Gentoo Archives: gentoo-commits

From: Justin Lecher <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
Date: Sun, 02 Jun 2013 16:49:05
Message-Id: 1370191344.eb7653c7d0b2c1ec08a436154d5d5623ad3ad3d1.jlec@gentoo
1 commit: eb7653c7d0b2c1ec08a436154d5d5623ad3ad3d1
2 Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
3 AuthorDate: Sun Jun 2 16:42:24 2013 +0000
4 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
5 CommitDate: Sun Jun 2 16:42:24 2013 +0000
6 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=eb7653c7
7
8 sci-chemistry/coot: Update pc patches
9
10 Package-Manager: portage-2.2.0_alpha177
11
12 ---
13 sci-chemistry/coot/ChangeLog | 5 +
14 sci-chemistry/coot/coot-9999.ebuild | 20 +-
15 sci-chemistry/coot/files/9999-clipper-config.patch | 17 -
16 sci-chemistry/coot/files/9999-goocanvas.patch | 25 -
17 sci-chemistry/coot/files/9999-mmdb-config.patch | 18 -
18 sci-chemistry/coot/files/9999-pc.patch | 1040 ++++++++++++++++++++
19 sci-chemistry/coot/files/9999-ssm.patch | 56 --
20 7 files changed, 1054 insertions(+), 127 deletions(-)
21
22 diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
23 index c729ace..2bbf002 100644
24 --- a/sci-chemistry/coot/ChangeLog
25 +++ b/sci-chemistry/coot/ChangeLog
26 @@ -2,6 +2,11 @@
27 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
28 # $Header: $
29
30 + 02 Jun 2013; Justin Lecher <jlec@g.o> coot-9999.ebuild,
31 + -files/9999-clipper-config.patch, -files/9999-goocanvas.patch,
32 + -files/9999-mmdb-config.patch, +files/9999-pc.patch, -files/9999-ssm.patch:
33 + Update pc patches
34 +
35 02 Jun 2013; Justin Lecher <jlec@g.o> coot-9999.ebuild:
36 Fix PYTHON() -> ${EPYTHON} for new eclasses
37
38
39 diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
40 index 4a7ee55..c8831ad 100644
41 --- a/sci-chemistry/coot/coot-9999.ebuild
42 +++ b/sci-chemistry/coot/coot-9999.ebuild
43 @@ -37,9 +37,9 @@ SCIDEPS="
44 >=sci-libs/gsl-1.3
45 >=sci-libs/mmdb-1.23
46 sci-libs/ssm
47 - <sci-libs/monomer-db-1
48 + sci-libs/monomer-db
49 sci-chemistry/reduce
50 - <sci-chemistry/refmac-5.6
51 + sci-chemistry/refmac
52 sci-chemistry/probe"
53
54 XDEPS="
55 @@ -82,21 +82,19 @@ pkg_setup() {
56 python-single-r1_pkg_setup
57 }
58
59 -PATCHES=(
60 - "${FILESDIR}"/${PV}-clipper-config.patch
61 - "${FILESDIR}"/${PV}-goocanvas.patch
62 - "${FILESDIR}"/${PV}-mmdb-config.patch
63 - "${FILESDIR}"/${PV}-ssm.patch
64 - )
65 +PATCHES=( "${FILESDIR}"/${PV}-pc.patch )
66
67 src_unpack() {
68 subversion_src_unpack
69 - use test && unpack ${A}
70 + if use test; then
71 + unpack ${A}
72 + ln -sf . "${S}"/coot-ccp4
73 + fi
74 }
75
76 src_prepare() {
77 sed \
78 - -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${PYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
79 + -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
80 -i configure.in || die
81
82 autotools-utils_src_prepare
83 @@ -128,7 +126,7 @@ src_configure() {
84
85 src_compile() {
86 autotools-utils_src_compile
87 - python_fix_shebang "${S}"/src/coot_gtk2.py "${S}"/python-tests/coot_unittest.py
88 + python_fix_shebang "${S}"/src/coot_gtk2.py
89 cp "${S}"/src/coot_gtk2.py python/coot.py || die
90 }
91
92
93 diff --git a/sci-chemistry/coot/files/9999-clipper-config.patch b/sci-chemistry/coot/files/9999-clipper-config.patch
94 deleted file mode 100644
95 index 311b5e8..0000000
96 --- a/sci-chemistry/coot/files/9999-clipper-config.patch
97 +++ /dev/null
98 @@ -1,17 +0,0 @@
99 - macros/clipper.m4 | 3 +++
100 - 1 files changed, 3 insertions(+), 0 deletions(-)
101 -
102 -diff --git a/macros/clipper.m4 b/macros/clipper.m4
103 -index 0bf087a..d0e8b6b 100644
104 ---- a/macros/clipper.m4
105 -+++ b/macros/clipper.m4
106 -@@ -98,6 +98,9 @@ case $ac_cv_build_alias in
107 - ;;
108 - esac
109 -
110 -+CLIPPER_CXXFLAGS=`clipper-config --cflags`
111 -+CLIPPER_LDOPTS=`clipper-config --libs`
112 -+
113 - AC_MSG_CHECKING([for Clipper])
114 -
115 - LIBS="$save_LIBS $CLIPPER_LDOPTS"
116
117 diff --git a/sci-chemistry/coot/files/9999-goocanvas.patch b/sci-chemistry/coot/files/9999-goocanvas.patch
118 deleted file mode 100644
119 index ce0d4a0..0000000
120 --- a/sci-chemistry/coot/files/9999-goocanvas.patch
121 +++ /dev/null
122 @@ -1,25 +0,0 @@
123 -Index: macros/goo-canvas.m4
124 -===================================================================
125 ---- macros/goo-canvas.m4 (revision 3307)
126 -+++ macros/goo-canvas.m4 (working copy)
127 -@@ -56,9 +56,9 @@
128 - fi
129 - fi
130 -
131 --AC_MSG_CHECKING([for Goocanvas])
132 -+PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
133 -
134 --LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
135 -+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
136 - CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
137 - #
138 - # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
139 -@@ -76,7 +76,7 @@
140 - if test x$have_goocanvas = xyes; then
141 -
142 - GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
143 -- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
144 -+ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
145 -
146 - ifelse([$1], , :, [$1])
147 -
148
149 diff --git a/sci-chemistry/coot/files/9999-mmdb-config.patch b/sci-chemistry/coot/files/9999-mmdb-config.patch
150 deleted file mode 100644
151 index b3b66ab..0000000
152 --- a/sci-chemistry/coot/files/9999-mmdb-config.patch
153 +++ /dev/null
154 @@ -1,18 +0,0 @@
155 -Index: macros/mmdb.m4
156 -===================================================================
157 ---- macros/mmdb.m4 (revision 3579)
158 -+++ macros/mmdb.m4 (working copy)
159 -@@ -86,8 +86,12 @@
160 - ac_MMDB_LDOPTS="-lmmdb -lm"
161 - fi
162 -
163 --AC_MSG_CHECKING([for MMDB])
164 -+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
165 -+ac_MMDB_LDOPTS="${MMDB_LIBS}"
166 -+ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
167 -
168 -+AC_MSG_CHECKING([for CISPEP in MMDB])
169 -+
170 - LIBS="$save_LIBS $ac_MMDB_LDOPTS"
171 - CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
172 - #
173
174 diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
175 new file mode 100644
176 index 0000000..a6bc18e
177 --- /dev/null
178 +++ b/sci-chemistry/coot/files/9999-pc.patch
179 @@ -0,0 +1,1040 @@
180 +Index: ChangeLog
181 +===================================================================
182 +--- ChangeLog (revision 4651)
183 ++++ ChangeLog (working copy)
184 +@@ -1959,7 +1959,7 @@
185 + 2005-01-29 Paul Emsley <paulemsley@××××××××××××.uk>
186 +
187 + * macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in
188 +- MMDBSSM_CXXFLAGS [Oops]. Hopefully fixes problems spotted by Joel
189 ++ MMDBSSM_CFLAGS [Oops]. Hopefully fixes problems spotted by Joel
190 + Bard and Joseph Toth.
191 +
192 + * src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add
193 +@@ -2252,14 +2252,14 @@
194 +
195 + 2004-11-20 Paul Emsley <paulemsley@××××××××××××.uk>
196 +
197 +- * coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for
198 ++ * coords/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS [for
199 + coot-close.cc usage].
200 +
201 + 2004-11-19 Paul Emsley <paulemsley@××××××××××××.uk>
202 +
203 +- * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS
204 ++ * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CFLAGS
205 +
206 +- * analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS
207 ++ * analysis/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS
208 +
209 + 2004-11-16 Paul Emsley <emsley@localhost>
210 +
211 +@@ -2269,7 +2269,7 @@
212 +
213 + 2004-11-15 Paul Emsley <emsley@localhost>
214 +
215 +- * coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks
216 ++ * coot-utils/Makefile.am: add MMDB_CFLAGS to INCLUDE [thanks
217 + Joseph Toth].
218 +
219 + * surface/CXXSphereNode.h: removed the ; again!
220 +Index: analysis/Makefile.am
221 +===================================================================
222 +--- analysis/Makefile.am (revision 4651)
223 ++++ analysis/Makefile.am (working copy)
224 +@@ -11,8 +11,8 @@
225 + -I$(top_srcdir)/coot-utils \
226 + -I$(top_srcdir)/mini-mol \
227 + -I$(top_srcdir)/utils \
228 +- $(CLIPPER_CXXFLAGS) \
229 +- $(MMDB_CXXFLAGS)
230 ++ $(CLIPPER_CFLAGS) \
231 ++ $(MMDB_CFLAGS)
232 +
233 + libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc
234 +
235 +Index: angles/Makefile.am
236 +===================================================================
237 +--- angles/Makefile.am (revision 4651)
238 ++++ angles/Makefile.am (working copy)
239 +@@ -6,7 +6,7 @@
240 +
241 + include_HEADERS = AngleInfo.h ncube.h wrapped-ncube.h
242 +
243 +-INCLUDES = $(CLIPPER_CXXFLAGS)
244 ++INCLUDES = $(CLIPPER_CFLAGS)
245 +
246 + libcoot_AngleInfo_a_sources = AngleInfo.cc AngleInfo.h \
247 + AngleInfo-angle-torsions-autogen.cc AngleInfo-theta_2-autogen.cc
248 +Index: auxil/catcheck/Makefile.am
249 +===================================================================
250 +--- auxil/catcheck/Makefile.am (revision 4651)
251 ++++ auxil/catcheck/Makefile.am (working copy)
252 +@@ -1,7 +1,7 @@
253 +
254 + EXTRA_DIST = Makefile.simple
255 +
256 +-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
257 ++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
258 +
259 + check_PROGRAMS = catcheck
260 +
261 +Index: auxil/catcheck/Makefile.simple
262 +===================================================================
263 +--- auxil/catcheck/Makefile.simple (revision 4651)
264 ++++ auxil/catcheck/Makefile.simple (working copy)
265 +@@ -1,17 +1,17 @@
266 +
267 +-# CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
268 ++# CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
269 +
270 +
271 + BASE = /home/paule/autobuild/Linux-kalypso-pre-release
272 +-CLIPPER_CXXFLAGS = -I$(BASE)/include
273 +-MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
274 ++CLIPPER_CFLAGS = -I$(BASE)/include
275 ++MMDB_CFLAGS = -I$(BASE)/include/mmdb
276 +
277 + CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
278 + -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
279 + -lclipper-core -lccp4c -L$(BASE)/lib \
280 + -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
281 +
282 +-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
283 ++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
284 + LDLIBS = $(CLIPPER_LIBS)
285 +
286 + catcheck: catcheck.cc catcheck.hh
287 +Index: auxil/rama/Makefile.am
288 +===================================================================
289 +--- auxil/rama/Makefile.am (revision 4651)
290 ++++ auxil/rama/Makefile.am (working copy)
291 +@@ -1,7 +1,7 @@
292 +
293 + EXTRA_DIST = Makefile.simple fit-rama.scm run.scm test-arr.scm
294 +
295 +-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
296 ++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
297 +
298 +
299 + check_PROGRAMS = rama-data rama-doughnut
300 +Index: auxil/rama/Makefile.simple
301 +===================================================================
302 +--- auxil/rama/Makefile.simple (revision 4651)
303 ++++ auxil/rama/Makefile.simple (working copy)
304 +@@ -1,12 +1,12 @@
305 +
306 +-CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
307 ++CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
308 +
309 + CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
310 + -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
311 + -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
312 + -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
313 +
314 +-INCLUDES = $(CLIPPER_CXXFLAGS)
315 ++INCLUDES = $(CLIPPER_CFLAGS)
316 + LDLIBS = $(CLIPPER_LIBS)
317 +
318 + rama-data: rama-data.cc
319 +Index: auxil/sec-str/Makefile.am
320 +===================================================================
321 +--- auxil/sec-str/Makefile.am (revision 4651)
322 ++++ auxil/sec-str/Makefile.am (working copy)
323 +@@ -1,6 +1,6 @@
324 +
325 + EXTRA_DIST = Makefile.simple sec-str-dist-check.cc sec-str-dist-check.hh
326 +-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
327 ++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
328 +
329 + #check_PROGRAMS = sec-str-dist-check
330 +
331 +Index: auxil/sec-str/Makefile.simple
332 +===================================================================
333 +--- auxil/sec-str/Makefile.simple (revision 4651)
334 ++++ auxil/sec-str/Makefile.simple (working copy)
335 +@@ -1,27 +1,27 @@
336 +
337 +-#CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
338 ++#CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
339 +
340 + #CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
341 + # -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
342 + # -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
343 + # -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
344 +
345 +-#INCLUDES = $(CLIPPER_CXXFLAGS)
346 ++#INCLUDES = $(CLIPPER_CFLAGS)
347 + #LDLIBS = $(CLIPPER_LIBS)
348 +
349 +
350 + #
351 +
352 + BASE = /home/paule/autobuild/Linux-kalypso-pre-release
353 +-CLIPPER_CXXFLAGS = -I$(BASE)/include
354 +-MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
355 ++CLIPPER_CFLAGS = -I$(BASE)/include
356 ++MMDB_CFLAGS = -I$(BASE)/include/mmdb
357 +
358 + CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
359 + -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
360 + -lclipper-core -lccp4c -L$(BASE)/lib \
361 + -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
362 +
363 +-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
364 ++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
365 + LDLIBS = $(CLIPPER_LIBS)
366 +
367 + sec-str-dist-check: sec-str-dist-check.cc sec-str-dist-check.hh
368 +Index: auxil/strand-analysis/Makefile.am
369 +===================================================================
370 +--- auxil/strand-analysis/Makefile.am (revision 4651)
371 ++++ auxil/strand-analysis/Makefile.am (working copy)
372 +@@ -3,8 +3,8 @@
373 +
374 +
375 + INCLUDES = -I$(top_srcdir)/auxil/sec-str \
376 +- $(MMDB_CXXFLAGS) \
377 +- $(CLIPPER_CXXFLAGS)
378 ++ $(MMDB_CFLAGS) \
379 ++ $(CLIPPER_CFLAGS)
380 +
381 +
382 + check_PROGRAMS =
383 +Index: auxil/strand-analysis/Makefile.simple
384 +===================================================================
385 +--- auxil/strand-analysis/Makefile.simple (revision 4651)
386 ++++ auxil/strand-analysis/Makefile.simple (working copy)
387 +@@ -2,13 +2,13 @@
388 +
389 + CLIPPER = /Users/paulemsley/ccp4/ysbl-distro-based
390 +
391 +-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include
392 ++CLIPPER_CFLAGS = -I$(CLIPPER)/include
393 +
394 + CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-ccp4 \
395 + -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
396 + -lclipper-core -lccp4c -lmmdb -lm -lrfftw -lfftw -lz -lm
397 +
398 +-INCLUDES = -I../sec-str $(CLIPPER_CXXFLAGS)
399 ++INCLUDES = -I../sec-str $(CLIPPER_CFLAGS)
400 + LDLIBS = $(CLIPPER_LIBS)
401 +
402 + .cc:
403 +Index: auxil/vectors/Makefile.am
404 +===================================================================
405 +--- auxil/vectors/Makefile.am (revision 4651)
406 ++++ auxil/vectors/Makefile.am (working copy)
407 +@@ -1,6 +1,6 @@
408 +
409 + EXTRA_DIST = Makefile.simple diff-vec.cc
410 +-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
411 ++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
412 + check_PROGRAMS =
413 +
414 + #diff_vec_SOURCES = diff-vec.cc
415 +Index: build/Makefile.am
416 +===================================================================
417 +--- build/Makefile.am (revision 4651)
418 ++++ build/Makefile.am (working copy)
419 +@@ -24,8 +24,8 @@
420 +
421 + INCLUDES = \
422 + -I$(top_srcdir)/angles \
423 +- $(CLIPPER_CXXFLAGS) \
424 +- $(MMDB_CXXFLAGS)
425 ++ $(CLIPPER_CFLAGS) \
426 ++ $(MMDB_CFLAGS)
427 +
428 + noinst_PROGRAMS = testcabuild
429 +
430 +Index: ccp4mg-utils/Makefile.am
431 +===================================================================
432 +--- ccp4mg-utils/Makefile.am (revision 4651)
433 ++++ ccp4mg-utils/Makefile.am (working copy)
434 +@@ -25,7 +25,7 @@
435 + EXTRA_DIST = convert.sh get-new-utils.sh
436 +
437 + INCLUDES = \
438 +- $(MMDB_CXXFLAGS) \
439 ++ $(MMDB_CFLAGS) \
440 + $(LIBPNG_CFLAGS)
441 +
442 + libccp4mg_utils_la_SOURCES = geomutil.cc mgtree.cc cartesian.cc \
443 +Index: ccp4mg-utils/mmut/Makefile.am
444 +===================================================================
445 +--- ccp4mg-utils/mmut/Makefile.am (revision 4651)
446 ++++ ccp4mg-utils/mmut/Makefile.am (working copy)
447 +@@ -70,9 +70,9 @@
448 + $(LIBGLADE_CFLAGS) \
449 + @GTK_CFLAGS@ \
450 + $(GLUT_CFLAGS) \
451 +- $(MMDBSSM_CXXFLAGS) \
452 +- $(MMDB_CXXFLAGS) \
453 +- $(CLIPPER_CXXFLAGS)
454 ++ $(MMDBSSM_CFLAGS) \
455 ++ $(MMDB_CFLAGS) \
456 ++ $(CLIPPER_CFLAGS)
457 +
458 + # $(WITH_SCRIPT_CFLAGS)
459 +
460 +Index: ccp4mg-utils/pygl/Makefile.am
461 +===================================================================
462 +--- ccp4mg-utils/pygl/Makefile.am (revision 4651)
463 ++++ ccp4mg-utils/pygl/Makefile.am (working copy)
464 +@@ -108,9 +108,9 @@
465 + $(LIBGLADE_CFLAGS) \
466 + @GTK_CFLAGS@ \
467 + $(GLUT_CFLAGS) \
468 +- $(MMDBSSM_CXXFLAGS) \
469 +- $(MMDB_CXXFLAGS) \
470 +- $(CLIPPER_CXXFLAGS)
471 ++ $(MMDBSSM_CFLAGS) \
472 ++ $(MMDB_CFLAGS) \
473 ++ $(CLIPPER_CFLAGS)
474 +
475 + # $(WITH_SCRIPT_CFLAGS)
476 +
477 +Index: ccp4mg-utils/util/Makefile.am
478 +===================================================================
479 +--- ccp4mg-utils/util/Makefile.am (revision 4651)
480 ++++ ccp4mg-utils/util/Makefile.am (working copy)
481 +@@ -73,9 +73,9 @@
482 + $(LIBGLADE_CFLAGS) \
483 + @GTK_CFLAGS@ \
484 + $(GLUT_CFLAGS) \
485 +- $(MMDBSSM_CXXFLAGS) \
486 +- $(MMDB_CXXFLAGS) \
487 +- $(CLIPPER_CXXFLAGS)
488 ++ $(MMDBSSM_CFLAGS) \
489 ++ $(MMDB_CFLAGS) \
490 ++ $(CLIPPER_CFLAGS)
491 +
492 + # $(WITH_SCRIPT_CFLAGS)
493 +
494 +Index: configure.in
495 +===================================================================
496 +--- configure.in (revision 4651)
497 ++++ configure.in (working copy)
498 +@@ -108,14 +108,18 @@
499 +
500 +
501 + dnl Check for MMDB.
502 +-AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
503 ++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2],,[AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)])
504 +
505 +-AM_WITH_MMDBSSM
506 ++PKG_CHECK_MODULES([MMDBSSM],[ssm],,[AM_WITH_MMDBSSM])
507 + AM_WITH_CCP4SRS
508 +
509 + dnl Check for Clipper. we exit if clipper is not found.
510 + #
511 +-AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
512 ++PKG_CHECK_MODULES([CLIPPER], [clipper libccp4c], [
513 ++ CLIPPER_LIBS="${CLIPPER_LIBS} -lrfftw -lfftw"; AC_SUBST([CLIPPER_LIBS])
514 ++ ], [
515 ++ AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
516 ++ ])
517 +
518 + # we set default coot_guile to true
519 + coot_guile=true
520 +@@ -189,11 +193,15 @@
521 +
522 + dnl =========================== GooCanvas ================================
523 +
524 +-AM_PATH_GOOCANVAS
525 +-# give something for the preprocessor to chew on...
526 +-if test "$GOOCANVAS_CFLAGS" != "" ; then
527 +- GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
528 +-fi
529 ++PKG_CHECK_MODULES([GOOCANVAS], [goocanvas],
530 ++ [GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"; AC_SUBST(GOOCANVAS_CFLAGS)],
531 ++ [
532 ++ AM_PATH_GOOCANVAS
533 ++ # give something for the preprocessor to chew on...
534 ++ if test "$GOOCANVAS_CFLAGS" != "" ; then
535 ++ GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
536 ++ fi
537 ++ ])
538 +
539 + AC_ARG_WITH(enterprise-tools, [ --with-enterprise-tools with optional complicated/experimental ligand-related dependencies ],
540 + coot_enterprise_additions="true",
541 +Index: coords/Makefile.am
542 +===================================================================
543 +--- coords/Makefile.am (revision 4651)
544 ++++ coords/Makefile.am (working copy)
545 +@@ -34,7 +34,7 @@
546 + -I$(top_srcdir)/compat \
547 + $(ENTERPRISE_TOOLS_CFLAGS) \
548 + $(RDKIT_CXXFLAGS) \
549 +- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
550 ++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
551 +
552 + AM_CXXFLAGS = \
553 + -DPKGDATADIR='"$(pkgdatadir)"' \
554 +Index: coot-surface/Makefile.am
555 +===================================================================
556 +--- coot-surface/Makefile.am (revision 4651)
557 ++++ coot-surface/Makefile.am (working copy)
558 +@@ -21,7 +21,7 @@
559 + INCLUDES = -I$(top_srcdir)/surface \
560 + -I$(top_srcdir)/coot-utils \
561 + -I$(top_srcdir)/mini-mol \
562 +- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
563 ++ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
564 +
565 + lib_LTLIBRARIES = libcoot-surface.la
566 +
567 +Index: coot-utils/Makefile.am
568 +===================================================================
569 +--- coot-utils/Makefile.am (revision 4651)
570 ++++ coot-utils/Makefile.am (working copy)
571 +@@ -38,8 +38,8 @@
572 + -I$(top_srcdir)/geometry \
573 + -I$(top_srcdir)/compat \
574 + -I$(top_srcdir)/mini-mol \
575 +- $(CLIPPER_CXXFLAGS) \
576 +- $(MMDB_CXXFLAGS) \
577 ++ $(CLIPPER_CFLAGS) \
578 ++ $(MMDB_CFLAGS) \
579 + $(GSL_CFLAGS) \
580 + $(WITH_GUILE_CFLAGS) \
581 + $(WITH_PYTHON_CFLAGS)
582 +Index: cootaneer/Makefile.am
583 +===================================================================
584 +--- cootaneer/Makefile.am (revision 4651)
585 ++++ cootaneer/Makefile.am (working copy)
586 +@@ -20,7 +20,7 @@
587 + EXTRA_DIST = \
588 + cootaneer-llk-2.40.dat
589 +
590 +-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
591 ++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
592 +
593 + cootaneer_demo_SOURCES = cootaneer-demo.cpp
594 +
595 +Index: cootilus/Makefile.am
596 +===================================================================
597 +--- cootilus/Makefile.am (revision 4651)
598 ++++ cootilus/Makefile.am (working copy)
599 +@@ -20,7 +20,7 @@
600 + EXTRA_DIST = \
601 + nautilus_lib.pdb
602 +
603 +-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
604 ++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
605 +
606 + cootilus_demo_SOURCES = cootilus-demo.cpp
607 +
608 +Index: db-main/Makefile.am
609 +===================================================================
610 +--- db-main/Makefile.am (revision 4651)
611 ++++ db-main/Makefile.am (working copy)
612 +@@ -6,7 +6,7 @@
613 + -DDATADIR='"$(datadir)"'
614 +
615 + INCLUDES = -I$(top_srcdir)/utils -I$(top_srcdir)/coot-utils -I$(top_srcdir)/mini-mol \
616 +- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
617 ++ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
618 +
619 + include_HEADERS = db-main.hh db-strands.hh
620 +
621 +Index: db-main/Makefile.simple
622 +===================================================================
623 +--- db-main/Makefile.simple (revision 4651)
624 ++++ db-main/Makefile.simple (working copy)
625 +@@ -19,7 +19,7 @@
626 + MCCP4 = $(HOME)/crystal
627 +
628 + CXX = g++
629 +-MMDB_CXXFLAGS = -I$(MMDB)/include
630 ++MMDB_CFLAGS = -I$(MMDB)/include
631 + FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
632 +
633 + MMDB_LIBS = -L$(MMDB)/lib -lmmdb
634 +@@ -28,9 +28,9 @@
635 + -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
636 +
637 + MCCP4_CFLAGS = -I$(MCCP4)/include
638 +-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
639 ++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
640 +
641 +-INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
642 ++INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
643 +
644 + CXXFLAGS = -g $(INCLUDES)
645 + LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS)
646 +@@ -44,4 +44,4 @@
647 + db-main.o: db-main.cc db-main.hh
648 +
649 + testmmdbbits: testmmdbbits.cc
650 +- $(CXX) $(MMDB_CXXFLAGS) $(MMDB_LIBS) $? -o $@
651 ++ $(CXX) $(MMDB_CFLAGS) $(MMDB_LIBS) $? -o $@
652 +Index: density-contour/Makefile.am
653 +===================================================================
654 +--- density-contour/Makefile.am (revision 4651)
655 ++++ density-contour/Makefile.am (working copy)
656 +@@ -20,7 +20,7 @@
657 +
658 + COORD_INCLUDES = -I$(top_srcdir)/coords
659 +
660 +-INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CXXFLAGS)
661 ++INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CFLAGS)
662 +
663 + lib_LTLIBRARIES = libcoot-isosurface.la
664 +
665 +Index: geometry/Makefile.am
666 +===================================================================
667 +--- geometry/Makefile.am (revision 4651)
668 ++++ geometry/Makefile.am (working copy)
669 +@@ -29,7 +29,7 @@
670 + -I$(top_srcdir)/mini-mol \
671 + -I$(top_srcdir)/coot-utils \
672 + -I$(top_srcdir)/compat \
673 +- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS)
674 ++ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS)
675 +
676 + AM_CXXFLAGS = \
677 + -DDATADIR='"$(datadir)"' \
678 +Index: geometry/Makefile.simple
679 +===================================================================
680 +--- geometry/Makefile.simple (revision 4651)
681 ++++ geometry/Makefile.simple (working copy)
682 +@@ -46,7 +46,7 @@
683 +
684 +
685 + CXX = g++
686 +-MMDB_CXXFLAGS = -I$(MMDB)/include
687 ++MMDB_CFLAGS = -I$(MMDB)/include
688 + FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
689 +
690 + MMDB_LIBS = -L$(MMDB)/lib -lmmdb
691 +@@ -55,9 +55,9 @@
692 + -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
693 +
694 + MCCP4_CFLAGS = -I$(MCCP4)/include
695 +-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
696 ++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
697 +
698 +-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -I$(top_srcdir)/coords
699 ++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/coords
700 +
701 + top_srcdir = ..
702 +
703 +Index: high-res/Makefile.am
704 +===================================================================
705 +--- high-res/Makefile.am (revision 4651)
706 ++++ high-res/Makefile.am (working copy)
707 +@@ -36,8 +36,8 @@
708 + -I$(top_srcdir)/coot-utils \
709 + -I$(top_srcdir)/lidia-core \
710 + -I$(top_srcdir)/compat \
711 +- $(MMDB_CXXFLAGS) \
712 +- $(CLIPPER_CXXFLAGS)
713 ++ $(MMDB_CFLAGS) \
714 ++ $(CLIPPER_CFLAGS)
715 +
716 + libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
717 + sequence-assignment.cc
718 +Index: ideal/Makefile.am
719 +===================================================================
720 +--- ideal/Makefile.am (revision 4651)
721 ++++ ideal/Makefile.am (working copy)
722 +@@ -37,11 +37,11 @@
723 + -I$(top_srcdir)/coot-utils \
724 + -I$(top_srcdir)/mini-mol \
725 + -I$(top_srcdir)/geometry \
726 +- $(CLIPPER_CXXFLAGS) \
727 +- $(MMDB_CXXFLAGS)
728 ++ $(CLIPPER_CFLAGS) \
729 ++ $(MMDB_CFLAGS)
730 +
731 + AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) $(COOT_WINDOWS_CFLAGS) \
732 +- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) $(COOT_GSL_FLAGS)
733 ++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) $(COOT_GSL_FLAGS)
734 + AM_LDFLAGS = $(GSL_LIBS) $(MMDB_LIBS) $(CLIPPER_LIBS)
735 +
736 +
737 +Index: ideal/Makefile.simple
738 +===================================================================
739 +--- ideal/Makefile.simple (revision 4651)
740 ++++ ideal/Makefile.simple (working copy)
741 +@@ -44,7 +44,7 @@
742 +
743 +
744 + CXX = g++
745 +-MMDB_CXXFLAGS = -I$(MMDB)/include
746 ++MMDB_CFLAGS = -I$(MMDB)/include
747 + FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
748 +
749 + MMDB_LIBS = -L$(MMDB)/lib -lmmdb
750 +@@ -53,9 +53,9 @@
751 + -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
752 +
753 + MCCP4_CFLAGS = -I$(MCCP4)/include
754 +-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
755 ++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
756 +
757 +-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) \
758 ++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) \
759 + -I$(top_srcdir)/coords \
760 + -I$(top_srcdir)/geometry
761 +
762 +Index: lbg/Makefile.am
763 +===================================================================
764 +--- lbg/Makefile.am (revision 4651)
765 ++++ lbg/Makefile.am (working copy)
766 +@@ -11,7 +11,7 @@
767 + $(GSL_CFLAGS) \
768 + $(GOOCANVAS_CFLAGS) \
769 + $(GTK_CFLAGS) \
770 +- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \
771 ++ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \
772 + $(COOT_WINDOWS_CFLAGS) \
773 + $(ENTERPRISE_TOOLS_CFLAGS) \
774 + $(RDKIT_CXXFLAGS) \
775 +Index: lbg/Makefile.simple
776 +===================================================================
777 +--- lbg/Makefile.simple (revision 4651)
778 ++++ lbg/Makefile.simple (working copy)
779 +@@ -24,11 +24,11 @@
780 + MMDB=$(CRYST)
781 + # MMDB=$(HOME)/test/mmdb
782 +
783 +-MMDB_CXXFLAGS=-I$(MMDB)/include/mmdb
784 ++MMDB_CFLAGS=-I$(MMDB)/include/mmdb
785 + MMDB_LDFLAGS=$(MMDB)/lib/libmmdb.la
786 +
787 + CLIPPER=$(CRYST)
788 +-CLIPPER_CXXFLAGS=-I$(CLIPPER)/include
789 ++CLIPPER_CFLAGS=-I$(CLIPPER)/include
790 + CLIPPER_LDFLAGS=$(CLIPPER)/lib/libclipper-core.la \
791 + $(CLIPPER)/lib/librfftw.la \
792 + $(CLIPPER)/lib/libfftw.la
793 +@@ -40,7 +40,7 @@
794 + LIDIA_CORE_LDFLAGS = $(COOT_INSTALLED)/lib/libcoot-lidia-core.la
795 +
796 +
797 +-CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(LIDIA_CORE_CXXFLAGS) \
798 ++CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(LIDIA_CORE_CXXFLAGS) \
799 + -I$(top_srcdir)/compat
800 +
801 + lbg: lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o
802 +Index: lidia-core/Makefile.am
803 +===================================================================
804 +--- lidia-core/Makefile.am (revision 4651)
805 ++++ lidia-core/Makefile.am (working copy)
806 +@@ -22,7 +22,7 @@
807 +
808 + # 20110408 I add a CResidue,dictionary_residue_restraints_t constructor to molfile_molecule_t
809 + # simple
810 +-#INCLUDES = $(CLIPPER_CXXFLAGS)
811 ++#INCLUDES = $(CLIPPER_CFLAGS)
812 + #
813 + INCLUDES = \
814 + -I$(top_srcdir)/geometry \
815 +@@ -31,7 +31,7 @@
816 + -I$(top_srcdir)/utils \
817 + $(ENTERPRISE_TOOLS_CFLAGS) \
818 + $(RDKIT_CXXFLAGS) \
819 +- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
820 ++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
821 +
822 + libcoot_lidia_core_la_SOURCES = lbg-shared.cc lbg-molfile.cc lig-build.cc rdkit-interface.cc \
823 + cod-types.cc
824 +Index: ligand/Makefile.am
825 +===================================================================
826 +--- ligand/Makefile.am (revision 4651)
827 ++++ ligand/Makefile.am (working copy)
828 +@@ -36,7 +36,7 @@
829 + -I$(top_srcdir)/db-main \
830 + $(COOT_GSL_FLAGS) \
831 + $(GSL_CFLAGS) \
832 +- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
833 ++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
834 +
835 + include_HEADERS = ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh \
836 + chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh \
837 +Index: macros/clipper.m4
838 +===================================================================
839 +--- macros/clipper.m4 (revision 4651)
840 ++++ macros/clipper.m4 (working copy)
841 +@@ -56,7 +56,7 @@
842 + #
843 + # should use clipper-config --cflags
844 + #
845 +- CLIPPER_CXXFLAGS="-I$clipper_prefix/include"
846 ++ CLIPPER_CFLAGS="-I$clipper_prefix/include"
847 + # -I$clipper_prefix/cctbx
848 +
849 + # yes, libmmtz.a is in -L$clipper_prefix/umtz!
850 +@@ -75,7 +75,7 @@
851 + #
852 + ccp4c=ccp4c
853 +
854 +- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
855 ++ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
856 + # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx
857 +
858 +
859 +@@ -102,8 +102,8 @@
860 + # this needs to be 'configured' - typically either s or blank.
861 + fftw_pre=
862 +
863 +- CLIPPER_CXXFLAGS="$CCP4_CFLAGS"
864 +- CLIPPER_LDOPTS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
865 ++ CLIPPER_CFLAGS="$CCP4_CFLAGS"
866 ++ CLIPPER_LIBS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
867 + fi
868 +
869 + # BL: workaround needed for new MinGW
870 +@@ -113,17 +113,17 @@
871 + case $ac_cv_build_alias in
872 + # BL says:: same as for cygwin in mingw
873 + MINGW*|Mingw*|*mingw*|Cygwin*|CYGWIN*|*cygwin*)
874 +- CLIPPER_LDOPTS=$CLIPPER_LDOPTS
875 ++ CLIPPER_LIBS=$CLIPPER_LIBS
876 + ;;
877 + *)
878 +- CLIPPER_LDOPTS=$CLIPPER_LDOPTS" -lpthread"
879 ++ CLIPPER_LIBS=$CLIPPER_LIBS" -lpthread"
880 + ;;
881 + esac
882 +
883 + AC_MSG_CHECKING([for Clipper])
884 +
885 +- LIBS="$save_LIBS $CLIPPER_LDOPTS"
886 +- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
887 ++ LIBS="$save_LIBS $CLIPPER_LIBS"
888 ++ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
889 + # AC_TRY_LINK uses the c compiler, so we will temporarily
890 + # reassign $CC to the c++ compiler.
891 + #
892 +@@ -140,7 +140,7 @@
893 +
894 + LIBS="$saved_LIBS"
895 + CFLAGS="$saved_CFLAGS"
896 +- CLIPPER_LIBS="$CLIPPER_LDOPTS"
897 ++ CLIPPER_LIBS="$CLIPPER_LIBS"
898 + ifelse([$1], , :, [$1])
899 +
900 + else
901 +@@ -148,12 +148,12 @@
902 + LIBS="$saved_LIBS"
903 + CFLAGS="$saved_CFLAGS"
904 + CLIPPER_LIBS=""
905 +- CLIPPER_CXXFLAGS=""
906 ++ CLIPPER_CFLAGS=""
907 + ifelse([$2], , :, [$2])
908 +
909 + fi
910 +
911 +-AC_SUBST(CLIPPER_CXXFLAGS)
912 ++AC_SUBST(CLIPPER_CFLAGS)
913 + AC_SUBST(CLIPPER_LIBS)
914 +
915 + ])
916 +Index: macros/clipper.m4.old
917 +===================================================================
918 +--- macros/clipper.m4.old (revision 4651)
919 ++++ macros/clipper.m4.old (working copy)
920 +@@ -34,7 +34,7 @@
921 + # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like
922 + # when clipper and dependencies get installed.
923 + #
924 +- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
925 ++ CLIPPER_CFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
926 + # -I$clipper_prefix/cctbx
927 +
928 + # yes, libmmtz.a is in -L$clipper_prefix/umtz!
929 +@@ -45,20 +45,20 @@
930 + # HACK! FIXME
931 + # added lz, we should have proper autoconf check for this.
932 + #
933 +- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
934 ++ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
935 + # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx
936 + else
937 + # the compiler looks in the "standard" places for clipper. In real life,
938 + # it would be quite unlikely that clipper would be installed in /usr/include,
939 + # /usr/lib etc. so this code will not usually find the right dependencies.
940 +- CLIPPER_CXXFLAGS=""
941 +- CLIPPER_LDOPTS=""
942 ++ CLIPPER_CFLAGS=""
943 ++ CLIPPER_LIBS=""
944 + fi
945 +
946 + AC_MSG_CHECKING([for Clipper])
947 +
948 +- LIBS="$save_LIBS $CLIPPER_LDOPTS"
949 +- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
950 ++ LIBS="$save_LIBS $CLIPPER_LIBS"
951 ++ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
952 + # AC_TRY_LINK uses the c compiler, so we will temporarily
953 + # reassign $CC to the c++ compiler.
954 + #
955 +@@ -72,7 +72,7 @@
956 +
957 + LIBS="$saved_LIBS"
958 + CFLAGS="$saved_CFLAGS"
959 +- CLIPPER_LIBS="$CLIPPER_LDOPTS"
960 ++ CLIPPER_LIBS="$CLIPPER_LIBS"
961 + ifelse([$1], , :, [$1])
962 +
963 + else
964 +@@ -80,12 +80,12 @@
965 + LIBS="$saved_LIBS"
966 + CFLAGS="$saved_CFLAGS"
967 + CLIPPER_LIBS=""
968 +- CLIPPER_CXXFLAGS=""
969 ++ CLIPPER_CFLAGS=""
970 + ifelse([$2], , :, [$2])
971 +
972 + fi
973 +
974 +-AC_SUBST(CLIPPER_CXXFLAGS)
975 ++AC_SUBST(CLIPPER_CFLAGS)
976 + AC_SUBST(CLIPPER_LIBS)
977 +
978 + ])
979 +Index: macros/goo-canvas.m4
980 +===================================================================
981 +--- macros/goo-canvas.m4 (revision 4651)
982 ++++ macros/goo-canvas.m4 (working copy)
983 +@@ -36,9 +36,9 @@
984 + # GCC c++ does not.
985 + #
986 + if test -e $goocanvas_prefix/lib/libgoocanvas.la ; then
987 +- GOOCANVAS_LDOPTS="$goocanvas_prefix/lib/libgoocanvas.la"
988 ++ GOOCANVAS_LIBS="$goocanvas_prefix/lib/libgoocanvas.la"
989 + else
990 +- GOOCANVAS_LDOPTS="-L$goocanvas_prefix/lib -lgoocanvas"
991 ++ GOOCANVAS_LIBS="-L$goocanvas_prefix/lib -lgoocanvas"
992 + fi
993 + else
994 + # the compiler looks in the "standard" places for GOOCANVAS. (or uses pkgconfig)
995 +@@ -57,19 +57,19 @@
996 + break;;
997 + esac
998 + if test -e /usr/lib/libgoocanvas.la ; then
999 +- GOOCANVAS_LDOPTS="libgoocanvas.la"
1000 ++ GOOCANVAS_LIBS="libgoocanvas.la"
1001 + else
1002 + if test -z "${PKG_CONFIG}"; then
1003 +- GOOCANVAS_LDOPTS="-lgoocanvas"
1004 ++ GOOCANVAS_LIBS="-lgoocanvas"
1005 + else
1006 +- GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs`
1007 ++ GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs`
1008 + fi
1009 + fi
1010 + fi
1011 +
1012 + AC_MSG_CHECKING([for Goocanvas])
1013 +
1014 +-LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
1015 ++LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
1016 + CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
1017 + #
1018 + # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
1019 +@@ -95,7 +95,7 @@
1020 + if test x$have_goocanvas = xyes; then
1021 +
1022 + GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
1023 +- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
1024 ++ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
1025 +
1026 + ifelse([$1], , :, [$1])
1027 +
1028 +Index: macros/mmdb-ssm.m4
1029 +===================================================================
1030 +--- macros/mmdb-ssm.m4 (revision 4651)
1031 ++++ macros/mmdb-ssm.m4 (working copy)
1032 +@@ -32,7 +32,7 @@
1033 +
1034 + if test x$with_ssmlib_prefix != x; then
1035 +
1036 +- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
1037 ++ MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
1038 + MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
1039 +
1040 + ac_mmdb_dirs='
1041 +@@ -47,16 +47,16 @@
1042 +
1043 + for ac_dir in $ac_mmdb_dirs; do
1044 + if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
1045 +- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
1046 ++ ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/$ac_dir"
1047 + break
1048 + fi
1049 + done
1050 +
1051 +- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
1052 ++ MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
1053 +
1054 + else
1055 +
1056 +- MMDBSSM_CXXFLAGS=""
1057 ++ MMDBSSM_CFLAGS=""
1058 + MMDBSSM_LIBS=""
1059 + with_ssmlib_prefix=no
1060 +
1061 +@@ -64,6 +64,6 @@
1062 +
1063 + AC_MSG_RESULT([$with_ssmlib_prefix])
1064 +
1065 +-AC_SUBST(MMDBSSM_CXXFLAGS)
1066 ++AC_SUBST(MMDBSSM_CFLAGS)
1067 + AC_SUBST(MMDBSSM_LIBS)
1068 + ])
1069 +Index: macros/mmdb.m4
1070 +===================================================================
1071 +--- macros/mmdb.m4 (revision 4651)
1072 ++++ macros/mmdb.m4 (working copy)
1073 +@@ -55,7 +55,7 @@
1074 + # --with-mmdb=/some/thing
1075 + #
1076 +
1077 +- # should ideally be MMDB_CXXFLAGS="-I$MMDB_prefix/include", and the like
1078 ++ # should ideally be MMDB_CFLAGS="-I$MMDB_prefix/include", and the like
1079 + # when MMDB and dependencies get installed - we infact, include both
1080 + # directories.
1081 + #
1082 +@@ -69,7 +69,7 @@
1083 + lib/src/mmdb'
1084 + for ac_dir in $ac_mmdb_dirs; do
1085 + if test -r "$mmdb_prefix/$ac_dir/mmdb/mmdb_manager.h"; then
1086 +- ac_MMDB_CXXFLAGS="-I$mmdb_prefix/$ac_dir"
1087 ++ ac_MMDB_CFLAGS="-I$mmdb_prefix/$ac_dir"
1088 + break
1089 + fi
1090 + done
1091 +@@ -82,14 +82,14 @@
1092 + # the compiler looks in the "standard" places for MMDB. In real life,
1093 + # it would be quite unlikely that MMDB would be installed in /usr/include,
1094 + # /usr/lib etc. so this code will not usually find the right dependencies.
1095 +- ac_MMDB_CXXFLAGS=""
1096 ++ ac_MMDB_CFLAGS=""
1097 + ac_MMDB_LDOPTS="-lmmdb -lm"
1098 + fi
1099 +
1100 + AC_MSG_CHECKING([for MMDB])
1101 +
1102 + LIBS="$save_LIBS $ac_MMDB_LDOPTS"
1103 +- CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
1104 ++ CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CFLAGS"
1105 + #
1106 + # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
1107 + # temporarily reassign $CC to the c++ compiler.
1108 +@@ -118,7 +118,7 @@
1109 + CLINKR_FLAG=-DMMDB_WITHOUT_LINKR
1110 + fi
1111 + CXXFLAGS="$saved_CXXFLAGS"
1112 +- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
1113 ++ MMDB_CFLAGS="$ac_MMDB_CFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
1114 + MMDB_LIBS="$ac_MMDB_LDOPTS"
1115 + ifelse([$1], , :, [$1])
1116 +
1117 +@@ -134,12 +134,12 @@
1118 + LIBS="$saved_LIBS"
1119 + CXXFLAGS="$saved_CXXFLAGS"
1120 + MMDB_LIBS=""
1121 +- MMDB_CXXFLAGS=""
1122 ++ MMDB_CFLAGS=""
1123 + ifelse([$2], , :, [$2])
1124 +
1125 + fi
1126 +
1127 +-AC_SUBST(MMDB_CXXFLAGS)
1128 ++AC_SUBST(MMDB_CFLAGS)
1129 + AC_SUBST(MMDB_LIBS)
1130 +
1131 + ])
1132 +Index: mini-mol/Makefile.am
1133 +===================================================================
1134 +--- mini-mol/Makefile.am (revision 4651)
1135 ++++ mini-mol/Makefile.am (working copy)
1136 +@@ -25,8 +25,8 @@
1137 + INCLUDES = \
1138 + -I$(top_srcdir)/coot-utils \
1139 + -I$(top_srcdir)/compat \
1140 +- $(CLIPPER_CXXFLAGS) \
1141 +- $(MMDB_CXXFLAGS)
1142 ++ $(CLIPPER_CFLAGS) \
1143 ++ $(MMDB_CFLAGS)
1144 +
1145 + AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
1146 +
1147 +Index: protein_db/Makefile.am
1148 +===================================================================
1149 +--- protein_db/Makefile.am (revision 4651)
1150 ++++ protein_db/Makefile.am (working copy)
1151 +@@ -19,7 +19,7 @@
1152 +
1153 + lib_LTLIBRARIES=libcoot-protein-db.la
1154 +
1155 +-INCLUDES= $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
1156 ++INCLUDES= $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
1157 +
1158 + include_HEADERS=protein_db.h protein_db_utils.h rna_db.h
1159 +
1160 +Index: sequence-view/Makefile.am
1161 +===================================================================
1162 +--- sequence-view/Makefile.am (revision 4651)
1163 ++++ sequence-view/Makefile.am (working copy)
1164 +@@ -55,9 +55,9 @@
1165 + -I$(top_srcdir)/analysis \
1166 + -I$(top_srcdir)/cootaneer \
1167 + -I$(top_srcdir)/src \
1168 +- $(CLIPPER_CXXFLAGS) \
1169 +- $(MMDB_CXXFLAGS) \
1170 +- $(MMDBSSM_CXXFLAGS) \
1171 ++ $(CLIPPER_CFLAGS) \
1172 ++ $(MMDB_CFLAGS) \
1173 ++ $(MMDBSSM_CFLAGS) \
1174 + $(GLUT_CFLAGS) \
1175 + $(CANVAS_CFLAGS) \
1176 + $(GTKGL_CONTEXT_CFLAGS) \
1177 +Index: skeleton/Makefile.am
1178 +===================================================================
1179 +--- skeleton/Makefile.am (revision 4651)
1180 ++++ skeleton/Makefile.am (working copy)
1181 +@@ -28,7 +28,7 @@
1182 + -I$(top_srcdir)/angles \
1183 + -I$(top_srcdir)/coot-utils \
1184 + -I$(top_srcdir)/compat \
1185 +- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
1186 ++ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
1187 +
1188 + AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
1189 +
1190 +Index: src/Makefile.am
1191 +===================================================================
1192 +--- src/Makefile.am (revision 4651)
1193 ++++ src/Makefile.am (working copy)
1194 +@@ -220,11 +220,11 @@
1195 + $(GOOCANVAS_CFLAGS) \
1196 + @GTK_CFLAGS@ \
1197 + $(GLUT_CFLAGS) \
1198 +- $(MMDBSSM_CXXFLAGS) \
1199 +- $(MMDB_CXXFLAGS) \
1200 ++ $(MMDBSSM_CFLAGS) \
1201 ++ $(MMDB_CFLAGS) \
1202 + $(CCP4SRS_CXXFLAGS) \
1203 + $(GSL_CFLAGS) \
1204 +- $(CLIPPER_CXXFLAGS) \
1205 ++ $(CLIPPER_CFLAGS) \
1206 + $(PYGTK_CFLAGS) \
1207 + $(GLOB_CFLAGS) \
1208 + $(CURL_CFLAGS)
1209 +Index: surface/Makefile.am
1210 +===================================================================
1211 +--- surface/Makefile.am (revision 4651)
1212 ++++ surface/Makefile.am (working copy)
1213 +@@ -1,5 +1,5 @@
1214 +
1215 +-INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(FFTW_CXXFLAGS)
1216 ++INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(FFTW_CXXFLAGS)
1217 +
1218 + AM_CXXFLAGS = $(OPENMP_CFLAGS)
1219 +
1220
1221 diff --git a/sci-chemistry/coot/files/9999-ssm.patch b/sci-chemistry/coot/files/9999-ssm.patch
1222 deleted file mode 100644
1223 index c801da7..0000000
1224 --- a/sci-chemistry/coot/files/9999-ssm.patch
1225 +++ /dev/null
1226 @@ -1,56 +0,0 @@
1227 - macros/mmdb-ssm.m4 | 42 +-----------------------------------------
1228 - 1 files changed, 1 insertions(+), 41 deletions(-)
1229 -
1230 -diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
1231 -index 1937a16..6ef547c 100644
1232 ---- a/macros/mmdb-ssm.m4
1233 -+++ b/macros/mmdb-ssm.m4
1234 -@@ -22,47 +22,7 @@
1235 - AC_DEFUN([AM_WITH_MMDBSSM],
1236 - [AC_PROVIDE([AM_USE_MMDBSSM])
1237 -
1238 --
1239 --AC_ARG_WITH(ssmlib-prefix,
1240 -- AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
1241 -- [ with_ssmlib_prefix="$withval" ],
1242 -- with_ssmlib_prefix="")
1243 --
1244 --AC_MSG_CHECKING([for SSMLib])
1245 --
1246 --if test x$with_ssmlib_prefix != x; then
1247 --
1248 -- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
1249 -- MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
1250 --
1251 --ac_mmdb_dirs='
1252 --.
1253 --include
1254 --include/ssm
1255 --include/mmdb
1256 --lib
1257 --src
1258 --lib/src
1259 --lib/src/mmdb'
1260 --
1261 -- for ac_dir in $ac_mmdb_dirs; do
1262 -- if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
1263 -- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
1264 -- break
1265 -- fi
1266 -- done
1267 --
1268 -- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
1269 --
1270 --else
1271 --
1272 -- MMDBSSM_CXXFLAGS=""
1273 -- MMDBSSM_LIBS=""
1274 -- with_ssmlib_prefix=no
1275 --
1276 --fi
1277 --
1278 --AC_MSG_RESULT([$with_ssmlib_prefix])
1279 -+PKG_CHECK_MODULES([MMDBSSM],[ssm])
1280 -
1281 - AC_SUBST(MMDBSSM_CXXFLAGS)
1282 - AC_SUBST(MMDBSSM_LIBS)