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commit: 9753c0fb02f9a8c76aeac1e2efd80793cb501416 |
2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Aug 1 18:31:32 2021 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Aug 1 18:31:32 2021 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9753c0fb |
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|
8 |
sci-biology/emboss: Fix C99 `bool` clash |
9 |
|
10 |
* Also fix `-Wimplicit-function-declaration` |
11 |
|
12 |
Closes: https://bugs.gentoo.org/695380 |
13 |
Signed-off-by: David Seifert <soap <AT> gentoo.org> |
14 |
|
15 |
sci-biology/emboss/Manifest | 1 + |
16 |
sci-biology/emboss/emboss-6.6.0-r1.ebuild | 14 +- |
17 |
.../files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch | 11 - |
18 |
.../files/emboss-6.6.0_fix-build-system.patch | 411 --------------------- |
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.../files/emboss-6.6.0_plplot-declarations.patch | 61 --- |
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.../emboss-6.6.0_qa-implicit-declarations.patch | 74 ---- |
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6 files changed, 10 insertions(+), 562 deletions(-) |
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|
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diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest |
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index e4650c04fb9..f97d826f09b 100644 |
25 |
--- a/sci-biology/emboss/Manifest |
26 |
+++ b/sci-biology/emboss/Manifest |
27 |
@@ -1 +1,2 @@ |
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DIST EMBOSS-6.6.0.tar.gz 117962028 BLAKE2B 91bf3c680290bd975d2ddb5251089d7f75f8a44a26e1247e93d2c9cf2f23e6b89c4218022ba1af0c940136ff56782f40d2c4604dc756b400ae23f223da7f3cca SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a |
29 |
+DIST emboss-6.6.0-patches.tar.xz 5408 BLAKE2B ec1c55c90a64b1c27645804411b44e413ae881b1637ad2b8dfcff172e15b841cc3d2807039761f8307b0b5a29ab5b1a2c840e189f326091aa9ce25317ec9cda6 SHA512 942681df428f6254c1711902f667c6e8c71babf3e9b0c73b8b7d2fbfa5e8856ce5817560280948e588f6037011ad7055a3af5b88a58fc2b14349869927c889eb |
30 |
|
31 |
diff --git a/sci-biology/emboss/emboss-6.6.0-r1.ebuild b/sci-biology/emboss/emboss-6.6.0-r1.ebuild |
32 |
index 1c74ded5e22..766dd6a61b0 100644 |
33 |
--- a/sci-biology/emboss/emboss-6.6.0-r1.ebuild |
34 |
+++ b/sci-biology/emboss/emboss-6.6.0-r1.ebuild |
35 |
@@ -8,7 +8,9 @@ EBO_EAUTORECONF=1 |
36 |
inherit emboss-r2 readme.gentoo-r1 |
37 |
|
38 |
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" |
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-SRC_URI="ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz" |
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+SRC_URI=" |
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+ ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz |
42 |
+ https://dev.gentoo.org/~soap/distfiles/${P}-patches.tar.xz" |
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S="${WORKDIR}/${P^^}" |
44 |
|
45 |
LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" |
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@@ -29,10 +31,12 @@ PDEPEND=" |
47 |
)" |
48 |
|
49 |
PATCHES=( |
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- "${FILESDIR}"/${P}_fix-build-system.patch |
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- "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch |
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- "${FILESDIR}"/${P}_plplot-declarations.patch |
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- "${FILESDIR}"/${P}_qa-implicit-declarations.patch |
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+ "${WORKDIR}"/patches/${P}-fix-build-system.patch |
55 |
+ "${WORKDIR}"/patches/${P}-FORTIFY_SOURCE-fix.patch |
56 |
+ "${WORKDIR}"/patches/${P}-plplot-declarations.patch |
57 |
+ "${WORKDIR}"/patches/${P}-qa-implicit-declarations.patch |
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+ "${WORKDIR}"/patches/${P}-C99-bool.patch |
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+ "${WORKDIR}"/patches/${P}-Wimplicit-function-declaration.patch |
60 |
) |
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|
62 |
src_install() { |
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|
64 |
diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch |
65 |
deleted file mode 100644 |
66 |
index 7704873e9d2..00000000000 |
67 |
--- a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch |
68 |
+++ /dev/null |
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@@ -1,11 +0,0 @@ |
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---- EMBOSS-6.6.0/emboss/embossversion.c |
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-+++ EMBOSS-6.6.0/emboss/embossversion.c |
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-@@ -415,7 +415,7 @@ |
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- ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING); |
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- #endif |
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- #ifdef _FORTIFY_SOURCE |
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-- ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE); |
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-+ ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL); |
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- #endif |
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- ajFmtPrintF(outfile, "\n"); |
80 |
- ajFmtPrintF(outfile, "Sizes (bytes):\n"); |
81 |
|
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diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch |
83 |
deleted file mode 100644 |
84 |
index 266bddd95a3..00000000000 |
85 |
--- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch |
86 |
+++ /dev/null |
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@@ -1,411 +0,0 @@ |
88 |
- Makefile.am | 9 +++--- |
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- ajax/Makefile.am | 4 +-- |
90 |
- ajax/acd/Makefile.am | 8 +++-- |
91 |
- ajax/ajaxdb/Makefile.am | 6 ++-- |
92 |
- ajax/core/Makefile.am | 6 ++-- |
93 |
- ajax/core/ajreg.h | 7 ++-- |
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- ajax/ensembl/Makefile.am | 6 ++-- |
95 |
- ajax/graphics/Makefile.am | 8 +++-- |
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- configure.ac | 82 ++++++++++++++++++++++++++--------------------- |
97 |
- emboss/Makefile.am | 13 +++++--- |
98 |
- jemboss/lib/Makefile.am | 2 +- |
99 |
- m4/idxdbs.m4 | 17 +++------- |
100 |
- nucleus/Makefile.am | 8 +++-- |
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- 13 files changed, 100 insertions(+), 76 deletions(-) |
102 |
- |
103 |
-diff --git a/Makefile.am b/Makefile.am |
104 |
-index 177dec5..18dd99a 100644 |
105 |
---- a/Makefile.am |
106 |
-+++ b/Makefile.am |
107 |
-@@ -12,8 +12,11 @@ LICENSE \ |
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- ONEWS \ |
109 |
- PROBLEMS |
110 |
- |
111 |
--SUBDIRS = \ |
112 |
--plplot \ |
113 |
-+SUBDIRS = |
114 |
-+if !ESYSTEMLIBS |
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-+SUBDIRS += plplot |
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-+endif |
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-+SUBDIRS += \ |
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- ajax \ |
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- nucleus \ |
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- emboss \ |
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-@@ -33,5 +36,3 @@ dist-hook: |
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- tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) |
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- tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) |
124 |
- |
125 |
--install-exec-hook: |
126 |
-- $(bindir)/embossupdate |
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-diff --git a/ajax/Makefile.am b/ajax/Makefile.am |
128 |
-index f27472c..de34e17 100644 |
129 |
---- a/ajax/Makefile.am |
130 |
-+++ b/ajax/Makefile.am |
131 |
-@@ -1,7 +1,7 @@ |
132 |
- ## Process this file with automake to produce Makefile.in |
133 |
- |
134 |
--SUBDIRS = pcre |
135 |
-+SUBDIRS = |
136 |
- if !ESYSTEMLIBS |
137 |
--SUBDIRS += expat zlib |
138 |
-+SUBDIRS += pcre expat zlib |
139 |
- endif |
140 |
- SUBDIRS += core graphics ensembl ajaxdb acd |
141 |
-diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am |
142 |
-index 9f0f700..3295a1d 100644 |
143 |
---- a/ajax/acd/Makefile.am |
144 |
-+++ b/ajax/acd/Makefile.am |
145 |
-@@ -3,16 +3,20 @@ |
146 |
- lib_LTLIBRARIES = libacd.la |
147 |
- |
148 |
- libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
149 |
-+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la |
150 |
- |
151 |
- libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb |
152 |
-+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core |
153 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl |
154 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics |
155 |
--libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
156 |
- if !ESYSTEMLIBS |
157 |
-+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
158 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
159 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
160 |
--endif |
161 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot |
162 |
-+else |
163 |
-+libacd_la_CFLAGS += $(PLPLOT_CFLAGS) |
164 |
-+endif |
165 |
- libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
166 |
- |
167 |
- libacd_la_LDFLAGS = -version-info 6:5:0 |
168 |
-diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am |
169 |
-index c2b0c00..9de14fe 100644 |
170 |
---- a/ajax/ajaxdb/Makefile.am |
171 |
-+++ b/ajax/ajaxdb/Makefile.am |
172 |
-@@ -3,14 +3,16 @@ |
173 |
- lib_LTLIBRARIES = libajaxdb.la |
174 |
- |
175 |
- libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
176 |
-+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la |
177 |
- |
178 |
- libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl |
179 |
--libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
180 |
-+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core |
181 |
- if !ESYSTEMLIBS |
182 |
-+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
183 |
- libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
184 |
- libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
185 |
--endif |
186 |
- libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot |
187 |
-+endif |
188 |
- libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) |
189 |
- libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
190 |
- |
191 |
-diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am |
192 |
-index 2906837..3189c34 100644 |
193 |
---- a/ajax/core/Makefile.am |
194 |
-+++ b/ajax/core/Makefile.am |
195 |
-@@ -3,13 +3,15 @@ |
196 |
- lib_LTLIBRARIES = libajax.la |
197 |
- |
198 |
- libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
199 |
-+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) |
200 |
- |
201 |
--libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre |
202 |
-+libajax_la_CPPFLAGS = |
203 |
- if !ESYSTEMLIBS |
204 |
-+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
205 |
- libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
206 |
- libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
207 |
--endif |
208 |
- libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot |
209 |
-+endif |
210 |
- libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
211 |
- libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS) |
212 |
- libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS) |
213 |
-diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h |
214 |
-index 1623c82..5d928cf 100644 |
215 |
---- a/ajax/core/ajreg.h |
216 |
-+++ b/ajax/core/ajreg.h |
217 |
-@@ -39,9 +39,8 @@ |
218 |
- #include "ajdefine.h" |
219 |
- #include "ajstr.h" |
220 |
- |
221 |
--#include "pcre_config.h" |
222 |
--#include "pcre_internal.h" |
223 |
--#include "pcreposix.h" |
224 |
-+#include <pcre.h> |
225 |
-+#include <pcreposix.h> |
226 |
- |
227 |
- AJ_BEGIN_DECLS |
228 |
- |
229 |
-@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS |
230 |
- |
231 |
- typedef struct AjSRegexp |
232 |
- { |
233 |
-- real_pcre *pcre; |
234 |
-+ struct real_pcre *pcre; |
235 |
- pcre_extra *extra; |
236 |
- int *ovector; |
237 |
- const char* orig; |
238 |
-diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am |
239 |
-index 0d1250b..5484c02 100644 |
240 |
---- a/ajax/ensembl/Makefile.am |
241 |
-+++ b/ajax/ensembl/Makefile.am |
242 |
-@@ -3,13 +3,15 @@ |
243 |
- lib_LTLIBRARIES = libensembl.la |
244 |
- |
245 |
- libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
246 |
-+libensembl_la_LIBADD = ../core/libajax.la |
247 |
- |
248 |
--libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre |
249 |
-+libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core |
250 |
- if !ESYSTEMLIBS |
251 |
-+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
252 |
- libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
253 |
- libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
254 |
--endif |
255 |
- libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot |
256 |
-+endif |
257 |
- libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
258 |
- |
259 |
- libensembl_la_LDFLAGS = -version-info 6:5:0 |
260 |
-diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am |
261 |
-index a4f202b..1114c2c 100644 |
262 |
---- a/ajax/graphics/Makefile.am |
263 |
-+++ b/ajax/graphics/Makefile.am |
264 |
-@@ -3,12 +3,16 @@ |
265 |
- lib_LTLIBRARIES = libajaxg.la |
266 |
- |
267 |
- libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
268 |
-+libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS) |
269 |
- |
270 |
--libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre |
271 |
-+libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core |
272 |
- if !ESYSTEMLIBS |
273 |
-+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
274 |
- libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
275 |
--endif |
276 |
- libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot |
277 |
-+else |
278 |
-+libajaxg_la_CFLAGS += $(PLPLOT_CFLAGS) |
279 |
-+endif |
280 |
- libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
281 |
- |
282 |
- libajaxg_la_LDFLAGS = -version-info 6:5:0 |
283 |
-diff --git a/configure.ac b/configure.ac |
284 |
-index a7bd9c6..9ba3121 100644 |
285 |
---- a/configure.ac |
286 |
-+++ b/configure.ac |
287 |
-@@ -629,32 +629,6 @@ AS_CASE([${host_os}], |
288 |
- |
289 |
- |
290 |
- |
291 |
-- |
292 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
293 |
--dnl to see which version's configure.in these lines come from |
294 |
-- |
295 |
--dnl Provide the current PCRE version information. Do not use numbers |
296 |
--dnl with leading zeros for the minor version, as they end up in a C |
297 |
--dnl macro, and may be treated as octal constants. Stick to single |
298 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
299 |
--dnl that many releases anyway. |
300 |
-- |
301 |
--PCRE_MAJOR="7" |
302 |
--PCRE_MINOR="9" |
303 |
--PCRE_DATE="11-Apr-2009" |
304 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
305 |
-- |
306 |
--dnl Default values for miscellaneous macros |
307 |
-- |
308 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
309 |
-- |
310 |
--dnl Provide versioning information for libtool shared libraries that |
311 |
--dnl are built by default on Unix systems. |
312 |
-- |
313 |
--PCRE_LIB_VERSION="0:1:0" |
314 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
315 |
-- |
316 |
-- |
317 |
- dnl Define where the EMBOSS package is located |
318 |
- AC_SUBST([AJAX_FIXED_ROOT]) |
319 |
- AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" |
320 |
-@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL |
321 |
- |
322 |
- |
323 |
- |
324 |
--dnl "Export" these variables for PCRE |
325 |
- |
326 |
--AC_SUBST([HAVE_MEMMOVE]) |
327 |
--AC_SUBST([HAVE_STRERROR]) |
328 |
--AC_SUBST([PCRE_MAJOR]) |
329 |
--AC_SUBST([PCRE_MINOR]) |
330 |
--AC_SUBST([PCRE_DATE]) |
331 |
--AC_SUBST([PCRE_VERSION]) |
332 |
--AC_SUBST([PCRE_LIB_VERSION]) |
333 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
334 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
335 |
- |
336 |
- |
337 |
- |
338 |
-@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs], |
339 |
- |
340 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
341 |
- |
342 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
343 |
-+[ |
344 |
-+dnl using system libraries |
345 |
-+ PKG_CHECK_MODULES([PCRE], [libpcre]) |
346 |
-+ PKG_CHECK_MODULES([EXPAT], [expat]) |
347 |
-+ PKG_CHECK_MODULES([ZLIB], [zlib]) |
348 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd], |
349 |
-+ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] |
350 |
-+ ) |
351 |
-+], |
352 |
-+[ |
353 |
-+dnl using bundled libraries |
354 |
-+ dnl PCRE library definitions - see the MAJOR and MINOR values |
355 |
-+ dnl to see which version's configure.ac these lines come from |
356 |
- |
357 |
-+ dnl Provide the current PCRE version information. Do not use numbers |
358 |
-+ dnl with leading zeros for the minor version, as they end up in a C |
359 |
-+ dnl macro, and may be treated as octal constants. Stick to single |
360 |
-+ dnl digits for minor numbers less than 10. There are unlikely to be |
361 |
-+ dnl that many releases anyway. |
362 |
-+ |
363 |
-+ PCRE_MAJOR="7" |
364 |
-+ PCRE_MINOR="9" |
365 |
-+ PCRE_DATE="11-Apr-2009" |
366 |
-+ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
367 |
-+ |
368 |
-+ dnl Default values for miscellaneous macros |
369 |
-+ |
370 |
-+ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
371 |
-+ |
372 |
-+ dnl Provide versioning information for libtool shared libraries that |
373 |
-+ dnl are built by default on Unix systems. |
374 |
-+ |
375 |
-+ PCRE_LIB_VERSION="0:1:0" |
376 |
-+ PCRE_POSIXLIB_VERSION="0:0:0" |
377 |
-+ |
378 |
-+ dnl "Export" these variables for PCRE |
379 |
-+ AC_SUBST([HAVE_MEMMOVE]) |
380 |
-+ AC_SUBST([HAVE_STRERROR]) |
381 |
-+ AC_SUBST([PCRE_MAJOR]) |
382 |
-+ AC_SUBST([PCRE_MINOR]) |
383 |
-+ AC_SUBST([PCRE_DATE]) |
384 |
-+ AC_SUBST([PCRE_VERSION]) |
385 |
-+ AC_SUBST([PCRE_LIB_VERSION]) |
386 |
-+ AC_SUBST([PCRE_POSIXLIB_VERSION]) |
387 |
-+ AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
388 |
-+]) |
389 |
- |
390 |
- |
391 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
392 |
-diff --git a/emboss/Makefile.am b/emboss/Makefile.am |
393 |
-index 89ada78..f987d40 100644 |
394 |
---- a/emboss/Makefile.am |
395 |
-+++ b/emboss/Makefile.am |
396 |
-@@ -28,15 +28,18 @@ endif |
397 |
- |
398 |
- AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd |
399 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb |
400 |
-+AM_CPPFLAGS += -I$(top_srcdir)/ajax/core |
401 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl |
402 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics |
403 |
-+if !ESYSTEMLIBS |
404 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
405 |
--if !ESYSTEMLIBS |
406 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
407 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
408 |
--endif |
409 |
--AM_CPPFLAGS += -I$(top_srcdir)/nucleus |
410 |
- AM_CPPFLAGS += -I$(top_srcdir)/plplot |
411 |
-+else |
412 |
-+AM_CFLAGS += $(PLPLOT_CFLAGS) |
413 |
-+endif |
414 |
-+AM_CPPFLAGS += -I$(top_srcdir)/nucleus |
415 |
- AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) |
416 |
- AM_CPPFLAGS += $(JAVA_CPPFLAGS) |
417 |
- |
418 |
-@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la |
419 |
- if !ESYSTEMLIBS |
420 |
- LDADD += ../ajax/zlib/libezlib.la |
421 |
- LDADD += ../ajax/expat/libeexpat.la |
422 |
--endif |
423 |
- LDADD += ../ajax/pcre/libepcre.la |
424 |
- LDADD += ../plplot/libeplplot.la |
425 |
-+else |
426 |
-+LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS) |
427 |
-+endif |
428 |
- LDADD += $(XLIB) |
429 |
- |
430 |
- #if PURIFY |
431 |
-diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am |
432 |
-index 5f7e21e..8b45ce2 100644 |
433 |
---- a/jemboss/lib/Makefile.am |
434 |
-+++ b/jemboss/lib/Makefile.am |
435 |
-@@ -12,7 +12,7 @@ mail.jar \ |
436 |
- jalviewApplet.jar \ |
437 |
- jemboss.jar |
438 |
- |
439 |
--jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java |
440 |
-+jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java |
441 |
- if JAVA_BUILD |
442 |
- $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; |
443 |
- endif |
444 |
-diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4 |
445 |
-index 0ca7ea9..9b54f2a 100644 |
446 |
---- a/m4/idxdbs.m4 |
447 |
-+++ b/m4/idxdbs.m4 |
448 |
-@@ -1,17 +1,8 @@ |
449 |
- AC_DEFUN([CHECK_IDXDBS], |
450 |
- [ |
451 |
--AC_MSG_CHECKING(for EMBOSS pre-indexed databases) |
452 |
-+AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) |
453 |
- |
454 |
-- |
455 |
--if test -f ./emboss/index/edam.xac; then |
456 |
--AC_MSG_RESULT(yes) |
457 |
--else |
458 |
--AC_MSG_RESULT(no) |
459 |
--echo "" |
460 |
--echo "Pre-indexed edam, taxon + drcat databases not found." |
461 |
--echo "Please download them from within this directory using:" |
462 |
--echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." |
463 |
--echo "and then repeat the configure step." |
464 |
--exit 1 |
465 |
--fi |
466 |
-+AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], |
467 |
-+ [], |
468 |
-+ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) |
469 |
- ]) |
470 |
-diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am |
471 |
-index 37b8543..5819c89 100644 |
472 |
---- a/nucleus/Makefile.am |
473 |
-+++ b/nucleus/Makefile.am |
474 |
-@@ -3,6 +3,7 @@ |
475 |
- lib_LTLIBRARIES = libnucleus.la |
476 |
- |
477 |
- libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
478 |
-+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la |
479 |
- |
480 |
- if ISSHARED |
481 |
- if ISAIXIA64 |
482 |
-@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm |
483 |
- endif |
484 |
- endif |
485 |
- |
486 |
--libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot |
487 |
--libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
488 |
-+libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core |
489 |
- if !ESYSTEMLIBS |
490 |
-+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot |
491 |
-+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
492 |
- libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
493 |
- libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
494 |
-+else |
495 |
-+libnucleus_la_CFLAGS += $(PLPLOT_CFLAGS) |
496 |
- endif |
497 |
- libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics |
498 |
- libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl |
499 |
|
500 |
diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch |
501 |
deleted file mode 100644 |
502 |
index 15f5f967a07..00000000000 |
503 |
--- a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch |
504 |
+++ /dev/null |
505 |
@@ -1,61 +0,0 @@ |
506 |
---- EMBOSS-6.6.0/ajax/graphics/ajgraph.c |
507 |
-+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c |
508 |
-@@ -49,7 +49,7 @@ |
509 |
- |
510 |
- #define GRAPH_DEBUG 1 |
511 |
- |
512 |
--#include "plplotP.h" |
513 |
-+#include <plplotP.h> |
514 |
- |
515 |
- |
516 |
- static void GraphArray(ajuint numofpoints, |
517 |
-@@ -964,10 +964,10 @@ |
518 |
- if(!thys->ready) |
519 |
- { |
520 |
- #if GRAPH_DEBUG |
521 |
-- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); |
522 |
-+ ajDebug("=g= plsfnam ('%S')\n", txt); |
523 |
- #endif |
524 |
- |
525 |
-- plxsfnam(ajStrGetPtr(txt), ext); |
526 |
-+ plsfnam(ajStrGetPtr(txt)); |
527 |
- ajStrAssignS(&graphBasename, txt); |
528 |
- ajStrAssignC(&graphExtension, ext); |
529 |
- if(ajStrGetCharFirst(graphExtension) == '.') |
530 |
-@@ -1213,10 +1213,10 @@ |
531 |
- void ajGraphicsSetPenwidth(float penwidth) |
532 |
- { |
533 |
- #if GRAPH_DEBUG |
534 |
-- ajDebug("=g= plwid(%.2f) [width]\n", penwidth); |
535 |
-+ ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth); |
536 |
- #endif |
537 |
- |
538 |
-- plwid((PLINT)penwidth); |
539 |
-+ c_plwidth((PLINT)penwidth); |
540 |
- |
541 |
- return; |
542 |
- } |
543 |
-@@ -1538,10 +1538,10 @@ |
544 |
- static void GraphSetPen(ajint colour) |
545 |
- { |
546 |
- #if GRAPH_DEBUG |
547 |
-- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); |
548 |
-+ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); |
549 |
- #endif |
550 |
- |
551 |
-- plcol((PLINT)colour); |
552 |
-+ plcol0((PLINT)colour); |
553 |
- |
554 |
- return; |
555 |
- } |
556 |
---- EMBOSS-6.6.0/ajax/graphics/ajgraph.h |
557 |
-+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h |
558 |
-@@ -32,7 +32,7 @@ |
559 |
- /* ========================================================================= */ |
560 |
- |
561 |
- #include "ajdefine.h" |
562 |
--#include "plplot.h" |
563 |
-+#include <plplot.h> |
564 |
- #include "ajgraphstruct.h" |
565 |
- #include "ajdefine.h" |
566 |
- #include "ajstr.h" |
567 |
|
568 |
diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch |
569 |
deleted file mode 100644 |
570 |
index eff10b2e670..00000000000 |
571 |
--- a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch |
572 |
+++ /dev/null |
573 |
@@ -1,74 +0,0 @@ |
574 |
---- EMBOSS-6.6.0/ajax/core/ajfeatread.c |
575 |
-+++ EMBOSS-6.6.0/ajax/core/ajfeatread.c |
576 |
-@@ -45,6 +45,7 @@ |
577 |
- |
578 |
- #include <limits.h> |
579 |
- #include <math.h> |
580 |
-+#include <string.h> |
581 |
- #include <errno.h> |
582 |
- |
583 |
- #ifdef WIN32 |
584 |
---- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c |
585 |
-+++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c |
586 |
-@@ -43,7 +43,7 @@ |
587 |
- |
588 |
- #include <limits.h> |
589 |
- #include <math.h> |
590 |
-- |
591 |
-+#include <string.h> |
592 |
- |
593 |
- static AjPRegexp featoutRegUfoFmt = NULL; |
594 |
- static AjPRegexp featoutRegUfoFile = NULL; |
595 |
---- EMBOSS-6.6.0/ajax/core/ajpdbio.c |
596 |
-+++ EMBOSS-6.6.0/ajax/core/ajpdbio.c |
597 |
-@@ -37,7 +37,7 @@ |
598 |
- |
599 |
- #include <limits.h> |
600 |
- #include <math.h> |
601 |
-- |
602 |
-+#include <string.h> |
603 |
- |
604 |
- |
605 |
- |
606 |
---- EMBOSS-6.6.0/ajax/core/ajreg.c |
607 |
-+++ EMBOSS-6.6.0/ajax/core/ajreg.c |
608 |
-@@ -32,6 +32,7 @@ |
609 |
- #include "ajlib.h" |
610 |
- |
611 |
- #include "ajreg.h" |
612 |
-+#include <string.h> |
613 |
- |
614 |
- |
615 |
- |
616 |
---- EMBOSS-6.6.0/ajax/core/ajseqtype.c |
617 |
-+++ EMBOSS-6.6.0/ajax/core/ajseqtype.c |
618 |
-@@ -32,7 +32,7 @@ |
619 |
- #include "ajfeat.h" |
620 |
- #include "ajfile.h" |
621 |
- #include "ajreg.h" |
622 |
-- |
623 |
-+#include <string.h> |
624 |
- |
625 |
- |
626 |
- |
627 |
---- EMBOSS-6.6.0/nucleus/embindex.c |
628 |
-+++ EMBOSS-6.6.0/nucleus/embindex.c |
629 |
-@@ -35,6 +35,7 @@ |
630 |
- #include "ajnam.h" |
631 |
- |
632 |
- #include <errno.h> |
633 |
-+#include <string.h> |
634 |
- |
635 |
- #define BTENTRYFILE ".ent" |
636 |
- #define KWLIMIT 12 |
637 |
---- EMBOSS-6.6.0/nucleus/embword.c |
638 |
-+++ EMBOSS-6.6.0/nucleus/embword.c |
639 |
-@@ -36,7 +36,7 @@ |
640 |
- #include "ajutil.h" |
641 |
- |
642 |
- #include <math.h> |
643 |
-- |
644 |
-+#include <string.h> |
645 |
- |
646 |
- |
647 |
- |