1489 -+ [sh bash ksh sh5], [sh ksh sh5 bash])])
1490 -+m4_define([_AS_RUN],
1491 -+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl
1492 -+NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])])
1493 -
1494 -
1495 - # One more hack: suppress PACKAGE_*, as we don't use them and some
1496 - # third-party libraries expose their corresponding settings, leading
1497 - # to preprocessor warnings.
1498 --m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED]))
1499 -+m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED])
1500 - m4_define([AC_DEFINE_UNQUOTED],
1501 - [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [],
1502 -- [NCBI_ORIG_ACDU($@)])])
1503 -+ [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])])
1504 -
1505 -
1506 - AC_DEFUN(NCBI_FIX_DIR,
1507 -@@ -158,7 +77,7 @@
1508 - AC_MSG_WARN([Proceeding without questions per --without-caution]) ;;
1509 - * )
1510 - echo "$1 [[y/N]]"
1511 -- read answer
1512 -+ read answer <& AS_ORIGINAL_STDIN_FD
1513 - case "$answer" in
1514 - [[Yy]]* ) AC_MSG_WARN([Proceeding at your own risk...]) ;;
1515 - * ) AC_MSG_ERROR([Configuration has been canceled by user.]) ;;
1516 ---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014-06-23 17:38:56.000000000 +0200
1517 -+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014-06-23 17:39:04.000000000 +0200
1518 -@@ -98,6 +98,9 @@
1519 - /* Define to 1 if you have the `getaddrinfo' function. */
1520 - #undef HAVE_GETADDRINFO
1521 -
1522 -+/* Define to 1 if you have the `getgrouplist' function. */
1523 -+#undef HAVE_GETGROUPLIST
1524 -+
1525 - /* If you have the `gethostbyaddr_r' function, define to the number of
1526 - arguments it takes (normally 7 or 8). */
1527 - #undef HAVE_GETHOSTBYADDR_R
1528 -@@ -176,9 +179,6 @@
1529 - /* Define to 1 if you have `ios(_base)::register_callback'. */
1530 - #undef HAVE_IOS_REGISTER_CALLBACK
1531 -
1532 --/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
1533 --#undef HAVE_IS_SORTED
1534 --
1535 - /* Define to 1 if you have the `lchown' function. */
1536 - #undef HAVE_LCHOWN
1537 -
1538 -@@ -234,6 +234,9 @@
1539 - /* Define to 1 if libgnutls is available. */
1540 - #undef HAVE_LIBGNUTLS
1541 -
1542 -+/* Define to 1 if libgsoapssl++ is available. */
1543 -+#undef HAVE_LIBGSOAP
1544 -+
1545 - /* Define to 1 if libhdf5_cpp is available. */
1546 - #undef HAVE_LIBHDF5
1547 -
1548 -@@ -260,6 +263,9 @@
1549 - /* Define to 1 if libmimetic is available. */
1550 - #undef HAVE_LIBMIMETIC
1551 -
1552 -+/* Define to 1 if libmongoclient is available. */
1553 -+#undef HAVE_LIBMONGODB
1554 -+
1555 - /* Define to 1 if libmuparser is available. */
1556 - #undef HAVE_LIBMUPARSER
1557 -
1558 -@@ -382,9 +388,6 @@
1559 - /* Define to 1 if `min'/`max' templates are not implemented. */
1560 - #undef HAVE_NO_MINMAX_TEMPLATE
1561 -
1562 --/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */
1563 --#undef HAVE_NULLPTR
1564 --
1565 - /* Define to 1 if ODBC libraries are available. */
1566 - #undef HAVE_ODBC
1567 -
1568 -@@ -799,37 +802,37 @@
1569 - by a signal. */
1570 - #undef SELECT_UPDATES_TIMEOUT
1571 -
1572 --/* The size of a `char', as computed by sizeof. */
1573 -+/* The size of `char', as computed by sizeof. */
1574 - #undef SIZEOF_CHAR
1575 -
1576 --/* The size of a `double', as computed by sizeof. */
1577 -+/* The size of `double', as computed by sizeof. */
1578 - #undef SIZEOF_DOUBLE
1579 -
1580 --/* The size of a `float', as computed by sizeof. */
1581 -+/* The size of `float', as computed by sizeof. */
1582 - #undef SIZEOF_FLOAT
1583 -
1584 --/* The size of a `int', as computed by sizeof. */
1585 -+/* The size of `int', as computed by sizeof. */
1586 - #undef SIZEOF_INT
1587 -
1588 --/* The size of a `long', as computed by sizeof. */
1589 -+/* The size of `long', as computed by sizeof. */
1590 - #undef SIZEOF_LONG
1591 -
1592 --/* The size of a `long double', as computed by sizeof. */
1593 -+/* The size of `long double', as computed by sizeof. */
1594 - #undef SIZEOF_LONG_DOUBLE
1595 -
1596 --/* The size of a `long long', as computed by sizeof. */
1597 -+/* The size of `long long', as computed by sizeof. */
1598 - #undef SIZEOF_LONG_LONG
1599 -
1600 --/* The size of a `short', as computed by sizeof. */
1601 -+/* The size of `short', as computed by sizeof. */
1602 - #undef SIZEOF_SHORT
1603 -
1604 --/* The size of a `size_t', as computed by sizeof. */
1605 -+/* The size of `size_t', as computed by sizeof. */
1606 - #undef SIZEOF_SIZE_T
1607 -
1608 --/* The size of a `void*', as computed by sizeof. */
1609 -+/* The size of `void*', as computed by sizeof. */
1610 - #undef SIZEOF_VOIDP
1611 -
1612 --/* The size of a `__int64', as computed by sizeof. */
1613 -+/* The size of `__int64', as computed by sizeof. */
1614 - #undef SIZEOF___INT64
1615 -
1616 - /* Define to 1 if the stack grows down. */
1617 -@@ -870,5 +873,5 @@
1618 - /* Define to empty if `const' does not conform to ANSI C. */
1619 - #undef const
1620 -
1621 --/* Define to `unsigned' if <sys/types.h> does not define. */
1622 -+/* Define to `unsigned int' if <sys/types.h> does not define. */
1623 - #undef size_t
1624 ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014-06-23 17:40:40.000000000 +0200
1625 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014-06-23 17:40:57.000000000 +0200
1626 -@@ -1,4 +1,4 @@
1627 --/* $Id: ncbiconf_xcode.h 361821 2012-05-04 14:28:13Z ucko $
1628 -+/* $Id$
1629 - * By Vlad Lebedev, NCBI (lebedev@××××××××××××.gov)
1630 - *
1631 - * Mac OS X - xCode Build
1632 -@@ -258,9 +258,6 @@
1633 - /* Define to 1 if you have `ios(_base)::register_callback'. */
1634 - #define HAVE_IOS_REGISTER_CALLBACK 1
1635 -
1636 --/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */
1637 --/* #undef HAVE_IS_SORTED */
1638 --
1639 - /* Define to 1 if you have the `lchown' function. */
1640 - /* #undef HAVE_LCHOWN */
1641 -
1642 -@@ -358,6 +355,9 @@
1643 - /* Define to 1 if you have the `lutimes' function. */
1644 - /* #undef HAVE_LUTIMES */
1645 -
1646 -+/* Define to 1 if you have the `madvise' function. */
1647 -+#define HAVE_MADVISE 1
1648 -+
1649 - /* Define to 1 if you have the <malloc.h> header file. */
1650 - /* #undef HAVE_MALLOC_H */
1651 -
1652 -@@ -589,15 +589,15 @@
1653 - /* Define to 1 if you have the <windows.h> header file. */
1654 - /* #undef HAVE_WINDOWS_H */
1655 -
1656 -+/* Define to 1 if you have the `writev' function. */
1657 -+#define HAVE_WRITEV 1
1658 -+
1659 - /* Define to 1 if the system has the type `wstring'. */
1660 - #define HAVE_WSTRING 1
1661 -
1662 - /* Define to 1 if wxWidgets is available. */
1663 - /* #undef HAVE_WXWIDGETS */
1664 -
1665 --/* Define to 1 if nullptr keyword is available. */
1666 --/* #undef HAVE_NULLPTR */
1667 --
1668 - /* Define as const if the declaration of iconv() needs const. */
1669 - #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */
1670 - # define ICONV_CONST
1671 -@@ -694,7 +694,7 @@
1672 - /* Define to empty if `const' does not conform to ANSI C. */
1673 - /* #undef const */
1674 -
1675 --/* Define to `unsigned' if <sys/types.h> does not define. */
1676 -+/* Define to `unsigned int' if <sys/types.h> does not define. */
1677 - /* #undef size_t */
1678 -
1679 - /*