Gentoo Archives: gentoo-commits

From: Justin Lecher <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:ccp4 commit in: /
Date: Thu, 30 May 2013 10:31:43
Message-Id: 1369909778.cd7d9ba38de3df2079f68c53db8ae4fa6fb3dab3.jlec@gentoo
1 commit: cd7d9ba38de3df2079f68c53db8ae4fa6fb3dab3
2 Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
3 AuthorDate: Thu May 30 10:29:38 2013 +0000
4 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
5 CommitDate: Thu May 30 10:29:38 2013 +0000
6 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cd7d9ba3
7
8 Merge branch 'master' into ccp4
9
10 * master: (776 commits)
11 Moved to tree Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
12 sci-chemistry/coot: Move to new python eclasses
13 sci-chemistry/coot: Drop version from clipper
14 root-docs: fix sandbox access violation
15 root: fix build with postgres
16 Moved html documentation one folder up.
17 Version bump.
18 Added html documentation.
19 sci-libs/blas-reference: proper versioning for live ebuild
20 sci-libs/coinor-flopcpp: Initial import
21 Switch to EAPI5
22 sci-libs/coinor-sample: Version bump
23 sci-libs/coinor-symphony: Version bump
24 sci-libs/coinor-cppad: Version bump
25 sci-libs/coinor-cbc: Version bump
26 sci-libs/coinor-cgl: Fixed missing header
27 sci-libs/coinor-buildtools: Initial import
28 sci-libs/coinor-alps: Version bump
29 removed in source builds
30 sci-libs/coinor-cgl: Version bump
31 ...
32
33 Conflicts:
34 sci-chemistry/jligand/ChangeLog
35 sci-chemistry/jligand/Manifest
36 sci-chemistry/jligand/jligand-1.0.37.ebuild
37
38
39 .DS_Store | Bin 15364 -> 0 bytes
40 README.md | 16 +-
41 app-admin/eselect/ChangeLog | 14 +-
42 app-admin/eselect/Manifest | 3 +-
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44 app-admin/eselect/eselect-1.3.3-r100.ebuild | 79 -
45 app-admin/eselect/eselect-1.3.4-r100.ebuild | 73 +
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49 app-doc/gromacs-manual/ChangeLog | 37 -
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1125 .../gappalib-coq/files/gappalib-coq-coq84.patch | 71 +
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1127 .../gappalib-coq/gappalib-coq-0.18.0.ebuild | 35 +
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1145 .../petsc/files/petsc-3.2_p6-configure-pic.patch | 11 -
1146 .../files/petsc-3.2_p6-disable-env-warnings.patch | 13 -
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1148 .../petsc/files/petsc-3.2_p6-fix-afterimage.patch | 71 -
1149 .../petsc/files/petsc-3.2_p6-fix-imagemagick.patch | 24 -
1150 .../petsc/files/petsc-3.2_p6-fix-xops.patch | 21 -
1151 .../files/petsc-3.3-disable-env-warnings.patch | 13 -
1152 .../files/petsc-3.3-fix-complex-threads.patch | 62 +
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1154 sci-mathematics/petsc/petsc-3.1_p8-r1.ebuild | 202 -
1155 sci-mathematics/petsc/petsc-3.2_p6.ebuild | 217 -
1156 sci-mathematics/petsc/petsc-3.3_p1.ebuild | 215 -
1157 sci-mathematics/petsc/petsc-3.3_p5.ebuild | 223 ++
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1159 sci-mathematics/pff/Manifest | 5 +-
1160 sci-mathematics/pff/metadata.xml | 10 +-
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1163 sci-mathematics/polymake/ChangeLog | 8 +
1164 sci-mathematics/polymake/metadata.xml | 18 +-
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1168 sci-mathematics/pulp/metadata.xml | 3 +-
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1170 sci-mathematics/pulp/pulp-1.5.3.ebuild | 43 +
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1172 sci-mathematics/rstudio/Manifest | 5 -
1173 .../rstudio/files/rstudio-linker_flags.patch | 13 -
1174 sci-mathematics/rstudio/files/rstudio-paths.patch | 106 -
1175 sci-mathematics/rstudio/files/rstudio-prefs.patch | 20 -
1176 .../rstudio/files/rstudio-rserver.initd | 15 -
1177 .../rstudio/files/rstudio.desktop.patch | 16 -
1178 sci-mathematics/rstudio/metadata.xml | 13 -
1179 sci-mathematics/rstudio/rstudio-0.96.316.ebuild | 141 -
1180 sci-mathematics/rstudio/rstudio-0.96.331.ebuild | 141 -
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1182 sci-mathematics/scilab/Manifest | 2 +-
1183 .../scilab/files/scilab-5.4.0-fortran-link.patch | 22 -
1184 .../scilab/files/scilab-5.4.0-java-heap.patch | 12 -
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1188 .../scilab/files/scilab-5.4.1-java-heap.patch | 14 +
1189 sci-mathematics/scilab/metadata.xml | 16 +-
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1195 sci-mathematics/surfer/metadata.xml | 2 +-
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1254 sci-misc/salome-yacs/metadata.xml | 2 +-
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1257 sci-misc/sfst/ChangeLog | 6 +-
1258 sci-misc/sfst/metadata.xml | 10 +-
1259 sci-misc/sfst/sfst-1.4.2.ebuild | 4 +-
1260 sci-misc/sfst/sfst-1.4.6g.ebuild | 4 +-
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1263 sci-physics/LoopTools/Manifest | 2 +-
1264 sci-physics/abinit/ChangeLog | 27 +-
1265 sci-physics/abinit/Manifest | 3 +-
1266 sci-physics/abinit/abinit-6.12.3-r2.ebuild | 335 --
1267 sci-physics/abinit/abinit-7.0.4.ebuild | 356 ++
1268 sci-physics/abinit/abinit-7.0.5.ebuild | 356 ++
1269 sci-physics/abinit/files/6.12.3-gui-makefiles.tbz | Bin 0 -> 14600 bytes
1270 sci-physics/abinit/files/7.0.4-test_dirs.patch | 12 +
1271 sci-physics/abinit/metadata.xml | 74 +-
1272 sci-physics/atompaw/ChangeLog | 13 +-
1273 sci-physics/atompaw/Manifest | 2 +-
1274 sci-physics/atompaw/atompaw-3.0.1.4.ebuild | 70 -
1275 sci-physics/atompaw/atompaw-3.0.1.9.ebuild | 68 +
1276 sci-physics/atompaw/metadata.xml | 14 +-
1277 sci-physics/atompaw2abinit/ChangeLog | 7 +-
1278 sci-physics/atompaw2abinit/Manifest | 2 +-
1279 .../atompaw2abinit/atompaw2abinit-3.3.0-r1.ebuild | 19 +-
1280 sci-physics/atompaw2abinit/metadata.xml | 8 +-
1281 sci-physics/elk/ChangeLog | 6 +-
1282 sci-physics/elk/elk-1.4.22.ebuild | 92 +-
1283 sci-physics/elk/metadata.xml | 10 +-
1284 sci-physics/espresso++/ChangeLog | 8 +-
1285 sci-physics/espresso++/espresso++-9999.ebuild | 21 +-
1286 sci-physics/espresso/ChangeLog | 5 +-
1287 sci-physics/espresso/espresso-9999.ebuild | 14 +-
1288 sci-physics/geant-vmc/ChangeLog | 13 +
1289 sci-physics/geant-vmc/Manifest | 2 +
1290 sci-physics/geant-vmc/geant-vmc-3.1.14.ebuild | 39 +
1291 sci-physics/geant-vmc/geant-vmc-4.2.14.ebuild | 60 +
1292 sci-physics/geant-vmc/metadata.xml | 19 +
1293 sci-physics/geant/ChangeLog | 353 ++
1294 sci-physics/geant/Manifest | 2 +
1295 sci-physics/geant/geant-3.21.14-r4.ebuild | 70 +
1296 sci-physics/geant/metadata.xml | 14 +
1297 sci-physics/herwig++/ChangeLog | 16 +-
1298 sci-physics/herwig++/Manifest | 2 +-
1299 ...ptools.patch => herwig++-2.6.3-looptools.patch} | 0
1300 sci-physics/herwig++/herwig++-2.6.1b.ebuild | 50 -
1301 sci-physics/herwig++/herwig++-2.6.3.ebuild | 50 +
1302 sci-physics/lammps/ChangeLog | 55 +
1303 sci-physics/lammps/Manifest | 3 +
1304 sci-physics/lammps/lammps-20130512.ebuild | 72 +
1305 sci-physics/lammps/lammps-20130514.ebuild | 75 +
1306 sci-physics/lammps/lammps-20130526.ebuild | 75 +
1307 sci-physics/lammps/metadata.xml | 30 +
1308 sci-physics/openmx/ChangeLog | 17 +
1309 sci-physics/openmx/Manifest | 2 +
1310 sci-physics/openmx/metadata.xml | 5 +
1311 sci-physics/openmx/openmx-3.6.ebuild | 97 +
1312 sci-physics/root/ChangeLog | 29 +-
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1314 .../root/files/root-5.28.00b-asneeded.patch | 20 -
1315 .../root/files/root-5.28.00b-nobyte-compile.patch | 138 -
1316 .../root/files/root-5.28.00b-prop-ldflags.patch | 13 -
1317 .../files/root-5.32.00-explicit-functions.patch | 18 -
1318 .../root/files/root-5.32.00-prop-flags.patch | 15 +
1319 .../root/files/root-5.34.05-nobyte-compile.patch | 137 +
1320 sci-physics/root/metadata.xml | 39 +-
1321 sci-physics/root/root-5.32.04.ebuild | 378 --
1322 sci-physics/root/root-5.34.03.ebuild | 378 --
1323 sci-physics/root/root-5.34.07.ebuild | 381 ++
1324 sci-physics/root/root-9999.ebuild | 16 +-
1325 sci-physics/thepeg/ChangeLog | 16 +-
1326 sci-physics/thepeg/Manifest | 6 +-
1327 ...eg-1.8.1-java.patch => thepeg-1.8.3-java.patch} | 0
1328 sci-physics/thepeg/thepeg-1.8.1.ebuild | 92 -
1329 sci-physics/thepeg/thepeg-1.8.3.ebuild | 92 +
1330 sci-physics/vgm/ChangeLog | 13 +
1331 sci-physics/vgm/metadata.xml | 13 +
1332 sci-physics/vgm/vgm-3.06.ebuild | 64 +
1333 sci-visualization/ferret-bin/ChangeLog | 7 +-
1334 sci-visualization/ferret-bin/Manifest | 10 +-
1335 .../ferret-bin/ferret-bin-6.6.4.ebuild | 52 +-
1336 sci-visualization/ferret-bin/metadata.xml | 12 +-
1337 sci-visualization/gnuplot/ChangeLog | 22 +-
1338 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild | 213 +-
1339 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild | 181 +-
1340 sci-visualization/gnuplot/metadata.xml | 26 +-
1341 sci-visualization/labplot/metadata.xml | 3 +-
1342 sci-visualization/paraview/ChangeLog | 14 +-
1343 .../paraview/files/paraview-3.14.1-vtknetcd.patch | 50 +-
1344 sci-visualization/paraview/metadata.xml | 36 +-
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1348 sci-visualization/v_sim/ChangeLog | 6 +-
1349 sci-visualization/v_sim/Manifest | 4 +-
1350 sci-visualization/v_sim/metadata.xml | 26 +-
1351 sci-visualization/v_sim/v_sim-3.5.1.ebuild | 80 -
1352 sci-visualization/v_sim/v_sim-3.5.2.ebuild | 87 -
1353 sci-visualization/v_sim/v_sim-3.6.0.ebuild | 4 +-
1354 sci-visualization/yt/yt-9999.ebuild | 3 +-
1355 skel.ChangeLog | 2 +-
1356 skel.ebuild | 7 +-
1357 skel.metadata.xml | 38 +-
1358 sys-apps/likwid/Manifest | 1 +
1359 sys-apps/likwid/files/likwid.patch | 27 +
1360 sys-apps/likwid/files/use_access_daemon.patch | 27 +
1361 sys-apps/likwid/files/use_uncore.patch | 12 +
1362 sys-apps/likwid/likwid-3.0.ebuild | 33 +
1363 sys-apps/likwid/metadata.xml | 22 +
1364 sys-cluster/blcr/ChangeLog | 5 +-
1365 sys-cluster/blcr/blcr-0.8.4.ebuild | 3 +-
1366 sys-cluster/blcr/metadata.xml | 4 +-
1367 sys-cluster/empi/ChangeLog | 10 +-
1368 sys-cluster/empi/empi-0.7.ebuild | 28 -
1369 sys-cluster/empi/empi-0.8.ebuild | 28 +
1370 sys-cluster/empi/files/ChangeLog-0.7 | 164 -
1371 sys-cluster/empi/files/ChangeLog-0.8 | 68 +
1372 sys-cluster/empi/files/empi-0.7 | 408 --
1373 sys-cluster/empi/files/empi-0.8 | 492 +++
1374 sys-cluster/empi/files/eselect.mpi-0.7 | 274 --
1375 sys-cluster/empi/files/eselect.mpi-0.8 | 274 ++
1376 sys-cluster/hpl/ChangeLog | 9 +-
1377 sys-cluster/hpl/Manifest | 2 +-
1378 sys-cluster/hpl/hpl-2.0-r1.ebuild | 20 +-
1379 sys-cluster/hpl/metadata.xml | 12 +-
1380 sys-cluster/hpx/Manifest | 1 +
1381 sys-cluster/hpx/hpx-0.9.5.ebuild | 28 +
1382 sys-cluster/hpx/metadata.xml | 17 +
1383 sys-cluster/lustre/ChangeLog | 419 +-
1384 ...01-LU-1812-kernel-3.7-FC18-server-patches.patch | 380 ++
1385 ...nel-sock_map_fd-replaced-by-sock_alloc_fi.patch | 137 +
1386 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch | 184 +
1387 ...pat-posix_acl_-to-from-_xattr-take-user_n.patch | 159 +
1388 ...005-LU-2800-llite-introduce-local-getname.patch | 91 +
1389 .../files/0006-LU-2987-llite-rcu-free-inode.patch | 89 +
1390 ...50-kernel-3.8-upstream-removes-vmtruncate.patch | 83 +
1391 ...-2850-kernel-3.8-upstream-kills-daemonize.patch | 3005 ++++++++++++++
1392 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch | 95 +
1393 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch | 115 +
1394 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch | 82 +
1395 ...uild-fix-compilation-error-with-gcc-4.7.2.patch | 43 +
1396 ...7-vfs-kernel-3.1-renames-lock-manager-ops.patch | 190 -
1397 ...37-vfs-kernel-3.1-kills-inode-i_alloc_sem.patch | 242 --
1398 ...fs-kernel-3.1-changes-open_to_namei_flags.patch | 95 -
1399 ...7-vfs-provides-ll_get_acl-to-i_op-get_acl.patch | 150 -
1400 ...ck-kernel-3.2-make_request_fn-returns-voi.patch | 108 -
1401 ...337-vfs-kernel-3.2-protects-inode-i_nlink.patch | 194 -
1402 ...-3.3-changes-super_operations-inode_opera.patch | 217 -
1403 ...nel-remove-unnecessary-includings-of-syst.patch | 211 -
1404 ...-kernel-3.4-touch_atime-switchs-to-1-argu.patch | 89 -
1405 ...-kernel-3.4-converts-d_alloc_root-to-d_ma.patch | 128 -
1406 ...1-LU-1337-kernel-v3.5-defines-INVALID_UID.patch | 31 -
1407 ...te-kernel-3.5-renames-end_writeback-to-cl.patch | 90 -
1408 ...nel-3.5-kernel-encode_fh-passes-in-parent.patch | 88 -
1409 sys-cluster/lustre/lustre-9999.ebuild | 103 +-
1410 sys-cluster/lustre/metadata.xml | 5 +
1411 sys-cluster/mvapich2/ChangeLog | 7 +
1412 sys-cluster/mvapich2/Manifest | 2 +-
1413 sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild | 4 +-
1414 sys-cluster/openmpi/ChangeLog | 14 +-
1415 sys-cluster/openmpi/Manifest | 2 +-
1416 sys-cluster/openmpi/metadata.xml | 2 -
1417 sys-cluster/openmpi/openmpi-1.5.3.ebuild | 115 -
1418 sys-cluster/openmpi/openmpi-1.6.4.ebuild | 160 +
1419 sys-cluster/ovis/ChangeLog | 5 +-
1420 sys-cluster/ovis/metadata.xml | 10 +-
1421 sys-cluster/ovis/ovis-3.0.1.ebuild | 6 +-
1422 virtual/blas/ChangeLog | 5 +-
1423 virtual/blas/blas-2.1.ebuild | 4 +-
1424 virtual/blas/metadata.xml | 4 +-
1425 virtual/cblas/ChangeLog | 6 +-
1426 virtual/cblas/cblas-2.0.ebuild | 4 +-
1427 virtual/geant/ChangeLog | 9 +
1428 virtual/geant/geant-3.ebuild | 17 +
1429 virtual/geant/metadata.xml | 8 +
1430 virtual/lapack/ChangeLog | 8 +-
1431 virtual/lapack/lapack-3.3.ebuild | 23 -
1432 virtual/lapack/lapack-3.4.ebuild | 23 +
1433 virtual/lapack/metadata.xml | 3 +-
1434 virtual/scalapack/ChangeLog | 9 +-
1435 virtual/scalapack/metadata.xml | 4 +-
1436 virtual/scalapack/scalapack-1.8.ebuild | 21 -
1437 virtual/scalapack/scalapack-2.0.ebuild | 21 +
1438 x11-libs/xview-bin/ChangeLog | 9 +-
1439 x11-libs/xview-bin/Manifest | 2 +-
1440 x11-libs/xview-bin/metadata.xml | 10 +-
1441 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild | 6 +-
1442 x11-libs/xview/ChangeLog | 12 +-
1443 x11-libs/xview/Manifest | 1 +
1444 x11-libs/xview/metadata.xml | 10 +-
1445 x11-libs/xview/xview-3.2-r6.ebuild | 4 +-
1446 x11-libs/xview/xview-3.2-r7.ebuild | 4 +-
1447 x11-libs/xview/xview-3.2-r8.ebuild | 108 +
1448 1409 files changed, 29080 insertions(+), 27064 deletions(-)
1449
1450 diff --cc sci-chemistry/jligand/ChangeLog
1451 index b555231,79845c4..9e2c106
1452 --- a/sci-chemistry/jligand/ChangeLog
1453 +++ b/sci-chemistry/jligand/ChangeLog
1454 @@@ -1,17 -1,11 +1,17 @@@
1455 # ChangeLog for sci-chemistry/jligand
1456 - # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
1457 + # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
1458 # $Header: $
1459
1460 - 10 Dec 2012; Justin Lecher <jlec@g.o> -jligand-1.0.19.ebuild,
1461 - +jligand-1.0.37.ebuild:
1462 - Version Bump
1463 + 03 Mar 2013; Justin Lecher <jlec@g.o> jligand-1.0.19.ebuild,
1464 + metadata.xml:
1465 + Fix version of refmac dep
1466
1467 +*jligand-1.0.37 (10 Dec 2012)
1468 +
1469 + 10 Dec 2012; Justin Lecher <jlec@g.o> -jligand-1.0.19.ebuild,
1470 + +jligand-1.0.37.ebuild:
1471 + Version Bump
1472 +
1473 *jligand-1.0.19 (25 Jun 2011)
1474
1475 25 Jun 2011; Justin Lecher <jlec@g.o> -jligand-0.1.ebuild,