Gentoo Archives: gentoo-commits

From: "Justin Lecher (jlec)" <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] gentoo-x86 commit in sci-chemistry/apbs/files/apbs-1.3: 0014-apbs-1.3-pythonlib-fix.patch 0006-apbs-1.3-clean-targets.patch 0005-apbs-1.3-linking.patch 0008-apbs-1.3-broken-test.patch 0015-apbs-1.3-pythonlib-fix.patch 0007-apbs-1.3-configure.patch 0011-apbs-1.3-shared-linking.patch 0002-python-linking.patch 0004-apbs-1.3-system-zlib.patch 0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch 0012-apbs-1.3-python-linking-correction.patch 0001-autoconf-2.68.patch 0013-apbs-1.3-tools-installation.patch 0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch 0003-apbs-1.3-pkg-config-file.patch
Date: Wed, 04 Jan 2012 17:25:36
Message-Id: 20120104172525.A9A652004B@flycatcher.gentoo.org
1 jlec 12/01/04 17:25:25
2
3 Added: 0014-apbs-1.3-pythonlib-fix.patch
4 0006-apbs-1.3-clean-targets.patch
5 0005-apbs-1.3-linking.patch
6 0008-apbs-1.3-broken-test.patch
7 0015-apbs-1.3-pythonlib-fix.patch
8 0007-apbs-1.3-configure.patch
9 0011-apbs-1.3-shared-linking.patch
10 0002-python-linking.patch
11 0004-apbs-1.3-system-zlib.patch
12 0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch
13 0012-apbs-1.3-python-linking-correction.patch
14 0001-autoconf-2.68.patch
15 0013-apbs-1.3-tools-installation.patch
16 0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch
17 0003-apbs-1.3-pkg-config-file.patch
18 Log:
19 Rewrite build, rely on pkg-config when possible, move to autotools-utils.eclass, handle static-libs correctly
20
21 (Portage version: 2.2.0_alpha84/cvs/Linux x86_64)
22
23 Revision Changes Path
24 1.1 sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch
25
26 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch?rev=1.1&view=markup
27 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch?rev=1.1&content-type=text/plain
28
29 Index: 0014-apbs-1.3-pythonlib-fix.patch
30 ===================================================================
31 From 86ae9a75144d1d9600e7a9045e1154fb2f481efb Mon Sep 17 00:00:00 2001
32 Message-Id: <86ae9a75144d1d9600e7a9045e1154fb2f481efb.1325691465.git.jlec@g.o>
33 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
34 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
35 From: Justin Lecher <jlec@g.o>
36 Date: Wed, 4 Jan 2012 14:05:22 +0100
37 Subject: [PATCH 14/15] apbs 1.3 pythonlib fix
38
39 ---
40 tools/python/Makefile.am | 2 +-
41 1 files changed, 1 insertions(+), 1 deletions(-)
42
43 diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am
44 index 6a09644..aecd6ed 100644
45 --- a/tools/python/Makefile.am
46 +++ b/tools/python/Makefile.am
47 @@ -13,7 +13,7 @@ CCLD = $(PY_CC)
48 CLEANFILES = _apbslib.so
49 SUBDIRS = vgrid
50
51 -noinst_PROGRAMS = _apbslib.so
52 +pyexec_LTLIBRARIES = _apbslib.so
53 _apbslib_so_SOURCES = apbslib.c
54 _apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
55 _apbslib_so_LDADD = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@
56 --
57 1.7.8.2
58
59
60
61
62 1.1 sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch
63
64 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch?rev=1.1&view=markup
65 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch?rev=1.1&content-type=text/plain
66
67 Index: 0006-apbs-1.3-clean-targets.patch
68 ===================================================================
69 From e000438cebba988300c1210bc92a62635ba2ddf8 Mon Sep 17 00:00:00 2001
70 Message-Id: <e000438cebba988300c1210bc92a62635ba2ddf8.1325691465.git.jlec@g.o>
71 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
72 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
73 From: Justin Lecher <jlec@g.o>
74 Date: Tue, 3 Jan 2012 20:49:24 +0100
75 Subject: [PATCH 06/15] apbs 1.3 clean targets
76
77 ---
78 Makefile.am | 32 +++++++++++++++++++++++++++-----
79 1 files changed, 27 insertions(+), 5 deletions(-)
80
81 diff --git a/Makefile.am b/Makefile.am
82 index 437402d..af3a3a3 100644
83 --- a/Makefile.am
84 +++ b/Makefile.am
85 @@ -16,6 +16,9 @@ SUFFIXES = .H .h .C .cc .c .f .o
86
87 SUBDIRS = contrib src bin @apbs_do_tools@
88
89 +pkgconfigdir = @pkgconfigdir@
90 +pkgconfig_DATA = apbs.pc
91 +
92 distclean-local: clean-local
93
94 clean-local: clean-ac
95 @@ -27,11 +30,30 @@ clean-ac:
96 install-exec-local:
97 -rm -f ./bin/apbs
98
99 -install-data-local:
100 - mkdir -p ${prefix}/share
101 - -cp -rf examples ${prefix}/share
102 - -cp -rf doc ${prefix}/share
103 - -cp -rf tools ${prefix}/share
104 +install-data-local: install-cleanup
105 + -rm -f doc/LICENSE.txt
106 +
107 +install-cleanup:
108 + -rm -f tools/manip/*.pyc
109 + -rm -f tools/**/*.o
110 + -rm -f tools/**/*.c
111 + -rm -f tools/**/*.f
112 + -rm -f tools/**/*Makefile*
113 + -rm -f tools/**/**/*.o
114 + -rm -f tools/**/**/*.c
115 + -rm -f tools/**/**/*.f
116 + -rm -f tools/**/**/*Makefile*
117 + -rm -f tools/*Makefile*
118 + -rm -f examples/*Makefile*
119 + -rm -f examples/**/*Makefile*
120 +
121 +install-tools:
122 + mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
123 + -cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
124 +
125 +install-examples:
126 + mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples
127 + -cp -rf examples $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
128
129 test:
130 cd examples; make test
131 --
132 1.7.8.2
133
134
135
136
137 1.1 sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch
138
139 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch?rev=1.1&view=markup
140 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch?rev=1.1&content-type=text/plain
141
142 Index: 0005-apbs-1.3-linking.patch
143 ===================================================================
144 From 071473a3ead25df253236329511dcc4c63c3b53a Mon Sep 17 00:00:00 2001
145 Message-Id: <071473a3ead25df253236329511dcc4c63c3b53a.1325691465.git.jlec@g.o>
146 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
147 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
148 From: Justin Lecher <jlec@g.o>
149 Date: Tue, 3 Jan 2012 20:48:36 +0100
150 Subject: [PATCH 05/15] apbs 1.3 linking
151
152 ---
153 bin/Makefile.am | 8 +++-----
154 src/aaa_lib/Makefile.am | 6 +++---
155 2 files changed, 6 insertions(+), 8 deletions(-)
156
157 diff --git a/bin/Makefile.am b/bin/Makefile.am
158 index 7b2f3ee..9dae096 100644
159 --- a/bin/Makefile.am
160 +++ b/bin/Makefile.am
161 @@ -15,7 +15,7 @@ build_libraries = @apbs_build_libraries@
162 bindir = ${prefix}/bin
163 bin_PROGRAMS = apbs
164 apbs_SOURCES = main.c
165 -apbs_LDADD = ${build_libraries}
166 +apbs_LDADD = ${build_libraries} -L../src/aaa_lib/.libs/ libapbsmainroutines.la
167
168 # This is a hack I suspect, but needed to force apbs to be
169 # rebuilt anytime the make command is issued
170 @@ -27,9 +27,9 @@ BUILT_SOURCES = rm.apbs
171 rm.apbs: Makefile
172 -rm -f apbs
173
174 -libdir = ${prefix}/lib
175 lib_LTLIBRARIES = libapbsmainroutines.la
176 libapbsmainroutines_la_SOURCES = routines.c
177 +libapbsmainroutines_la_LIBADD = -L../src/aaa_lib/.libs/ -lapbs @mc_lib@
178 libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION}
179
180 INCLUDES = @inc_list@
181 @@ -40,6 +40,4 @@ includedir = ${prefix}/include/apbs
182 include_HEADERS = routines.h
183
184 install-data-local:
185 - -cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
186 - -chmod 755 ${prefix}/bin/ApbsClient.py
187 - -rm -f ${prefix}/bin/wsdl2py
188 \ No newline at end of file
189 + -rm -f $(DESTDIR)${prefix}/bin/wsdl2py
190 diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am
191 index 2c5026b..2495246 100644
192 --- a/src/aaa_lib/Makefile.am
193 +++ b/src/aaa_lib/Makefile.am
194 @@ -16,13 +16,13 @@ FEM_LIBS = ${top_builddir}/src/fem/libapbsfem.la
195 MG_LIBS = ${top_builddir}/src/mg/libapbsmg.la
196 PMGZ_LIBS = ${top_builddir}/contrib/pmgZ/libapbspmgz.la
197 AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la
198 -BLAS_LIBS = @blas_lib@
199 +BLAS_LIBS = @BLAS_LIBS@
200
201 -libdir = ${prefix}/lib
202 lib_LTLIBRARIES = libapbs.la
203
204 libapbs_la_SOURCES = apbs_link.c
205 -libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS}
206 +libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} \
207 + @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ @z_lib@
208 libapbs_la_LDFLAGS = -version-info ${APBS_VERSION}
209
210 INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@
211 --
212 1.7.8.2
213
214
215
216
217 1.1 sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch
218
219 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch?rev=1.1&view=markup
220 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch?rev=1.1&content-type=text/plain
221
222 Index: 0008-apbs-1.3-broken-test.patch
223 ===================================================================
224 From 6bcd14554262bf366aa371873c22cccb21b32850 Mon Sep 17 00:00:00 2001
225 Message-Id: <6bcd14554262bf366aa371873c22cccb21b32850.1325691465.git.jlec@g.o>
226 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
227 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
228 From: Justin Lecher <jlec@g.o>
229 Date: Tue, 3 Jan 2012 20:59:43 +0100
230 Subject: [PATCH 08/15] apbs 1.3 broken test
231
232 ---
233 examples/Makefile.am | 3 ---
234 1 files changed, 0 insertions(+), 3 deletions(-)
235
236 diff --git a/examples/Makefile.am b/examples/Makefile.am
237 index 6cf5664..adf901f 100644
238 --- a/examples/Makefile.am
239 +++ b/examples/Makefile.am
240 @@ -22,7 +22,6 @@ clean:
241 cd born; make clean
242 cd FKBP; make clean
243 cd hca-bind; make clean
244 - cd ion-pmf; make clean
245 cd ion-protein; make clean
246 cd ionize; make clean
247 cd pka-lig; make clean
248 @@ -39,7 +38,6 @@ test:
249 cd born; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
250 cd FKBP; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
251 cd hca-bind; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
252 - cd ion-pmf; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
253 cd ion-protein; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
254 cd ionize; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
255 cd pka-lig; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
256 @@ -56,7 +54,6 @@ testocd:
257 cd born; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
258 cd FKBP; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
259 cd hca-bind; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
260 - cd ion-pmf; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
261 cd ion-protein; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
262 cd ionize; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
263 cd pka-lig; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
264 --
265 1.7.8.2
266
267
268
269
270 1.1 sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch
271
272 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch?rev=1.1&view=markup
273 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch?rev=1.1&content-type=text/plain
274
275 Index: 0015-apbs-1.3-pythonlib-fix.patch
276 ===================================================================
277 From 013f5770202f705df7c522dcb123da86ac62e901 Mon Sep 17 00:00:00 2001
278 Message-Id: <013f5770202f705df7c522dcb123da86ac62e901.1325691465.git.jlec@g.o>
279 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
280 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
281 From: Justin Lecher <jlec@g.o>
282 Date: Wed, 4 Jan 2012 14:28:14 +0100
283 Subject: [PATCH 15/15] apbs 1.3 pythonlib fix
284
285 ---
286 configure.ac | 1 +
287 tools/python/Makefile.am | 11 ++++++-----
288 2 files changed, 7 insertions(+), 5 deletions(-)
289
290 diff --git a/configure.ac b/configure.ac
291 index 9837a57..d39a0a5 100644
292 --- a/configure.ac
293 +++ b/configure.ac
294 @@ -161,6 +161,7 @@ AC_ARG_ENABLE(
295 if test x"$enable_python" != "xno"; then
296 AC_MSG_RESULT([yes])
297 AC_MSG_NOTICE([Python linkage requires GNU compilers])
298 + AM_PATH_PYTHON
299 cclist="gcc"
300 f77list="gfortran g95 g77"
301 apbs_do_python="python"
302 diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am
303 index aecd6ed..7d661b1 100644
304 --- a/tools/python/Makefile.am
305 +++ b/tools/python/Makefile.am
306 @@ -10,10 +10,11 @@ AUTOMAKE_OPTIONS = no-dependencies
307 SUFFIXES = .c .C .o .so
308 INCLUDES = @inc_list@ $(PY_CFLAGS) -I${top_srcdir}/bin
309 CCLD = $(PY_CC)
310 -CLEANFILES = _apbslib.so
311 +CLEANFILES = _apbs.so
312 SUBDIRS = vgrid
313
314 -pyexec_LTLIBRARIES = _apbslib.so
315 -_apbslib_so_SOURCES = apbslib.c
316 -_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
317 -_apbslib_so_LDADD = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@
318 +pkgpyexec_LTLIBRARIES = _apbs.la
319 +_apbs_la_SOURCES = apbslib.c
320 +#_apbs_la_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
321 +_apbs_la_LDFLAGS = -module -avoid-version -shared
322 +_apbs_la_LIBADD = ${top_builddir}/bin/.libs/libapbsmainroutines.la ${top_builddir}/src/aaa_lib/.libs/libapbs.la $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@
323 --
324 1.7.8.2
325
326
327
328
329 1.1 sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch
330
331 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch?rev=1.1&view=markup
332 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch?rev=1.1&content-type=text/plain
333
334 Index: 0007-apbs-1.3-configure.patch
335 ===================================================================
336 From b196b6b83a969e6c7ee60e3cdfe03b76eb87bd11 Mon Sep 17 00:00:00 2001
337 Message-Id: <b196b6b83a969e6c7ee60e3cdfe03b76eb87bd11.1325691465.git.jlec@g.o>
338 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
339 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
340 From: Justin Lecher <jlec@g.o>
341 Date: Tue, 3 Jan 2012 20:50:19 +0100
342 Subject: [PATCH 07/15] apbs 1.3 configure
343
344 ---
345 configure.ac | 117 +++++++++++++++------------------------------------------
346 1 files changed, 31 insertions(+), 86 deletions(-)
347
348 diff --git a/configure.ac b/configure.ac
349 index 6020fbf..c91abb5 100644
350 --- a/configure.ac
351 +++ b/configure.ac
352 @@ -1,4 +1,4 @@
353 -1.3dnl ##########################################################################
354 +dnl ##########################################################################
355 dnl APBS -- Adaptive Poisson-Boltzmann Solver
356 dnl
357 dnl Nathan A. Baker (nathan.baker@×××.gov)
358 @@ -71,6 +71,10 @@ AM_CONFIG_HEADER(src/aaa_inc/apbscfg.h)
359 AC_CONFIG_AUX_DIR(config)
360 AC_PREFIX_DEFAULT(${HOME})
361 AC_CANONICAL_SYSTEM
362 +LT_INIT
363 +LT_LANG([Fortran 77])
364 +AC_F77_DUMMY_MAIN
365 +AC_F77_LIBRARY_LDFLAGS
366
367 dnl ##########################################################################
368 dnl 1. automake initialization (uncomment only if rebuilding Makefile.in's)
369 @@ -152,8 +156,7 @@ dnl ##########################################################################
370 AC_MSG_CHECKING([for --enable-python])
371 AC_ARG_ENABLE(
372 [python],
373 - AS_HELP_STRING([--enable-python],[enables Python wrapper compilation]),,
374 - [enable_python=no]
375 + AS_HELP_STRING([--enable-python],[enables Python wrapper compilation])
376 )
377 if test x"$enable_python" != "xno"; then
378 AC_MSG_RESULT([yes])
379 @@ -582,6 +585,7 @@ if test x"$enable_python" != "xno"; then
380 PY_SHARED="-shared"
381 CC="${CC} -fPIC"
382 F77="${F77} -fPIC"
383 + PY_LDFLAGS="-lpython$PY_VERSION"
384 ;;
385 irix*)
386 PY_SHARED="-shared"
387 @@ -717,8 +721,7 @@ if test -z "${USE_FETK}"; then
388 AC_MSG_CHECKING([for --disable-maloc-rebuild])
389 AC_ARG_ENABLE(
390 [maloc-rebuild],
391 - AS_HELP_STRING([--disable-maloc-rebuild], [disable rebuilding maloc]),,
392 - [enable_maloc_rebuild=yes]
393 + AS_HELP_STRING([--disable-maloc-rebuild], [disable rebuilding maloc])
394 )
395
396 if test x"$enable_maloc_rebuild" = "xno"; then
397 @@ -981,8 +984,7 @@ dnl # -----------------------
398 AC_MSG_CHECKING([for --disable-tools])
399 AC_ARG_ENABLE(
400 [tools],
401 - AS_HELP_STRING([--disable-tools],[disable tool compilation]),,
402 - [enable_tools=yes]
403 + AS_HELP_STRING([--disable-tools],[disable tool compilation])
404 )
405 apbs_do_tools=""
406 if test x"$enable_tools" != "xno"; then
407 @@ -999,45 +1001,10 @@ AC_SUBST(apbs_do_tools)
408 dnl # -----------------------
409 dnl # HANDLE THE BLAS LIBRARIES
410 dnl # -----------------------
411 -blas_lib=""
412 -AC_ARG_WITH(
413 - [blas],
414 - AS_HELP_STRING([--with-blas=LDFLAGS], [link to user-specified BLAS (specify flags to pass to ld)])
415 - )
416 -AC_MSG_CHECKING([for --with-blas])
417 -if test x"$with_blas" != "xno" -a -n "$with_blas"; then
418 - blas_lib="${with_blas}"
419 - AC_MSG_RESULT([${blas_lib}])
420 - AC_ARG_WITH(
421 - [blas_name],
422 - AS_HELP_STRING([--with-blas-name=NAME], [name of BLAS library, defaults to blas]),,
423 - [with_blas_name="blas"]
424 - )
425 - if test x"$with_blas_name" != "xno" -a -n "$with_blas_name"; then
426 - blas_name="${with_blas_name}"
427 - fi
428 - AC_MSG_NOTICE([checking ${blas_name} using ${blas_lib}])
429 - AC_LANG_FORTRAN77
430 - LDFLAGS_SAVE=${LDFLAGS};
431 - CPPFLAGS_SAVE=${CPPFLAGS};
432 - LDFLAGS="-L${maloc_lib_path} ${blas_lib}";
433 - AC_CHECK_LIB(${blas_name},dscal,
434 - [blas_found="yes"],
435 - [blas_found=""],
436 - [${blas_lib} ${socket_lib} ${nsl_lib} ${math_lib}])
437 - LDFLAGS=${LDFLAGS_SAVE};
438 - CPPFLAGS=${CPPFLAGS_SAVE};
439 - if test -z "${blas_found}"; then
440 - AC_MSG_ERROR([BLAS libraries or headers missing: exiting on error!])
441 - fi
442 - apbs_do_blas=""
443 - AC_LANG_C
444 -else
445 - AC_MSG_RESULT([no])
446 - apbs_do_blas="blas"
447 - blas_lib=${contrib_path}/blas/.libs/libapbsblas.a
448 -fi
449 +apbs_do_blas=""
450 +PKG_CHECK_MODULES([BLAS],[blas])
451 AC_SUBST(apbs_do_blas)
452 +AC_SUBST([BLAS_LIBS])
453
454 dnl # --------------------------------
455 dnl # HANDLE ZLIB COMPILATION
456 @@ -1047,13 +1014,12 @@ z_lib=
457 AC_MSG_CHECKING([--disable-zlib])
458 AC_ARG_ENABLE(
459 [zlib],
460 - AS_HELP_STRING([--disable-zlib], [disable zlib compilation]),,
461 - [disable_zlib=no]
462 + AS_HELP_STRING([--disable-zlib], [disable zlib compilation])
463 )
464 -if test x"$disable_zlib" == "xno"; then
465 +if test x"$disable_zlib" != "xno"; then
466 AC_MSG_RESULT([yes])
467 zlib="zlib"
468 - z_lib=${contrib_path}/zlib/.libs/libz.a
469 + z_lib=-lz
470 AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled])
471 fi
472 AC_SUBST(zlib)
473 @@ -1143,8 +1109,7 @@ dnl # -----------------------
474 AC_MSG_CHECKING([for --enable-abps-quiet])
475 AC_ARG_ENABLE(
476 [abps-quiet],
477 - AS_HELP_STRING([--enable-abps-quiet],[prevent APBS diagnostic messages from displaying to stdout]),,
478 - [enable_apbs_quiet=no]
479 + AS_HELP_STRING([--enable-abps-quiet],[prevent APBS diagnostic messages from displaying to stdout])
480 )
481 if test x"$enable_apbs_quiet" != "xno"; then
482 AC_MSG_RESULT([yes])
483 @@ -1156,36 +1121,7 @@ fi
484 dnl # -----------------------
485 dnl # CHECK WHETHER YOU WANT TO DISABLE OPENMP SUPPORT
486 dnl # -----------------------
487 -AC_MSG_CHECKING([for --disable-openmp])
488 -AC_ARG_ENABLE(
489 - [openmp],
490 - AS_HELP_STRING([--disable-openmp],[disables OpenMP compiler support]),,
491 - [disable_openmp=yes]
492 -)
493 -if test x"$disable_openmp" != "xyes"; then
494 - AC_MSG_RESULT([yes])
495 -else
496 - AC_MSG_RESULT([no])
497 - if [[ "${CC}" = "icc" ] && [ "${F77}" = "ifort" ]]; then
498 - CFLAGS="${CFLAGS} -openmp"
499 - FFLAGS="${FFLAGS} -openmp -assume cc_omp"
500 - LDFLAGS="${LDFLAGS} -static-intel"
501 - fi
502 -
503 - if [[ "${CC}" = "gcc" ] && [ "${F77}" = "gfortran" ]]; then
504 - gcc_version=`gcc --version`
505 - gcc_complete_version=`echo ${gcc_version} | awk '{printf("%s",$3)}' | awk -F'.' '{print $1$2}'`
506 -
507 - if test ["${gcc_complete_version}" -ge 42]; then
508 - CFLAGS="${CFLAGS} -fopenmp"
509 - FFLAGS="${FFLAGS} -fopenmp"
510 - else
511 - AC_MSG_RESULT([WARNING])
512 - AC_MSG_RESULT([WARNING Version of gcc/gfortran does not support OpenMP. Disabling.])
513 - AC_MSG_RESULT([WARNING])
514 - fi
515 - fi
516 -fi
517 +AC_OPENMP
518
519 dnl # -----------------------
520 dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES
521 @@ -1217,7 +1153,7 @@ dnl # COMPILATIONS
522 dnl # -----------------------
523 top_srcdir="`pwd`"
524 base_list="${FLIBS} ${tree_lib} ${vmetis_lib} ${vor_lib} ${mcx_lib} ${mc_lib} \
525 - ${thread_lib} ${mpi_lib} ${math_lib} ${rl_lib} ${socket_lib} ${nsl_lib} ${blas_lib} ${z_lib}"
526 + ${thread_lib} ${mpi_lib} ${math_lib} ${rl_lib} ${socket_lib} ${nsl_lib} ${BLAS_LIBS} ${z_lib}"
527
528 case $host_os in
529
530 @@ -1284,6 +1220,17 @@ else
531 fi
532 AC_SUBST(apbs_build_libraries)
533
534 +# Additional arguments (and substitutions)
535 +# Allow the pkg-config directory to be set
536 +AC_ARG_WITH(pkgconfigdir,
537 + AC_HELP_STRING([--with-pkgconfigdir],
538 + [Use the specified pkgconfig dir (default is libdir/pkgconfig)]),
539 + [pkgconfigdir=${withval}],
540 + [pkgconfigdir='${libdir}/pkgconfig'])
541 +
542 +AC_SUBST([pkgconfigdir])
543 +AC_MSG_NOTICE([pkgconfig directory is ${pkgconfigdir}])
544 +
545 dnl ##########################################################################
546 dnl 11. generate the makefiles
547 dnl ##########################################################################
548 @@ -1292,12 +1239,8 @@ AC_CONFIG_FILES([
549 Makefile
550
551 contrib/Makefile
552 - contrib/blas/Makefile
553 contrib/pmgZ/Makefile
554 contrib/aqua/Makefile
555 - contrib/opal/Makefile
556 - contrib/opal/ZSI/Makefile
557 - contrib/zlib/Makefile
558
559 tools/Makefile
560 tools/mesh/Makefile
561 @@ -1332,6 +1275,8 @@ AC_CONFIG_FILES([
562
563 bin/Makefile
564
565 + apbs.pc:apbs.pc.in
566 +
567 ])
568 AC_OUTPUT
569
570 --
571 1.7.8.2
572
573
574
575
576 1.1 sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch
577
578 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch?rev=1.1&view=markup
579 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch?rev=1.1&content-type=text/plain
580
581 Index: 0011-apbs-1.3-shared-linking.patch
582 ===================================================================
583 From 0f26ce7c0c5013ba72c6bf5fcf04004240e79d26 Mon Sep 17 00:00:00 2001
584 Message-Id: <0f26ce7c0c5013ba72c6bf5fcf04004240e79d26.1325691465.git.jlec@g.o>
585 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
586 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
587 From: Justin Lecher <jlec@g.o>
588 Date: Wed, 4 Jan 2012 11:36:56 +0100
589 Subject: [PATCH 11/15] apbs 1.3 shared linking
590
591 ---
592 tools/python/vgrid/Makefile.am | 2 +-
593 1 files changed, 1 insertions(+), 1 deletions(-)
594
595 diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am
596 index b31c9b6..50c09ac 100644
597 --- a/tools/python/vgrid/Makefile.am
598 +++ b/tools/python/vgrid/Makefile.am
599 @@ -16,5 +16,5 @@ if PY_PRESENT
600 noinst_PROGRAMS = _vgrid.so
601 _vgrid_so_SOURCES = vgridlib.c
602 _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
603 - _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a @lib_list@
604 + _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.la ${top_builddir}/src/aaa_lib/.libs/libapbs.la @lib_list@
605 endif
606 --
607 1.7.8.2
608
609
610
611
612 1.1 sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch
613
614 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch?rev=1.1&view=markup
615 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch?rev=1.1&content-type=text/plain
616
617 Index: 0002-python-linking.patch
618 ===================================================================
619 From 5b208a6ef5fc706b699b3b33bd9248126c54a034 Mon Sep 17 00:00:00 2001
620 Message-Id: <5b208a6ef5fc706b699b3b33bd9248126c54a034.1325691465.git.jlec@g.o>
621 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
622 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
623 From: Justin Lecher <jlec@g.o>
624 Date: Tue, 3 Jan 2012 20:45:58 +0100
625 Subject: [PATCH 02/15] python linking
626
627 ---
628 tools/python/Makefile.am | 4 ++--
629 tools/python/vgrid/Makefile.am | 4 ++--
630 2 files changed, 4 insertions(+), 4 deletions(-)
631
632 diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am
633 index 73d25f7..2c1fbea 100644
634 --- a/tools/python/Makefile.am
635 +++ b/tools/python/Makefile.am
636 @@ -15,5 +15,5 @@ SUBDIRS = vgrid
637
638 noinst_PROGRAMS = _apbslib.so
639 _apbslib_so_SOURCES = apbslib.c
640 -_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
641 -_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) ${z_lib}
642 +_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
643 +_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${z_lib} @OPENMP_LIBS@ @maloc_lib@ @mc_lib@
644 diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am
645 index b573268..b31c9b6 100644
646 --- a/tools/python/vgrid/Makefile.am
647 +++ b/tools/python/vgrid/Makefile.am
648 @@ -15,6 +15,6 @@ CLEANFILES = _vgrid.so
649 if PY_PRESENT
650 noinst_PROGRAMS = _vgrid.so
651 _vgrid_so_SOURCES = vgridlib.c
652 - _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
653 - _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
654 + _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
655 + _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a @lib_list@
656 endif
657 --
658 1.7.8.2
659
660
661
662
663 1.1 sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch
664
665 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch?rev=1.1&view=markup
666 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch?rev=1.1&content-type=text/plain
667
668 Index: 0004-apbs-1.3-system-zlib.patch
669 ===================================================================
670 From 7abe31a7006c97e908ec717f5f85dddd4cd36110 Mon Sep 17 00:00:00 2001
671 Message-Id: <7abe31a7006c97e908ec717f5f85dddd4cd36110.1325691465.git.jlec@g.o>
672 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
673 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
674 From: Justin Lecher <jlec@g.o>
675 Date: Tue, 3 Jan 2012 20:47:58 +0100
676 Subject: [PATCH 04/15] apbs 1.3 system zlib
677
678 ---
679 src/mg/vgrid.c | 2 +-
680 1 files changed, 1 insertions(+), 1 deletions(-)
681
682 diff --git a/src/mg/vgrid.c b/src/mg/vgrid.c
683 index d183bb2..e0669ab 100644
684 --- a/src/mg/vgrid.c
685 +++ b/src/mg/vgrid.c
686 @@ -432,7 +432,7 @@ VPUBLIC int Vgrid_gradient(Vgrid *thee, double pt[3], double grad[3]) {
687 /////////////////////////////////////////////////////////////////////////// */
688 #ifdef HAVE_ZLIB
689 #define off_t long
690 -#include "../../contrib/zlib/zlib.h"
691 +#include <zlib.h>
692 #endif
693 VPUBLIC int Vgrid_readGZ(Vgrid *thee, const char *fname) {
694
695 --
696 1.7.8.2
697
698
699
700
701 1.1 sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch
702
703 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch?rev=1.1&view=markup
704 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch?rev=1.1&content-type=text/plain
705
706 Index: 0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch
707 ===================================================================
708 From a7705f4957dca398031f1b6f3a74494004588c4d Mon Sep 17 00:00:00 2001
709 Message-Id: <a7705f4957dca398031f1b6f3a74494004588c4d.1325691465.git.jlec@g.o>
710 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
711 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
712 From: Justin Lecher <jlec@g.o>
713 Date: Wed, 4 Jan 2012 10:52:29 +0100
714 Subject: [PATCH 09/15] apbs 1.3 use pkg-config for zlib detection
715
716 ---
717 configure.ac | 15 ++++-----------
718 1 files changed, 4 insertions(+), 11 deletions(-)
719
720 diff --git a/configure.ac b/configure.ac
721 index c91abb5..53deb06 100644
722 --- a/configure.ac
723 +++ b/configure.ac
724 @@ -1011,17 +1011,10 @@ dnl # HANDLE ZLIB COMPILATION
725 dnl # --------------------------------
726 disable_zlib=yes
727 z_lib=
728 -AC_MSG_CHECKING([--disable-zlib])
729 -AC_ARG_ENABLE(
730 - [zlib],
731 - AS_HELP_STRING([--disable-zlib], [disable zlib compilation])
732 -)
733 -if test x"$disable_zlib" != "xno"; then
734 - AC_MSG_RESULT([yes])
735 - zlib="zlib"
736 - z_lib=-lz
737 - AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled])
738 -fi
739 +zlib=
740 +PKG_CHECK_MODULES([ZLIB],[zlib])
741 +z_lib=$(ZLIB_LIBS)
742 +AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled])
743 AC_SUBST(zlib)
744 AC_SUBST(z_lib)
745
746 --
747 1.7.8.2
748
749
750
751
752 1.1 sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch
753
754 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch?rev=1.1&view=markup
755 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch?rev=1.1&content-type=text/plain
756
757 Index: 0012-apbs-1.3-python-linking-correction.patch
758 ===================================================================
759 From 73a1f1d63d7617fea85c10990b1f35c9567a3573 Mon Sep 17 00:00:00 2001
760 Message-Id: <73a1f1d63d7617fea85c10990b1f35c9567a3573.1325691465.git.jlec@g.o>
761 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
762 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
763 From: Justin Lecher <jlec@g.o>
764 Date: Wed, 4 Jan 2012 11:49:50 +0100
765 Subject: [PATCH 12/15] apbs 1.3 python linking correction
766
767 ---
768 bin/Makefile.am | 4 ++--
769 tools/python/Makefile.am | 2 +-
770 tools/python/vgrid/Makefile.am | 2 +-
771 3 files changed, 4 insertions(+), 4 deletions(-)
772
773 diff --git a/bin/Makefile.am b/bin/Makefile.am
774 index 9dae096..574be3d 100644
775 --- a/bin/Makefile.am
776 +++ b/bin/Makefile.am
777 @@ -15,7 +15,7 @@ build_libraries = @apbs_build_libraries@
778 bindir = ${prefix}/bin
779 bin_PROGRAMS = apbs
780 apbs_SOURCES = main.c
781 -apbs_LDADD = ${build_libraries} -L../src/aaa_lib/.libs/ libapbsmainroutines.la
782 +apbs_LDADD = ${build_libraries} .libs/libapbsmainroutines.la
783
784 # This is a hack I suspect, but needed to force apbs to be
785 # rebuilt anytime the make command is issued
786 @@ -29,7 +29,7 @@ rm.apbs: Makefile
787
788 lib_LTLIBRARIES = libapbsmainroutines.la
789 libapbsmainroutines_la_SOURCES = routines.c
790 -libapbsmainroutines_la_LIBADD = -L../src/aaa_lib/.libs/ -lapbs @mc_lib@
791 +libapbsmainroutines_la_LIBADD = ../src/aaa_lib/.libs/libapbs.la @mc_lib@
792 libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION}
793
794 INCLUDES = @inc_list@
795 diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am
796 index 2c1fbea..6a09644 100644
797 --- a/tools/python/Makefile.am
798 +++ b/tools/python/Makefile.am
799 @@ -16,4 +16,4 @@ SUBDIRS = vgrid
800 noinst_PROGRAMS = _apbslib.so
801 _apbslib_so_SOURCES = apbslib.c
802 _apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
803 -_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${z_lib} @OPENMP_LIBS@ @maloc_lib@ @mc_lib@
804 +_apbslib_so_LDADD = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@
805 diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am
806 index 50c09ac..165cd4d 100644
807 --- a/tools/python/vgrid/Makefile.am
808 +++ b/tools/python/vgrid/Makefile.am
809 @@ -16,5 +16,5 @@ if PY_PRESENT
810 noinst_PROGRAMS = _vgrid.so
811 _vgrid_so_SOURCES = vgridlib.c
812 _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
813 - _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.la ${top_builddir}/src/aaa_lib/.libs/libapbs.la @lib_list@
814 + _vgrid_so_LDADD = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs @lib_list@
815 endif
816 --
817 1.7.8.2
818
819
820
821
822 1.1 sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch
823
824 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch?rev=1.1&view=markup
825 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch?rev=1.1&content-type=text/plain
826
827 Index: 0001-autoconf-2.68.patch
828 ===================================================================
829 From 89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea Mon Sep 17 00:00:00 2001
830 Message-Id: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
831 From: Justin Lecher <jlec@g.o>
832 Date: Tue, 3 Jan 2012 20:25:55 +0100
833 Subject: [PATCH 01/15] autoconf 2.68
834
835 ---
836 acinclude.m4 | 13 +++++--------
837 1 files changed, 5 insertions(+), 8 deletions(-)
838
839 diff --git a/acinclude.m4 b/acinclude.m4
840 index 3701ceb..34602e3 100644
841 --- a/acinclude.m4
842 +++ b/acinclude.m4
843 @@ -54,14 +54,11 @@ AC_LANG_SAVE
844 AC_LANG_C
845 ac_save_LIBS="$LIBS"
846 LIBS="mangle-func.o $LIBS"
847 -AC_TRY_LINK(,foobar();,
848 - ac_f77_mangle_type=lowercase,
849 - AC_TRY_LINK(,foobar_();,
850 - ac_f77_mangle_type=lowercase-underscore,
851 - AC_TRY_LINK(,FOOBAR();,
852 - ac_f77_mangle_type=uppercase,
853 - AC_TRY_LINK(,FOOBAR_();,
854 - ac_f77_mangle_type=uppercase-underscore))))
855 +AC_TRY_LINK(,foobar();,ac_f77_mangle_type=lowercase)
856 +AC_TRY_LINK(,foobar_();,ac_f77_mangle_type=lowercase-underscore)
857 +AC_TRY_LINK(,FOOBAR();,ac_f77_mangle_type=uppercase)
858 +AC_TRY_LINK(,FOOBAR_();,ac_f77_mangle_type=uppercase-underscore)
859 +
860 LIBS="$ac_save_LIBS"
861 AC_LANG_RESTORE
862 AC_MSG_RESULT($ac_f77_mangle_type)
863 --
864 1.7.8.2
865
866
867
868
869 1.1 sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch
870
871 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch?rev=1.1&view=markup
872 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch?rev=1.1&content-type=text/plain
873
874 Index: 0013-apbs-1.3-tools-installation.patch
875 ===================================================================
876 From 4fd349da80e63c6fd3fbb2f015d8d802c326508e Mon Sep 17 00:00:00 2001
877 Message-Id: <4fd349da80e63c6fd3fbb2f015d8d802c326508e.1325691465.git.jlec@g.o>
878 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
879 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
880 From: Justin Lecher <jlec@g.o>
881 Date: Wed, 4 Jan 2012 13:29:19 +0100
882 Subject: [PATCH 13/15] apbs 1.3 tools installation
883
884 ---
885 Makefile.am | 2 +-
886 tools/arpack/Makefile.am | 2 +-
887 tools/manip/Makefile.am | 2 +-
888 tools/mesh/Makefile.am | 2 +-
889 4 files changed, 4 insertions(+), 4 deletions(-)
890
891 diff --git a/Makefile.am b/Makefile.am
892 index af3a3a3..60ba9bd 100644
893 --- a/Makefile.am
894 +++ b/Makefile.am
895 @@ -49,7 +49,7 @@ install-cleanup:
896
897 install-tools:
898 mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
899 - -cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
900 + -cp -rf tools/conversion tools/visualization tools/matlab $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
901
902 install-examples:
903 mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples
904 diff --git a/tools/arpack/Makefile.am b/tools/arpack/Makefile.am
905 index 6c05f4a..2362114 100644
906 --- a/tools/arpack/Makefile.am
907 +++ b/tools/arpack/Makefile.am
908 @@ -10,7 +10,7 @@ AUTOMAKE_OPTIONS = no-dependencies
909 SUFFIXES = .H .h .C .c .f .o
910 CCLD = $(F77)
911
912 -noinst_PROGRAMS = driver
913 +bin_PROGRAMS = driver
914 driver_SOURCES = driver.c readhb.f ardriv.f
915 driver_LDADD = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@
916 INCLUDES = @inc_list@
917 diff --git a/tools/manip/Makefile.am b/tools/manip/Makefile.am
918 index f5f692b..f64f8fc 100644
919 --- a/tools/manip/Makefile.am
920 +++ b/tools/manip/Makefile.am
921 @@ -10,7 +10,7 @@ AUTOMAKE_OPTIONS = no-dependencies
922 SUFFIXES = .H .h .C .c .f .o
923 CCLD = $(CC)
924
925 -noinst_PROGRAMS = coulomb born
926 +bin_PROGRAMS = coulomb born
927 coulomb_SOURCES = coulomb.c
928 coulomb_LDADD = ../../src/aaa_lib/libapbs.la @apbs_build_libraries@
929 born_SOURCES = born.c
930 diff --git a/tools/mesh/Makefile.am b/tools/mesh/Makefile.am
931 index 8ad5cfb..3cd9268 100644
932 --- a/tools/mesh/Makefile.am
933 +++ b/tools/mesh/Makefile.am
934 @@ -21,7 +21,7 @@ uhbd_asc2bin_CCLD = $(F77)
935 else
936 UHBD =
937 endif
938 -noinst_PROGRAMS = mgmesh dxmath mergedx mergedx2 $(UHBD) smooth value dx2mol dx2uhbd benchmark similarity analysis multivalue del2dx tensor2dx
939 +bin_PROGRAMS = mgmesh dxmath mergedx mergedx2 $(UHBD) smooth value dx2mol dx2uhbd benchmark similarity analysis multivalue del2dx tensor2dx
940
941 mgmesh_SOURCES = mgmesh.c
942 mgmesh_LDADD = ../../src/aaa_lib/libapbs.la @apbs_build_libraries@
943 --
944 1.7.8.2
945
946
947
948
949 1.1 sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch
950
951 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch?rev=1.1&view=markup
952 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch?rev=1.1&content-type=text/plain
953
954 Index: 0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch
955 ===================================================================
956 From c09358a2aca006d93d8bc7525efe656f1b4f9c0a Mon Sep 17 00:00:00 2001
957 Message-Id: <c09358a2aca006d93d8bc7525efe656f1b4f9c0a.1325691465.git.jlec@g.o>
958 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
959 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
960 From: Justin Lecher <jlec@g.o>
961 Date: Wed, 4 Jan 2012 11:05:04 +0100
962 Subject: [PATCH 10/15] apbs 1.3 use OPENMP_CFLAGS instead of OPENMP_LIBS
963
964 ---
965 configure.ac | 4 ++--
966 src/aaa_lib/Makefile.am | 2 +-
967 2 files changed, 3 insertions(+), 3 deletions(-)
968
969 diff --git a/configure.ac b/configure.ac
970 index 53deb06..9837a57 100644
971 --- a/configure.ac
972 +++ b/configure.ac
973 @@ -1013,7 +1013,7 @@ disable_zlib=yes
974 z_lib=
975 zlib=
976 PKG_CHECK_MODULES([ZLIB],[zlib])
977 -z_lib=$(ZLIB_LIBS)
978 +z_lib=${ZLIB_LIBS}
979 AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled])
980 AC_SUBST(zlib)
981 AC_SUBST(z_lib)
982 @@ -1115,7 +1115,7 @@ dnl # -----------------------
983 dnl # CHECK WHETHER YOU WANT TO DISABLE OPENMP SUPPORT
984 dnl # -----------------------
985 AC_OPENMP
986 -
987 +CFLAGS+=" ${OPENMP_CFLAGS}"
988 dnl # -----------------------
989 dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES
990 dnl # -----------------------
991 diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am
992 index 2495246..9fcbcaa 100644
993 --- a/src/aaa_lib/Makefile.am
994 +++ b/src/aaa_lib/Makefile.am
995 @@ -22,7 +22,7 @@ lib_LTLIBRARIES = libapbs.la
996
997 libapbs_la_SOURCES = apbs_link.c
998 libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} \
999 - @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ @z_lib@
1000 + @maloc_lib@ @mc_lib@ @z_lib@
1001 libapbs_la_LDFLAGS = -version-info ${APBS_VERSION}
1002
1003 INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@
1004 --
1005 1.7.8.2
1006
1007
1008
1009
1010 1.1 sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch
1011
1012 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch?rev=1.1&view=markup
1013 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch?rev=1.1&content-type=text/plain
1014
1015 Index: 0003-apbs-1.3-pkg-config-file.patch
1016 ===================================================================
1017 From 9876050808e5d43c02d3c703e998a82f7502275d Mon Sep 17 00:00:00 2001
1018 Message-Id: <9876050808e5d43c02d3c703e998a82f7502275d.1325691465.git.jlec@g.o>
1019 In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
1020 References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
1021 From: Justin Lecher <jlec@g.o>
1022 Date: Tue, 3 Jan 2012 20:47:13 +0100
1023 Subject: [PATCH 03/15] apbs 1.3 pkg-config file
1024
1025 ---
1026 apbs.pc.in | 11 +++++++++++
1027 1 files changed, 11 insertions(+), 0 deletions(-)
1028
1029 diff --git a/apbs.pc.in b/apbs.pc.in
1030 new file mode 100644
1031 index 0000000..c177512
1032 --- /dev/null
1033 +++ b/apbs.pc.in
1034 @@ -0,0 +1,11 @@
1035 +prefix=@prefix@
1036 +exec_prefix=@exec_prefix@
1037 +libdir=@libdir@
1038 +includedir=@includedir@/apbs
1039 +
1040 +Name: apbs
1041 +Description: apbs
1042 +Version: @PACKAGE_VERSION@
1043 +Libs: -L${libdir} -lapbsmainroutines -lapbs
1044 +Libs.private: @LIBS@
1045 +Cflags: -I${includedir}
1046 --
1047 1.7.8.2