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commit: 1c4cc4b44ec299a0611ea194f3ffc4c8b6389f87 |
2 |
Author: Horea Christian <chr <AT> chymera <DOT> eu> |
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AuthorDate: Mon Sep 28 08:34:14 2020 +0000 |
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Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> |
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CommitDate: Mon Sep 28 08:43:32 2020 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c4cc4b4 |
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|
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sci-chemistry/rosetta: removed unmaintained package |
9 |
|
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Package-Manager: Portage-3.0.8, Repoman-3.0.1 |
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Signed-off-by: Horea Christian <chr <AT> chymera.eu> |
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|
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.../rosetta/files/rosetta-3.4-boinc.patch | 53 ------- |
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.../rosetta/files/rosetta-3.4-boost.patch | 16 -- |
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.../rosetta/files/rosetta-3.4-boost157.patch | 16 -- |
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.../files/rosetta-3.4-fix-scons-warnings.patch | 82 ---------- |
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.../rosetta/files/rosetta-3.4-fix-valgrind.patch | 11 -- |
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.../rosetta/files/rosetta-3.4-gcc4.7.patch | 32 ---- |
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.../rosetta/files/rosetta-3.4-gcc4.78.patch | 32 ---- |
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.../rosetta/files/rosetta-3.4-gcc4.789.patch | 32 ---- |
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.../rosetta/files/rosetta-3.4-lange-fix.patch | 22 --- |
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.../rosetta/files/rosetta-3.4-platform.patch | 11 -- |
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.../rosetta/files/rosetta-3.4-unbundle.patch | 47 ------ |
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.../rosetta/files/rosetta-3.4-user-settings.patch | 29 ---- |
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sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch | 12 -- |
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sci-chemistry/rosetta/metadata.xml | 17 -- |
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sci-chemistry/rosetta/rosetta-3.4.ebuild | 171 --------------------- |
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15 files changed, 583 deletions(-) |
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|
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diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch |
31 |
deleted file mode 100644 |
32 |
index 1f6da965c..000000000 |
33 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch |
34 |
+++ /dev/null |
35 |
@@ -1,53 +0,0 @@ |
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---- src/protocols/boinc/boinc_shmem.hh 2009-02-03 22:47:07.000000000 +0100 |
37 |
-+++ src/protocols/boinc/boinc_shmem.hh.new 2009-04-09 14:59:15.000000000 +0200 |
38 |
-@@ -18,7 +18,7 @@ |
39 |
- #include <core/types.hh> |
40 |
- |
41 |
- #ifdef BOINC |
42 |
--#include "boinc_api.h" |
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-+#include "boinc/boinc_api.h" |
44 |
- #endif |
45 |
- |
46 |
- namespace protocols { |
47 |
---- src/protocols/boinc/boinc.hh 2009-02-03 22:47:07.000000000 +0100 |
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-+++ src/protocols/boinc/boinc.hh.new 2009-04-09 15:00:57.000000000 +0200 |
49 |
-@@ -20,11 +20,11 @@ |
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- #include <boinc_win.h> |
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- #include <str_util.h> |
52 |
- #endif |
53 |
--#include <boinc_api.h> |
54 |
--#include <diagnostics.h> |
55 |
--#include <error_numbers.h> |
56 |
-+#include <boinc/boinc_api.h> |
57 |
-+#include <boinc/diagnostics.h> |
58 |
-+#include <boinc/error_numbers.h> |
59 |
- #ifdef BOINC_GRAPHICS |
60 |
--#include <graphics2.h> |
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--#include <util.h> |
62 |
--#include <shmem.h> |
63 |
-+#include <boinc/graphics2.h> |
64 |
-+#include <boinc/util.h> |
65 |
-+#include <boinc/shmem.h> |
66 |
- |
67 |
---- src/utility/exit.cc 2009-02-03 22:47:28.000000000 +0100 |
68 |
-+++ src/utility/exit.cc.new 2009-04-09 16:23:18.000000000 +0200 |
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-@@ -23,7 +23,7 @@ |
70 |
- // Boinc headers |
71 |
- #ifdef BOINC |
72 |
- #include <utility/io/izstream.hh> |
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--#include <boinc_api.h> |
74 |
-+#include <boinc/boinc_api.h> |
75 |
- #include <string> |
76 |
- #endif |
77 |
- |
78 |
---- src/utility/boinc/boinc_util.cc 2009-02-03 22:47:30.000000000 +0100 |
79 |
-+++ src/utility/boinc/boinc_util.cc.new 2009-04-09 16:25:16.000000000 +0200 |
80 |
-@@ -20,7 +20,7 @@ |
81 |
- //#ifdef _WIN32 |
82 |
- //#include <boinc_win.h> |
83 |
- //#endif |
84 |
--#include <boinc_api.h> |
85 |
-+#include <boinc/boinc_api.h> |
86 |
- |
87 |
- // C++ headers |
88 |
- #include <iostream> |
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|
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diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch |
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deleted file mode 100644 |
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index 7c1e1ffc2..000000000 |
93 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch |
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+++ /dev/null |
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@@ -1,16 +0,0 @@ |
96 |
- tools/build/basic.settings | 2 +- |
97 |
- 1 file changed, 1 insertion(+), 1 deletion(-) |
98 |
- |
99 |
-diff --git a/tools/build/basic.settings b/tools/build/basic.settings |
100 |
-index ecf3237..356cd61 100644 |
101 |
---- a/tools/build/basic.settings |
102 |
-+++ b/tools/build/basic.settings |
103 |
-@@ -610,7 +610,7 @@ settings = { |
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- "gcc, boost_thread" : { |
105 |
- "appends" : { |
106 |
- "defines" : [ "MULTI_THREADED" ], |
107 |
-- "libraries" : [ "pthread", "boost_thread" ], |
108 |
-+ "libraries" : [ "pthread", "boost_thread", "boost_system" ], |
109 |
- "library_path" : [ "/usr/local/lib", "/opt/boost/lib" ], |
110 |
- "flags" : { |
111 |
- "compile" : [ "pthread" ], |
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|
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diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch |
114 |
deleted file mode 100644 |
115 |
index c2d7594b6..000000000 |
116 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch |
117 |
+++ /dev/null |
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@@ -1,16 +0,0 @@ |
119 |
- src/protocols/moves/StructureRestrictor.cc | 2 +- |
120 |
- 1 file changed, 1 insertion(+), 1 deletion(-) |
121 |
- |
122 |
-diff --git a/src/protocols/moves/StructureRestrictor.cc b/src/protocols/moves/StructureRestrictor.cc |
123 |
-index 1e1f1d4..da69796 100644 |
124 |
---- a/src/protocols/moves/StructureRestrictor.cc |
125 |
-+++ b/src/protocols/moves/StructureRestrictor.cc |
126 |
-@@ -40,7 +40,7 @@ |
127 |
- |
128 |
- using namespace std; |
129 |
- using namespace boost; |
130 |
--using namespace core; |
131 |
-+using namespace boost::core; |
132 |
- using namespace pose; |
133 |
- using namespace protocols::jd2; |
134 |
- |
135 |
|
136 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch |
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deleted file mode 100644 |
138 |
index 321d0a784..000000000 |
139 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch |
140 |
+++ /dev/null |
141 |
@@ -1,82 +0,0 @@ |
142 |
---- src/SConscript.src 2009-02-03 22:44:31.000000000 +0100 |
143 |
-+++ src/SConscript.src.new 2009-04-07 16:25:30.000000000 +0200 |
144 |
-@@ -85,7 +85,7 @@ |
145 |
- |
146 |
- # Transform the modified settings into SCons Environment variables. |
147 |
- # Gives priority to project settings over global settings. |
148 |
--env = build.environment.Copy() |
149 |
-+env = build.environment.Clone() |
150 |
- env.Prepend(**actual.symbols()) |
151 |
- |
152 |
- |
153 |
---- tools/build/setup.py 2009-02-03 22:44:32.000000000 +0100 |
154 |
-+++ tools/build/setup.py.new 2009-04-07 16:43:42.000000000 +0200 |
155 |
-@@ -42,21 +42,21 @@ |
156 |
- # Read in the options from the .settings files (1st pass) |
157 |
- # This has to be done in two passes, because some legal values |
158 |
- # (version numbers) are dependent on the other values |
159 |
-- options.AddOptions( |
160 |
-+ options.AddVariables( |
161 |
- # Options for the build. Modifiable on the command-line. |
162 |
-- EnumOption("cxx", "Select the C++ compiler to build with", |
163 |
-+ EnumVariable("cxx", "Select the C++ compiler to build with", |
164 |
- defaults.cxx, supported.cxx), |
165 |
-- EnumOption("os", "Select the operating system to build for", |
166 |
-+ EnumVariable("os", "Select the operating system to build for", |
167 |
- defaults.os, supported.os), |
168 |
-- EnumOption("arch", "Select the processor architecture to build for", |
169 |
-+ EnumVariable("arch", "Select the processor architecture to build for", |
170 |
- defaults.arch, supported.arch), |
171 |
-- EnumOption("mode", "Select the optimization mode", |
172 |
-+ EnumVariable("mode", "Select the optimization mode", |
173 |
- defaults.mode, supported.mode), |
174 |
-- ListOption("cat", "Select the build category", |
175 |
-+ ListVariable("cat", "Select the build category", |
176 |
- defaults.cat, supported.cat), |
177 |
-- ListOption("extras", "Select any extras", |
178 |
-+ ListVariable("extras", "Select any extras", |
179 |
- defaults.extras, supported.extras), |
180 |
-- ListOption("log", "Log debugging output", |
181 |
-+ ListVariable("log", "Log debugging output", |
182 |
- defaults.log, supported.log), |
183 |
- ) |
184 |
- |
185 |
---- tools/build/setup.py 2009-04-07 16:44:26.000000000 +0200 |
186 |
-+++ tools/build/setup.py.new 2009-04-07 16:46:45.000000000 +0200 |
187 |
-@@ -37,7 +37,7 @@ |
188 |
- |
189 |
- # Incorporate options in site and user options |
190 |
- option_files = [ "%s.options" % (name) for name in ("site", "user") ] |
191 |
-- options = Options(option_files) |
192 |
-+ options = Variables(option_files) |
193 |
- |
194 |
- # Read in the options from the .settings files (1st pass) |
195 |
- # This has to be done in two passes, because some legal values |
196 |
-@@ -68,12 +68,12 @@ |
197 |
- cxx = env["cxx"] |
198 |
- os = env["os"] |
199 |
- arch = env["arch"] |
200 |
-- options.AddOptions( |
201 |
-- EnumOption("cxx_ver", "Select the C++ compiler version", |
202 |
-+ options.AddVariables( |
203 |
-+ EnumVariable("cxx_ver", "Select the C++ compiler version", |
204 |
- defaults.cxx_ver, supported.cxx[cxx]), |
205 |
-- EnumOption("os_ver", "Select the operating system version", |
206 |
-+ EnumVariable("os_ver", "Select the operating system version", |
207 |
- defaults.os_ver, supported.os[os]), |
208 |
-- EnumOption("arch_size", "Select the architecture bit-size", |
209 |
-+ EnumVariable("arch_size", "Select the architecture bit-size", |
210 |
- defaults.arch_size, supported.arch[arch]), |
211 |
- ) |
212 |
- |
213 |
---- src/SConscript.apps 2009-02-03 22:44:31.000000000 +0100 |
214 |
-+++ src/SConscript.apps.new 2009-04-07 16:48:06.000000000 +0200 |
215 |
-@@ -92,7 +92,7 @@ |
216 |
- |
217 |
- # Transform the modified settings into SCons Environment variables. |
218 |
- # Gives priority to project settings over global settings. |
219 |
--env = build.environment.Copy() |
220 |
-+env = build.environment.Clone() |
221 |
- env.Prepend(**actual.symbols()) |
222 |
- if "static" not in build.options.extras: |
223 |
- env["RPATH"] = build.toplevel + "/build/src/" + build.platform |
224 |
|
225 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch |
226 |
deleted file mode 100644 |
227 |
index bc98773c1..000000000 |
228 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch |
229 |
+++ /dev/null |
230 |
@@ -1,11 +0,0 @@ |
231 |
---- tools/build/options.settings 2009-02-03 22:44:32.000000000 +0100 |
232 |
-+++ tools/build/options.settings.new 2009-04-07 18:12:00.000000000 +0200 |
233 |
-@@ -76,7 +76,7 @@ |
234 |
- # Build so that valgrind can follow the memory use. |
235 |
- # Valgrind normally works fine with most executables but not |
236 |
- # with static builds, which we are doing. |
237 |
-- "valgrind", |
238 |
-+ "shared", |
239 |
- |
240 |
- # Build using static linking. |
241 |
- "static", |
242 |
|
243 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch |
244 |
deleted file mode 100644 |
245 |
index d0893c183..000000000 |
246 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch |
247 |
+++ /dev/null |
248 |
@@ -1,32 +0,0 @@ |
249 |
- tools/build/options.settings | 2 +- |
250 |
- 1 file changed, 1 insertion(+), 1 deletion(-) |
251 |
- |
252 |
-diff --git a/tools/build/options.settings b/tools/build/options.settings |
253 |
-index 30fb65e..f79ef5b 100644 |
254 |
---- a/tools/build/options.settings |
255 |
-+++ b/tools/build/options.settings |
256 |
-@@ -9,7 +9,7 @@ |
257 |
- options = { |
258 |
- |
259 |
- "cxx" : { |
260 |
-- "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ], |
261 |
-+ "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "*" ], |
262 |
- "icc" : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK |
263 |
- "msvc" : [ "7.0", "7.1", "8.0", "8.1", "*" ], |
264 |
- "xlc" : [ "7.0", "8.0", "9.0", "XL", "*" ], |
265 |
- src/protocols/jd2/SingleFileBuffer.cc | 2 ++ |
266 |
- 1 file changed, 2 insertions(+) |
267 |
- |
268 |
-diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc |
269 |
-index aa78d91..61ca823 100644 |
270 |
---- a/src/protocols/jd2/SingleFileBuffer.cc |
271 |
-+++ b/src/protocols/jd2/SingleFileBuffer.cc |
272 |
-@@ -28,6 +28,8 @@ |
273 |
- #include <ctime> // for clock() |
274 |
- #endif |
275 |
- |
276 |
-+#include <unistd.h> |
277 |
-+ |
278 |
- namespace protocols { |
279 |
- namespace jd2 { |
280 |
- using namespace core; |
281 |
|
282 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch |
283 |
deleted file mode 100644 |
284 |
index 882534bfd..000000000 |
285 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch |
286 |
+++ /dev/null |
287 |
@@ -1,32 +0,0 @@ |
288 |
- tools/build/options.settings | 2 +- |
289 |
- 1 file changed, 1 insertion(+), 1 deletion(-) |
290 |
- |
291 |
-diff --git a/tools/build/options.settings b/tools/build/options.settings |
292 |
-index 30fb65e..f79ef5b 100644 |
293 |
---- a/tools/build/options.settings |
294 |
-+++ b/tools/build/options.settings |
295 |
-@@ -9,7 +9,7 @@ |
296 |
- options = { |
297 |
- |
298 |
- "cxx" : { |
299 |
-- "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ], |
300 |
-+ "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "4.8", "*" ], |
301 |
- "icc" : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK |
302 |
- "msvc" : [ "7.0", "7.1", "8.0", "8.1", "*" ], |
303 |
- "xlc" : [ "7.0", "8.0", "9.0", "XL", "*" ], |
304 |
- src/protocols/jd2/SingleFileBuffer.cc | 2 ++ |
305 |
- 1 file changed, 2 insertions(+) |
306 |
- |
307 |
-diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc |
308 |
-index aa78d91..61ca823 100644 |
309 |
---- a/src/protocols/jd2/SingleFileBuffer.cc |
310 |
-+++ b/src/protocols/jd2/SingleFileBuffer.cc |
311 |
-@@ -28,6 +28,8 @@ |
312 |
- #include <ctime> // for clock() |
313 |
- #endif |
314 |
- |
315 |
-+#include <unistd.h> |
316 |
-+ |
317 |
- namespace protocols { |
318 |
- namespace jd2 { |
319 |
- using namespace core; |
320 |
|
321 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch |
322 |
deleted file mode 100644 |
323 |
index e11532ac4..000000000 |
324 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch |
325 |
+++ /dev/null |
326 |
@@ -1,32 +0,0 @@ |
327 |
- tools/build/options.settings | 2 +- |
328 |
- 1 file changed, 1 insertion(+), 1 deletion(-) |
329 |
- |
330 |
-diff --git a/tools/build/options.settings b/tools/build/options.settings |
331 |
-index 30fb65e..f79ef5b 100644 |
332 |
---- a/tools/build/options.settings |
333 |
-+++ b/tools/build/options.settings |
334 |
-@@ -9,7 +9,7 @@ |
335 |
- options = { |
336 |
- |
337 |
- "cxx" : { |
338 |
-- "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ], |
339 |
-+ "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "4.8", "4.9", "*" ], |
340 |
- "icc" : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK |
341 |
- "msvc" : [ "7.0", "7.1", "8.0", "8.1", "*" ], |
342 |
- "xlc" : [ "7.0", "8.0", "9.0", "XL", "*" ], |
343 |
- src/protocols/jd2/SingleFileBuffer.cc | 2 ++ |
344 |
- 1 file changed, 2 insertions(+) |
345 |
- |
346 |
-diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc |
347 |
-index aa78d91..61ca823 100644 |
348 |
---- a/src/protocols/jd2/SingleFileBuffer.cc |
349 |
-+++ b/src/protocols/jd2/SingleFileBuffer.cc |
350 |
-@@ -28,6 +28,8 @@ |
351 |
- #include <ctime> // for clock() |
352 |
- #endif |
353 |
- |
354 |
-+#include <unistd.h> |
355 |
-+ |
356 |
- namespace protocols { |
357 |
- namespace jd2 { |
358 |
- using namespace core; |
359 |
|
360 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch b/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch |
361 |
deleted file mode 100644 |
362 |
index 17e85f882..000000000 |
363 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch |
364 |
+++ /dev/null |
365 |
@@ -1,22 +0,0 @@ |
366 |
- tools/build/setup.py | 8 +++++++- |
367 |
- 1 file changed, 7 insertions(+), 1 deletion(-) |
368 |
- |
369 |
-diff --git a/tools/build/setup.py b/tools/build/setup.py |
370 |
-index 4e57ff6..d8a2a08 100644 |
371 |
---- a/tools/build/setup.py |
372 |
-+++ b/tools/build/setup.py |
373 |
-@@ -354,7 +354,13 @@ what SCons will use to build the system. |
374 |
- symbols = setting.appends.symbols() |
375 |
- if symbols.has_key("ENV"): |
376 |
- for key, value in symbols["ENV"].items(): |
377 |
-- env["ENV"][key] += value |
378 |
-+ if key == "PATH": |
379 |
-+ env["ENV"][key] = value |
380 |
-+ else: |
381 |
-+ try: |
382 |
-+ env["ENV"][key] += value |
383 |
-+ except: |
384 |
-+ print key, value |
385 |
- del symbols["ENV"] |
386 |
- env.Append(**symbols) |
387 |
- if setting.prepends: |
388 |
|
389 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch b/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch |
390 |
deleted file mode 100644 |
391 |
index 82f0ba63f..000000000 |
392 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch |
393 |
+++ /dev/null |
394 |
@@ -1,11 +0,0 @@ |
395 |
---- ./tools/build/setup_platforms.py 2009-02-03 22:44:32.000000000 +0100 |
396 |
-+++ ./tools/build/setup_platforms.py.new 2009-04-07 16:16:44.000000000 +0200 |
397 |
-@@ -274,7 +274,7 @@ |
398 |
- """ |
399 |
- # Note that these are very different values, and need processing |
400 |
- if globals().has_key("platform"): |
401 |
-- return platform.processor() or _uname()[4] |
402 |
-+ return platform.machine() or _uname()[4] |
403 |
- else: |
404 |
- return _uname()[4] |
405 |
- |
406 |
|
407 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch b/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch |
408 |
deleted file mode 100644 |
409 |
index ba810b162..000000000 |
410 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch |
411 |
+++ /dev/null |
412 |
@@ -1,47 +0,0 @@ |
413 |
- src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh | 3 +-- |
414 |
- .../pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh | 3 +-- |
415 |
- src/utility/io/zipstream.hpp | 3 +-- |
416 |
- 3 files changed, 3 insertions(+), 6 deletions(-) |
417 |
- |
418 |
-diff --git a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh |
419 |
-index 0aa44a6..299e0c5 100644 |
420 |
---- a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh |
421 |
-+++ b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh |
422 |
-@@ -402,8 +402,7 @@ |
423 |
- #include <boost/function.hpp> |
424 |
- #include <boost/pool/detail/mutex.hpp> |
425 |
- #include <boost/pool/poolfwd.hpp> |
426 |
--#include <zlib/zlib.h> |
427 |
--#include <zlib/zutil.h> |
428 |
-+#include <zlib.h> |
429 |
- |
430 |
- namespace core { |
431 |
- namespace pack { |
432 |
-diff --git a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh |
433 |
-index 2396126..700e78d 100644 |
434 |
---- a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh |
435 |
-+++ b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh |
436 |
-@@ -405,8 +405,7 @@ |
437 |
- #include <boost/function.hpp> |
438 |
- #include <boost/pool/detail/mutex.hpp> |
439 |
- #include <boost/pool/poolfwd.hpp> |
440 |
--#include <zlib/zlib.h> |
441 |
--#include <zlib/zutil.h> |
442 |
-+#include <zlib.h> |
443 |
- |
444 |
- namespace core { |
445 |
- namespace pack { |
446 |
-diff --git a/src/utility/io/zipstream.hpp b/src/utility/io/zipstream.hpp |
447 |
-index adaf88c..c7d36d0 100644 |
448 |
---- a/src/utility/io/zipstream.hpp |
449 |
-+++ b/src/utility/io/zipstream.hpp |
450 |
-@@ -43,8 +43,7 @@ |
451 |
- |
452 |
- |
453 |
- // Zlib headers |
454 |
--#include <zlib/zlib.h> |
455 |
--#include <zlib/zutil.h> |
456 |
-+#include <zlib.h> |
457 |
- |
458 |
- |
459 |
- |
460 |
|
461 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch |
462 |
deleted file mode 100644 |
463 |
index d7297cfc0..000000000 |
464 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch |
465 |
+++ /dev/null |
466 |
@@ -1,29 +0,0 @@ |
467 |
- tools/build/user.settings | 8 +++++++- |
468 |
- 1 file changed, 7 insertions(+), 1 deletion(-) |
469 |
- |
470 |
-diff --git a/tools/build/user.settings b/tools/build/user.settings |
471 |
-index 27a001f..9696e3e 100644 |
472 |
---- a/tools/build/user.settings |
473 |
-+++ b/tools/build/user.settings |
474 |
-@@ -22,7 +22,7 @@ |
475 |
- # and select between them from the options. For now there is only the |
476 |
- # single "user" settings. |
477 |
- |
478 |
--#import os |
479 |
-+import os |
480 |
- settings = { |
481 |
- "user" : { |
482 |
- "prepends" : { |
483 |
-@@ -38,6 +38,12 @@ settings = { |
484 |
- #"program_path" : os.environ["PATH"].split(":"), |
485 |
- }, |
486 |
- "overrides" : { |
487 |
-+ "flags" : { |
488 |
-+ "compile" : [ GENTOO_CXXFLAGS ], |
489 |
-+ "link" : [ GENTOO_LDFLAGS ], |
490 |
-+ }, |
491 |
-+ "cc" : os.environ["CC"], |
492 |
-+ "cxx" : os.environ["CXX"], |
493 |
- }, |
494 |
- "removes" : { |
495 |
- }, |
496 |
|
497 |
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch b/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch |
498 |
deleted file mode 100644 |
499 |
index 18060add4..000000000 |
500 |
--- a/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch |
501 |
+++ /dev/null |
502 |
@@ -1,12 +0,0 @@ |
503 |
---- src/utility/io/zipstream.hpp 2009-02-03 22:47:27.000000000 +0100 |
504 |
-+++ src/utility/io/zipstream.hpp.new 2009-04-07 19:57:09.000000000 +0200 |
505 |
-@@ -36,8 +36,7 @@ |
506 |
- |
507 |
- |
508 |
- // Zlib headers |
509 |
--#include <zlib/zlib.h> |
510 |
--#include <zlib/zutil.h> |
511 |
-+#include <zlib.h> |
512 |
- |
513 |
- // C++ headers |
514 |
- #include <algorithm> |
515 |
|
516 |
diff --git a/sci-chemistry/rosetta/metadata.xml b/sci-chemistry/rosetta/metadata.xml |
517 |
deleted file mode 100644 |
518 |
index dcf5c02f4..000000000 |
519 |
--- a/sci-chemistry/rosetta/metadata.xml |
520 |
+++ /dev/null |
521 |
@@ -1,17 +0,0 @@ |
522 |
-<?xml version="1.0" encoding="UTF-8"?> |
523 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
524 |
-<pkgmetadata> |
525 |
- <maintainer type="project"> |
526 |
- <email>sci-chemistry@g.o</email> |
527 |
- <name>Gentoo Chemistry Project</name> |
528 |
- </maintainer> |
529 |
- <use> |
530 |
- <flag name="boinc">compile rosetta as a rosetta@home client</flag> |
531 |
- <flag name="boost">compile rosetta with boost supported code</flag> |
532 |
- <flag name="float">Build with floats rather than doubles</flag> |
533 |
- <flag name="lange">Apply patches from www.csrosetta.org</flag> |
534 |
- </use> |
535 |
- <upstream> |
536 |
- <bugs-to>mailto:general-support@×××××××××××××××××××.org</bugs-to> |
537 |
- </upstream> |
538 |
-</pkgmetadata> |
539 |
|
540 |
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild |
541 |
deleted file mode 100644 |
542 |
index bf40276a7..000000000 |
543 |
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild |
544 |
+++ /dev/null |
545 |
@@ -1,171 +0,0 @@ |
546 |
-# Copyright 1999-2015 Gentoo Foundation |
547 |
-# Distributed under the terms of the GNU General Public License v2 |
548 |
- |
549 |
-# boinc support is BROKEN !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
550 |
- |
551 |
-EAPI=5 |
552 |
- |
553 |
-inherit eutils multilib prefix scons-utils toolchain-funcs versionator |
554 |
- |
555 |
-#MY_P="${PN}$(get_major_version)_source" |
556 |
-MY_P="${PN}${PV}_source" |
557 |
- |
558 |
-DESCRIPTION="Prediction of protein structures and protein-protein interactions" |
559 |
-HOMEPAGE="http://www.rosettacommons.org/" |
560 |
-SRC_URI="${MY_P}.tgz patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt" |
561 |
- |
562 |
-LICENSE="|| ( rosetta-academic rosetta-commercial )" |
563 |
-SLOT="0" |
564 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
565 |
-IUSE="boinc +boost custom-cflags debug doc float +lange mpi +openmp X" |
566 |
- |
567 |
-REQUIRED_USE="?? ( mpi boinc )" |
568 |
- |
569 |
-RESTRICT="fetch" |
570 |
- |
571 |
-RDEPEND=" |
572 |
- dev-db/cppdb |
573 |
- mpi? ( virtual/mpi ) |
574 |
- boinc? ( sci-misc/boinc[X?] ) |
575 |
- boost? ( dev-libs/boost ) |
576 |
- sci-libs/rosetta-db" |
577 |
-DEPEND="${RDEPEND} |
578 |
- dev-util/scons |
579 |
- doc? ( app-doc/doxygen ) |
580 |
- X? ( media-libs/freeglut )" |
581 |
- |
582 |
-MYCONF="" |
583 |
- |
584 |
-S="${WORKDIR}/${PN}_source" |
585 |
- |
586 |
-pkg_nofetch() { |
587 |
- einfo "Go to ${HOMEPAGE} and get ${A}" |
588 |
- einfo "which must be placed in ${DISTDIR}" |
589 |
-} |
590 |
- |
591 |
-src_prepare() { |
592 |
- local myCXXFLAGS |
593 |
- local myLDFLAGS |
594 |
- |
595 |
- use custom-cflags || \ |
596 |
- export CXXFLAGS="-O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -pipe" |
597 |
- |
598 |
- export LD_LIBRARY_PATH="" |
599 |
- use lange && \ |
600 |
- epatch \ |
601 |
- "${DISTDIR}"/patch_${PN}${PV}_to_CSROSETTA3_ver1.3.txt \ |
602 |
- "${FILESDIR}"/${P}-lange-fix.patch |
603 |
- |
604 |
- epatch \ |
605 |
- "${FILESDIR}"/${P}-platform.patch \ |
606 |
- "${FILESDIR}"/${P}-user-settings.patch \ |
607 |
- "${FILESDIR}"/${P}-fix-valgrind.patch \ |
608 |
- "${FILESDIR}"/${P}-boinc.patch \ |
609 |
- "${FILESDIR}"/${P}-boost.patch \ |
610 |
- "${FILESDIR}"/${P}-boost157.patch \ |
611 |
- "${FILESDIR}"/${P}-gcc4.789.patch |
612 |
- |
613 |
- eprefixify tools/build/* |
614 |
- |
615 |
- rm bin/* external/{dbio,scons-local,lib} -rfv || die |
616 |
- |
617 |
- find external/boost_1_46_1 -name "*.hpp" -delete || die |
618 |
- |
619 |
- for i in ${CXXFLAGS}; do |
620 |
- myCXXFLAGS="${myCXXFLAGS} \"${i/-/}\"," |
621 |
- done |
622 |
- |
623 |
- for i in ${LDFLAGS}; do |
624 |
- myLDFLAGS="${myLDFLAGS} \"${i/-/}\"," |
625 |
- done |
626 |
- |
627 |
- sed \ |
628 |
- -e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \ |
629 |
- -e "s:GENTOO_LDFLAGS:${myCXXFLAGS} ${myLDFLAGS}:g" \ |
630 |
- -e "s:GENTOO_LIBDIR:$(get_libdir):g" \ |
631 |
- -e "/program_path/s:#::g" \ |
632 |
- -i tools/build/user.settings || die |
633 |
- |
634 |
- tc-export CC CXX |
635 |
- |
636 |
- if use mpi; then |
637 |
- sed \ |
638 |
- -e 's:mpiCC:mpicxx:g' \ |
639 |
- -i tools/build/basic.settings || die |
640 |
- sed \ |
641 |
- -e "/cxx/d" \ |
642 |
- -i tools/build/user.settings || die |
643 |
- fi |
644 |
-} |
645 |
- |
646 |
-src_configure() { |
647 |
- local myextras="" |
648 |
- local mymode="" |
649 |
- local mycxx="" |
650 |
- |
651 |
- use boinc && EXTRAS="boinc" |
652 |
- use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost") |
653 |
- use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost_thread") |
654 |
- use float && EXTRAS=$(my_list_append "${EXTRAS}" "rosetta_float") |
655 |
- use openmp && EXTRAS=$(my_list_append "${EXTRAS}" "omp") |
656 |
- use X && EXTRAS=$(my_list_append "${EXTRAS}" "graphics") |
657 |
- use mpi && EXTRAS=$(my_list_append "${EXTRAS}" "mpi") |
658 |
- |
659 |
- COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') |
660 |
- mycxx="cxx=${COMPILER}" |
661 |
- |
662 |
- test -n "${EXTRAS}" && myextras="extras=${EXTRAS}" |
663 |
- |
664 |
- if use debug; then |
665 |
- mymode="debug" |
666 |
- else |
667 |
- mymode="release" |
668 |
- fi |
669 |
- |
670 |
- MYCONF="mode=${mymode} ${myextras} ${mycxx}" |
671 |
-} |
672 |
- |
673 |
-src_compile() { |
674 |
- einfo "running 'scons bin cat=src ${MYCONF}' ..." |
675 |
- escons bin cat=src ${MYCONF} |
676 |
- |
677 |
- if use doc; then |
678 |
- einfo "running 'scons ${MYCONF} cat=doc' ..." |
679 |
- scons ${MYCONF} cat=doc || die "scons failed to build documentation" |
680 |
- fi |
681 |
-} |
682 |
- |
683 |
-src_install() { |
684 |
- dolib.so build/src/release/linux/*/*/*/*/*/${EXTRAS//,/-}/*.so* |
685 |
- |
686 |
- use doc && dohtml build/doc/rosetta++/docs/* |
687 |
- |
688 |
- cd bin || die |
689 |
- for BIN in *; do |
690 |
- newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files" |
691 |
- done |
692 |
- |
693 |
- if [[ -e "${ED}"/usr/bin/cluster ]]; then |
694 |
- mv "${ED}"/usr/bin/cluster{,-${PN}} || die |
695 |
- fi |
696 |
- |
697 |
- if [[ -e "${ED}"/usr/bin/benchmark ]]; then |
698 |
- mv "${ED}"/usr/bin/benchmark{,-${PN}} || die |
699 |
- fi |
700 |
-} |
701 |
- |
702 |
-my_filter_option() { |
703 |
- local value="$1" |
704 |
- local exp="$2" |
705 |
- local result=`echo ${value} | sed -e s/${exp}//g` |
706 |
- echo "${result}" |
707 |
- return 0; |
708 |
-} |
709 |
- |
710 |
-my_list_append() { |
711 |
- local old_value="$1" |
712 |
- local new_value="$2" |
713 |
- test -n "${old_value}" && old_value="${old_value}," |
714 |
- echo "${old_value}${new_value}" |
715 |
- return 0; |
716 |
-} |