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  • Committer: Package Import Robot
  • Author(s): Elmar Pruesse, Andreas Tille, Elmar Pruesse
  • Date: 2014-09-02 15:15:06 UTC
  • mfrom: (1.1.6)
  • Revision ID: package-import@ubuntu.com-20140902151506-jihq58b3iz342wif
Tags: 6.0.2-1
http://bugs.debian.org/741890
http://bugs.debian.org/757497
[ Andreas Tille ]
* New upstream version
  Closes: #741890
* debian/upstream -> debian/upstream/metadata
* debian/control:
   - Build-Depends: added libglib2.0-dev
   - Depends: added mafft, mrbayes
* debian/rules
   - Add explicite --remove-section=.comment option to manual strip call
* cme fix dpkg-control
* arb-common.dirs: Do not create unneeded lintian dir
* Add turkish debconf translation (thanks for the patch to Mert Dirik
  <mertdirik@gmail.com>)
  Closes: #757497

[ Elmar Pruesse ]
* patches removed:
   - 10_config.makefiles.patch,
     80_no_GL.patch
       removed in favor of creating file from config.makefile.template via 
       sed in debian/control
   - 20_Makefile_main.patch
       merged upstream
   - 21_Makefiles.patch
       no longer needed
   - 30_tmpfile_CVE-2008-5378.patch: 
       merged upstream
   - 50_fix_gcc-4.8.patch:
       merged upstream
   - 40_add_libGLU.patch:
       libGLU not needed for arb_ntree)
   - 60_use_debian_packaged_raxml.patch:
       merged upstream
   - 70_hardening.patch
       merged upstream
   - 72_add_math_lib_to_linker.patch
       does not appear to be needed
* patches added:
   - 10_upstream_r12793__show_db_load_progress:
       backported patch showing progress while ARB is loading a database
       (needed as indicator/splash screen while ARB is launching)
   - 20_upstream_r12794__socket_permissions:
       backported security fix
   - 30_upstream_r12814__desktop_keywords:
       backported add keywords to desktop (fixes lintian warning)
   - 40_upstream_r12815__lintian_spelling:
       backported fix for lintian reported spelling errors
   - 50_private_nameservers
       change configuration to put nameservers into users home dirs
       (avoids need for shared writeable directory)
   - 60_use_debian_phyml
       use phyml from debian package for both interfaces in ARB
* debian/rules:
   - create config.makefile from override_dh_configure target
   - use "make tarfile" in override_dh_install
   - remove extra cleaning not needed for ARB 6
   - use "dh_install --list-missing" to avoid missing files
   - added override_dh_fixperms target
* debian/control:
   - added libarb-dev package
   - Depends: added phyml, xdg-utils
   - Suggests: removed phyml
   - fix lintian duplicate-short-description (new descriptions)
* debian/*.install:
   - "unrolled" confusing globbing to select files
   - pick files from debian/tmp
   - moved all config files to /etc/arb
* debian/arb-common.templates: updated
* scripts:
   - removed arb-add-pt-server
   - launch-wrapper: 
     - only add demo.arb to newly created $ARBUSERDATA
     - pass commandline arguments through bin/arb wrapper
   - preinst: removing old PT server index files on upgrade from 5.5*
   - postinst: set setgid on shared PT dir
* rewrote arb.1 manfile
* added file icon for ARB databases
* using upstream arb_tcp.dat

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UNIT_TESTER/run/consense/3/bootstrapped_1.tree
 
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[<NONE>
 
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Sun Mar 11 18:16:55 2012: tree_bootstrapped_1 saved to /home/ralf/ARB-bilbo/ARB.CT.refactored_added_checks/UNIT_TESTER/run/consense/3/bootstrapped_1.tree
 
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4
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  (
 
6
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7
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10
            (
 
11
              (
 
12
                (
 
13
                  (
 
14
                    (
 
15
                      AticSe28:0.00120,
 
16
                      AticSe33:0.00024
 
17
                    ):0.00015,
 
18
                    AticSe30:0.00021
 
19
                  ):0.00016,
 
20
                  AticSe25:-0.00016
 
21
                ):0.00009,
 
22
                AticSe15:-0.00009
 
23
              ):0.00006,
 
24
              AticSea7:-0.00006
 
25
            ):0.00003,
 
26
            (
 
27
              (
 
28
                (
 
29
                  (
 
30
                    (
 
31
                      (
 
32
                        OcdSpec9:0.00209,
 
33
                        Unc03nea:-0.00136
 
34
                      ):0.00083,
 
35
                      OcdSpeci:-0.00082
 
36
                    ):0.00039,
 
37
                    OcdSpec2:-0.00040
 
38
                  ):0.00021,
 
39
                  AticSea6:-0.00021
 
40
                ):0.00010,
 
41
                AticSea9:-0.00010
 
42
              ):0.00006,
 
43
              AticSe10:-0.00006
 
44
            ):0.00002
 
45
          ):0.00002,
 
46
          OcdSpec3:-0.00003
 
47
        ):0.00003,
 
48
        OcdSpec5:-0.00001
 
49
      ):0.00001,
 
50
      AticSe32:-0.00001
 
51
    ):0.00001,
 
52
    (
 
53
      OcdSpe11:-0.00000,
 
54
      (
 
55
        AticSe29:-0.00002,
 
56
        (
 
57
          (
 
58
            OcdSpe13:-0.00000,
 
59
            (
 
60
              OcdSpe15:-0.00000,
 
61
              (
 
62
                OcdSpe10:-0.00002,
 
63
                (
 
64
                  Unc03dtr:0.00061,
 
65
                  (
 
66
                    (
 
67
                      OcdSpec6:0.00692,
 
68
                      Unc00rpc:0.00109
 
69
                    ):0.00073,
 
70
                    (
 
71
                      (
 
72
                        (
 
73
                          OcdSpe18:0.01028,
 
74
                          (
 
75
                            OcdSpe19:0.00132,
 
76
                            OcdSpe21:-0.00132
 
77
                          ):0.00223
 
78
                        ):0.00456,
 
79
                        OcdSpec4:0.02061
 
80
                      ):0.00047,
 
81
                      (
 
82
                        (
 
83
                          (
 
84
                            (
 
85
                              (
 
86
                                (
 
87
                                  (
 
88
                                    (
 
89
                                      ShaMarin:0.00941,
 
90
                                      ShaSpeci:0.01227
 
91
                                    ):0.00720,
 
92
                                    (
 
93
                                      (
 
94
                                        (
 
95
                                          (
 
96
                                            LsnAquim:0.00617,
 
97
                                            LsnMeth2:0.00702
 
98
                                          ):0.00412,
 
99
                                          (
 
100
                                            MrnAlp12:0.01013,
 
101
                                            PhbCaeru:0.00590
 
102
                                          ):0.00825
 
103
                                        ):0.00354,
 
104
                                        (
 
105
                                          PhbArcti:0.01962,
 
106
                                          PhbGall5:0.01278
 
107
                                        ):0.00462
 
108
                                      ):0.00418,
 
109
                                      TscHalod:0.02192
 
110
                                    ):0.00299
 
111
                                  ):0.00070,
 
112
                                  (
 
113
                                    (
 
114
                                      (
 
115
                                        (
 
116
                                          (
 
117
                                            (
 
118
                                              RhbBac48:0.00924,
 
119
                                              SbtLacus:0.01032
 
120
                                            ):0.00276,
 
121
                                            RueAtla7:0.00303
 
122
                                          ):0.00394,
 
123
                                          SbtPomer:0.01404
 
124
                                        ):0.00075,
 
125
                                        (
 
126
                                          (
 
127
                                            RueSpe54:0.00000,
 
128
                                            RueSpe56:-0.00000
 
129
                                          ):0.00105,
 
130
                                          RueMobi3:0.00261
 
131
                                        ):0.01482
 
132
                                      ):0.00243,
 
133
                                      (
 
134
                                        PdgAquim:0.00938,
 
135
                                        PdgSpec5:0.02562
 
136
                                      ):0.00574
 
137
                                    ):0.00430,
 
138
                                    RueSpe62:0.01406
 
139
                                  ):0.00435
 
140
                                ):0.00439,
 
141
                                (
 
142
                                  (
 
143
                                    (
 
144
                                      (
 
145
                                        DnrShiba:0.02749,
 
146
                                        RsbElon4:0.02142
 
147
                                      ):0.00845,
 
148
                                      (
 
149
                                        (
 
150
                                          RclMahon:0.02993,
 
151
                                          LokPyose:0.03201
 
152
                                        ):0.00074,
 
153
                                        (
 
154
                                          (
 
155
                                            (
 
156
                                              RblAerol:0.01978,
 
157
                                              RblMesop:0.01027
 
158
                                            ):0.01014,
 
159
                                            RblTherm:0.03080
 
160
                                          ):0.02946,
 
161
                                          (
 
162
                                            (
 
163
                                              (
 
164
                                                LbnMarin:0.00646,
 
165
                                                LbnzAlb4:0.00406
 
166
                                              ):0.00729,
 
167
                                              LbnAlexa:0.01137
 
168
                                            ):0.04328,
 
169
                                            (
 
170
                                              MhuCaps3:0.06244,
 
171
                                              ThtNivea:0.04808
 
172
                                            ):0.08341
 
173
                                          ):0.02092
 
174
                                        ):0.01027
 
175
                                      ):0.00367
 
176
                                    ):0.00267,
 
177
                                    RsnAnta2:0.02399
 
178
                                  ):0.00456,
 
179
                                  (
 
180
                                    (
 
181
                                      (
 
182
                                        (
 
183
                                          (
 
184
                                            (
 
185
                                              MmbAlkal:0.02180,
 
186
                                              OnlNanha:0.02498
 
187
                                            ):0.00486,
 
188
                                            (
 
189
                                              RueSpe48:0.01177,
 
190
                                              OnlSpec4:0.01581
 
191
                                            ):0.00589
 
192
                                          ):0.00233,
 
193
                                          (
 
194
                                            RosSpe24:0.01354,
 
195
                                            RosSpe86:0.00970
 
196
                                          ):0.00814
 
197
                                        ):0.00141,
 
198
                                        (
 
199
                                          DonEburn:0.01645,
 
200
                                          (
 
201
                                            RsxSpec6:0.01101,
 
202
                                            YanPacif:0.01763
 
203
                                          ):0.00670
 
204
                                        ):0.00269
 
205
                                      ):0.00413,
 
206
                                      (
 
207
                                        AttHeli2:0.02453,
 
208
                                        SgtStel2:0.01804
 
209
                                      ):0.01197
 
210
                                    ):0.00078,
 
211
                                    (
 
212
                                      (
 
213
                                        (
 
214
                                          (
 
215
                                            (
 
216
                                              RosSpe15:-0.00122,
 
217
                                              RsrMucos:0.00366
 
218
                                            ):0.01504,
 
219
                                            RsrTole2:0.01244
 
220
                                          ):0.01640,
 
221
                                          (
 
222
                                            (
 
223
                                              (
 
224
                                                PgbBermu:0.01025,
 
225
                                                SlpMuco2:0.01959
 
226
                                              ):0.00615,
 
227
                                              PaoMaris:0.02559
 
228
                                            ):0.00364,
 
229
                                            (
 
230
                                              (
 
231
                                                (
 
232
                                                  CieThioo:0.00061,
 
233
                                                  MrnAlp10:0.00164
 
234
                                                ):0.01421,
 
235
                                                CieSpec9:0.01492
 
236
                                              ):0.00813,
 
237
                                              (
 
238
                                                (
 
239
                                                  RsxHalo2:0.01534,
 
240
                                                  RsxHalo3:0.02296
 
241
                                                ):0.00732,
 
242
                                                CiaSalin:0.01961
 
243
                                              ):0.00530
 
244
                                            ):0.00353
 
245
                                          ):0.00415
 
246
                                        ):0.00460,
 
247
                                        MrvAlgi3:0.01804
 
248
                                      ):0.00093,
 
249
                                      (
 
250
                                        OnlBats2:0.02004,
 
251
                                        OnlGran2:0.02373
 
252
                                      ):0.00657
 
253
                                    ):0.00511
 
254
                                  ):0.00083
 
255
                                ):0.00536
 
256
                              ):0.00285,
 
257
                              PhbSpe37:0.02300
 
258
                            ):0.00031,
 
259
                            (
 
260
                              (
 
261
                                NerIgna3:0.02618,
 
262
                                (
 
263
                                  (
 
264
                                    (
 
265
                                      (
 
266
                                        (
 
267
                                          (
 
268
                                            (
 
269
                                              BcrNAS14:0.00033,
 
270
                                              SltSpe43:-0.00033
 
271
                                            ):0.00122,
 
272
                                            SltPont3:-0.00122
 
273
                                          ):0.00352,
 
274
                                          SltBrev2:0.01162
 
275
                                        ):0.00208,
 
276
                                        SltMedi2:0.00515
 
277
                                      ):0.00151,
 
278
                                      SltGutt2:0.01643
 
279
                                    ):0.00241,
 
280
                                    (
 
281
                                      (
 
282
                                        OcbIndo3:0.00065,
 
283
                                        SltSpe32:0.00011
 
284
                                      ):0.00231,
 
285
                                      (
 
286
                                        SltDeli3:0.00449,
 
287
                                        SltDubi2:0.00050
 
288
                                      ):0.00157
 
289
                                    ):0.01851
 
290
                                  ):0.00135,
 
291
                                  (
 
292
                                    (
 
293
                                      RosLito2:0.00124,
 
294
                                      RosLito8:-0.00049
 
295
                                    ):0.00661,
 
296
                                    RosDeni2:0.01221
 
297
                                  ):0.01422
 
298
                                ):0.00236
 
299
                              ):0.00258,
 
300
                              (
 
301
                                (
 
302
                                  (
 
303
                                    LokAgnit:0.01245,
 
304
                                    LokVest4:0.01342
 
305
                                  ):0.01285,
 
306
                                  (
 
307
                                    LokFryx2:0.00714,
 
308
                                    LokSals5:0.00728
 
309
                                  ):0.02200
 
310
                                ):0.00239,
 
311
                                LokRosea:0.01726
 
312
                              ):0.01084
 
313
                            ):0.00151
 
314
                          ):0.00155,
 
315
                          (
 
316
                            (
 
317
                              (
 
318
                                (
 
319
                                  (
 
320
                                    (
 
321
                                      (
 
322
                                        JnnHelg4:0.00646,
 
323
                                        JnnRubr2:0.00557
 
324
                                      ):0.01015,
 
325
                                      (
 
326
                                        JnnSeoha:0.01755,
 
327
                                        JnnSeosi:0.01463
 
328
                                      ):0.00491
 
329
                                    ):0.00331,
 
330
                                    (
 
331
                                      JnnPohan:0.01239,
 
332
                                      JnnDongh:0.01416
 
333
                                    ):0.00162
 
334
                                  ):0.00291,
 
335
                                  JnnSpec8:0.02703
 
336
                                ):0.00270,
 
337
                                RsrSpec6:0.02456
 
338
                              ):0.00220,
 
339
                              (
 
340
                                MabPelag:0.00119,
 
341
                                MabSalin:0.00028
 
342
                              ):0.03394
 
343
                            ):0.00422,
 
344
                            (
 
345
                              (
 
346
                                RsrCrass:0.01769,
 
347
                                (
 
348
                                  TlbSten4:0.01989,
 
349
                                  (
 
350
                                    RsrAestu:0.01243,
 
351
                                    RsrNubi2:0.01469
 
352
                                  ):0.00378
 
353
                                ):0.00382
 
354
                              ):0.00343,
 
355
                              (
 
356
                                (
 
357
                                  OcdOrien:0.00672,
 
358
                                  TlbArena:0.00355
 
359
                                ):0.00457,
 
360
                                OcdSpec8:0.01786
 
361
                              ):0.00856
 
362
                            ):0.00275
 
363
                          ):0.00309
 
364
                        ):0.00357,
 
365
                        (
 
366
                          TlsAestu:0.01338,
 
367
                          (
 
368
                            TlsGela3:0.00442,
 
369
                            TlsMedi4:0.01330
 
370
                          ):0.00472
 
371
                        ):0.00655
 
372
                      ):0.00619
 
373
                    ):0.01056
 
374
                  ):0.00112
 
375
                ):0.00009
 
376
              ):0.00003
 
377
            ):0.00000
 
378
          ):0.00003,
 
379
          OcdSpe12:-0.00003
 
380
        ):0.00002
 
381
      ):0.00071
 
382
    ):0.00000
 
383
  ):-0.00000,
 
384
  AticSe36:-0.00000
 
385
);