-
Notifications
You must be signed in to change notification settings - Fork 47
/
Copy pathbuild-it-3-3
executable file
·5197 lines (4589 loc) · 179 KB
/
build-it-3-3
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#!/bin/bash
#
# -*-shell-script-*-
# Local Variables:
# mode: shell-script
# sh-shell: bash
# End:
# ----------------- this is now the python-3 version ----------------
#
# Copyright 2004, 2005, 2006, 2007, 2008 by The University of York
# Copyright 2009, 2010, 2011, 2012 by The University of York
# Copyright 2012 by Paul Emsley
# Copyright 2012, 2013, 2014, 2015, 2016 by Medical Reserch Council
# Copyright 2014, 2015, 2016, 2017, 2018 by Medical Reserch Council
# Copyright 2019, 2020, 2021, 2022, 2023, 2024 by Medical Research Council
# Author: Paul Emsley
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA
#
#
#
# For instructions, read below, starting at :: NOTE ::
#
#
# Prerequisites: sed, GNU make, libtool, wget
#
# libz is optional for the moment
# 1.3 Put RELEASE-NOTES on web site too
# 1.4 Apply both of Ezra's patches of today Wed Mar 2 22:51:36 GMT 2005
# Update clipper version (the one with shelx .fcf ability)
# 1.5 Apply Ezra's gtkglarea patch and GSL patch.
# Update version of FFTW and other updates from MATSUURA Takanori.
# 1.6 Update to mmdb-1.0.8 [# for molrep output]
# 1.7 Fix logic of fftw test
# 1.8 Add the clipper edcalc patch (suggested by Ezra ages ago)
# 1.9 Add Fedora Core 4 support and testing for the need to build mccp4,
# mmdb and clipper.
# 1.10 Tidy up nightly code.
# 1.11 Add code testing the need for guile_gui and goosh.
# 1.12 Tidy nightly code again.
# 1.13 Don't escape the "."s in gsub for new gawk (Ward Smith).
# 1.14 20050628 Test for imlib on the installation, not the system (ignore
# the system).
# 1.15 20050709 Add glib gstrfuncs patch
# 1.16 20050709 Update to guile 1.6.7 and add lt_preloaded_symbols patch
# 1.17 20050721 Added clipper status code to compiling clipper part.
# Redirect stderr output?
# fix build_mccp4 problem.
# 1.18 20050722 Fix guile build (wrong http tar file).
# Added freeglut
# 1.19 20050803 Update version of guile-gtk to 0.41
# 1.20 20050815 Several updates and clean up from MATSUURA Takanori.
# 1.21 20050815 Stop if wget test fails.
# 1.22 20050916 Update build for freeglut to use --disable-warnings and
# CFLAGS
# 1.23 20050916 Move "set" so we don't see confusing default coot_version
# 1.24 20051012 Do pre-release tars for a few days.
# 1.25 20051017 Don't make install if Coot's makes fails. Don't make -k
# 1.26 20051018 Handle clipper nxmap patch.
# 1.27 20051027 [Gif, Paris] Fix tarred directory for nightly pre-release
# tars.
# 1.28 20051101 Fix the md5sum for nxmap.h
# 1.29 20051104 Apply most of MATSUURA Takanori's fixes.
# Use CCP4 libs (mtz, clipper, mmdb).
# 1.30 20051109 Darwin setting of FC for CCP4 libs configure.
# 1.31 20051114 Fix coot tar file problem on building pre-release (or not).
# 1.32 20060205 Add scripting variable debugging (its currently not making
# python tar files)
# 1.33 20060214 Get wget testing tar file from YSBL, not chem.gla
# 1.34 20060219 Correct the install position of libccp4c.la
# 1.35 20060219 create time stamp with current time, not the time of
# the previous ccp4 libs file, now the find ctime test works
# as I wanted.
# 1.36 20060220 Add a libmmdb.la too.
# 1.37 20060222 Add Bob Nolte's proxy settings
# 1.38 20060224 dylib variable for libmmdb.la and libccp4c.la
# 1.39 20060225 Fix sedding of libmmdb.la and libccp4c.la
# 1.40 20060323 copy over coot.py to share/coot/python (if we built with
# python)
# 1.41 20060401 Big changes for ccp4 5.0.2 ccp4c libs.
# 1.42 20060404 Various small build debuggings.
# 1.43 20060405 Fix do_nightlies syntax error and fix up glut_prefix build
# problem.
# 1.44 20060405 Fix the tarred directory name when this is not a pre-release
# 1.45 20060406 Check for missing reference structures and monomer lib and
# install them if needed.
# 1.46 20060418 use install_top_dir variable to copy over coot.py (not
# $coot_prefix!)
# 1.47 20060419 Remove the mmdb binaries
# 1.48 20060420 J. Maclean says no guile. He is right. So check install for
# guile, not system.
# 1.49 20060420 Replace many $AUTOBUILD_INSTALLED with $install_top_dir.
# 1.50 20060421 Replace other $AUTOBUILD_INSTALLED with $install_top_dir for
# tar file creation.
# 1.51 20060425 net-http was installing into the wrong place because it had
# been set to install_top_dir, but this was not set as a shell
# (or configured) variable so it was just blank [James Murray].
# Now we export install_top_dir.
# 1.52 20060427 Don't add unecessary tagging of -pre-release to tar_dir at
# the end.
# 1.53 20060503 Force GSL to be in $install_top_dir rather than anywhere.
# 1.54 20060519 Update to extract the right coot version from the release and
# pre-release directories.
# 1.55 20060621 Shuffle around the test for using pre-release
# 1.56 20060626 Fixes from MATSUURA Takanori. Shuffle around the usage of
# install_top_dir.
# 1.57 20060704 run imlib-config from the installation, not anywhere.
# 1.58 20060705 Fix wrong directory to build libtiff.
# 1.59 20060706 guile-config should run with an argument, otherise it
# returns with exit status 1 (and we test for non-zero).
# 1.60 20060706 Fix (directory for) mmdb include file test.
# 1.61 20060707 Add to coot configure line the option for guile_gtk
# 1.62 20060708 Fix coot_prerelease_exists typo in setting install_top_dir
# (oops).
# 1.63 20060708 Add jpeg dependency for imlib
# 1.64 20060708 Add libungif test to installation, not system (imlib
# dependency).
# 1.65 20060710 Add removal of coot_wrap_guile.cc compilation when python
# scripting.
# 1.66 20060710 Python on a Sunday.
# 1.67 20060711 Try to fix up the Makefile for PNG.
# 1.68 20060723 Add in the updates to ltmain.sh, ltconfig and config.guess/sub
# for Mactel build. Add build for readline.
# Readline version typo fixed.
# 1.69 20060724 ENABLE_PYTHON_COOT variable is tested. Don't display
# a variables if we are using a proxy.
# 1.70 20060728 pass CFLAGS and LDFLAGS to guile's configure
# 1.71 20060730 Add test for 64-bit Linux to update config.xxxs and libtool.
# Installation readline built now, not system.
# 1.72 20060801 Use mmdb-1.0.8-ysbl-2, which installs includes in the include
# dir. This matches clipper cif_data_io.cpp which presumes that
# it is there. (And is a clean thing to do anyway).
# 1.73 20060801 Use the new version of libccp4c, with some of Ralf's patches
# and includes that go into include/ccp4 dir.
# 1.74 20060801 Use CCP4_CXXFLAGS argument to clipper (it does the wrong thing
# with --with-ccp4)
# 1.75 20060801 Use -pre-2 version of SSMlib, that has -Ixxx/include/mmdb to
# find mmdb include files.
# 1.76 20060808 test for libjpeg.$shared_lib_ext not libjpeg.so. LTE bug.
# 1.77 20060818 Force update of libtool and config files for libjpeg. Extend
# the make install proceedure. Lynn Ten Eyck reported problems
# here.
# 1.78 20060823 Add poll fix and getpwuid fix to glib build on Intel Mac.
# 1.79 20060827 Add fix for gtk-canvas from fink for Intel Mac.
# 1.80 20061002 Change freeglut test to test instaltion, not system.
# 1.81 20061012 The path used to find *-config files should be the same one
# that new executables are added (it was $AUTOBUILD_INSTALLED)
# and it should be $AUTOBUILD_INSTALLED-pre-release/bin) when
# we are building a pre-release.
# 1.82 20061012 Change the destination tar file so that there are nightly
# and stable directories for the binary tar files on the web
# server.
# 1.83 20061107 cd to the clipper dir when building clipper. Pirate and
# bucca are not (attempted to be) built then.
# 1.84 20061107 Capture and report error status from make in GSL (intel mac
# build fails).
# 1.85 20061107 Use GSL version 1.8, which includes Charles Ballard's fix for
# fp_regs.h
# 1.86 20061108 Add fink-based args for configure of gtk for Darwin
# 1.87 20061108 Fix ltmain.sh updating for Gtk (oops!).
# 1.88 20061122 Fix coot tar directory now that we have revision numbers in
# tar file name.
# 1.89 20061123 Fix/add test for ssmlib build (now depends on mmdb build) and
# libccp4c build (now depends on xxx/include/ccp4/cmtzlib.h).
# 1.90 20061128 Allow the user to specify if the dependencies should be checked
# on the system or only in the autobuild installed directory.
# Needs more checks to use this. Currently only glib and gtk
# tests.
# 1.91 20061211 Don't make install for guile-gtk if the make fails - or the
# dependency check for guile-gtk in coot's configure passes
# when it should fail (maybe).
# 1.92 20061212 Apply Charles Ballards libtool patch for Macs for imlib and
# guile-gtk.
# 1.93 20061212 Fiddle the env vars to compile gtk+ on Mac.
# 1.94 20070104 Non-pre-release build problems, BINARY_DEST_DIR
# 2.01 20070109 imlib tar gz should be downloaded from the correct directory
# (sigh).
# 2.02 20070117 Try to compile clipper with -fno-strict-aliasing
# 2.03 20070123 Tell us where the gtkglarea include file was found.
# 2.04 20070124 GCC 3.2 on RH8 machine cannot compile new clipper, so add a
# patch if needed.
# 2.05 20070216 Put libtiff after libjpeg and give tiff's configure command
# line args to find jpeg.
# 2.06 20070306 Put in the clipper<->ccp4 new dist patch.
# 2.07 20070319 Remove == comparisons - Lothar Esser.
# 2.08 20070424 --with-jpeg-lib-dir should be a lib dir!
# 2.09 20070501 Fix the setting of coot_version when no pre-release set.
# 2.10 20071002 Post install slim the binaries. Add helper functions.
# 2.11 20071005 Add some debugging to make_tar. It doesn't seem to work
# currently.
# 2.12 20071005 Fix post_install_slim call.
# 2.13 20071005 Fix slim_dir
# 2.14 20071006 Adjust python scripting settings, so that it should try
# to compile with python most of the time now.
# 2.15 20071008 Fix extra fi, uncommented typo.
# 2.16 20071010 ENABLE_PYTHON_COOT=no for now.
# 2.17 20071105 Swap out DL Clipper for York clipper [whoosh, bang, kerpow!]
# enable-cns
# 2.18 20071105 Backpeddle to mmdb 1.08. Baah.
# 2.19 20071108 Version 1.08-ysbl-3 of mmdb.
# 2.20 20071118 No longer make the full fat tar file.
# 2.21 20071120 Sourcefource no longer distributes libungif, now in
# ysbl software/extras
# 2.22 20071121 set the architecture for ubuntu systems.
# 2.23 20071125 Fix typo in recent fixes.
# 2.24 20071126 Fix setting of systype for MacOSX, hopefully.
# 2.25 20071126 Another try to fix setting of systype for MacOSX.
# 2.26 20071130 Try to enable python
# 2.27 20071207 More python tinkering. Upgrade to 2.5.1
# 2.28 20071207 Add greg. If in York, use it to test before installing.
# 2.29 20071208 Setup CCP4 and use it to test coot before making binaries.
# 2.30 20071209 Add dewinter's ccp4 setup in setup_ccp4.
# 2.31 20071212 Redirect testing output to $LOGS/$HOST-testing.log
# 2.32 20071213 Copy over the ChangeLog, README and RELEASE-NOTES on good test
# 2.33 20071215 Pythonize only sometimes, default off.
# 2.34 20071215 Tell us some Python info
# 2.35 20071215 Python settings outside the subshell.
# 2.36 20071219 Set up for testing and tars on biop too.
# 3.00 20080108 Gtk+-2 version
# 3.01 20080118 Add GtkGlExt
# 3.02 20080121 Tinker with guile build settings.
# 3.03 20080124 Build GTK2 from scratch: librsvg, cairo, pango, glitz. glib, gtk+-2
# 3.04 20080128 Add a test for the existance of pygtk
# 3.05 20080129 Add pkg-config and pygobject
# 3.06 20080130 Add test for pycairo
# 3.07 20080130 pycairo needs 1.4.12 - so test for cairo, setting build_gtk=1 on
# failure
# 3.08 20080130 Remove static patch (for sgi). Add test/build for freetype2
# 3.09 20080130 fontconfig added too.
# 3.10 20080131 Change HOSTLOGDIR to include gtk2 to separate it from gtk1 build logs.
# 3.11 20080201 Fix problem in scripting args to coot's configure.
# 3.12 20080207 Add test and build of ATK, needed for gtk+2.10.x
# 3.13 20080208 lib cleaning problems, add debugging.
# 3.14 20080208 Try requiring gtk 2.10
# 4.00 20080208 Remove gtk2 and pkg-config building. Test for Fedora core 5.
# 4.01 20080211 Remove pycairo build and fix up test for build for guile_gtk
# 4.02 20080212 Add in the Neil Jerram guile-gui patch.
# 4.03 20080213 Add Joseph Moran's fix for handling CC when set.
# 4.04 20080213 Allow python to get through rsync filter, for PHENIX usage.
# 4.05 20080226 Fix up build_guile_gtk usage.
# 4.06 20080428 Apply Joseph Moran's fix correctly.
# 4.07 20080518 Update the status reporting system.
# 4.08 20080607 Bump version of python to 2.5.2
# 4.09 20080617 Update to guile-1.8.5
# 4.10 20080618 As per JED request, number the build logs in a more sensible way.
# 4.11 20080620 Don't run the tests if not in biop or york.
# 4.12 20080624 Add guile-lib to build.
# 4.13 20080729 Correctly test for the up to date python version.
# 4.14 20080729 Adjust test for build_guile_gtk.
# 4.15 20080730 Adjust test for up to date python.
# 4.16 20080730 Use old version of pyobject if pkg-config is not new enough
# 4.17 20080730 Test for gtk minor version, use that to apply guile-gtk patches
# if needed.
# 4.18 20080730 Add Diagnosis for applying guile-gtk patch.
# 4.19 20080818 use mmdb version 1.12
# 4.20 20080918 Remove references to glitz, cairo, fontconfig
# 4.21 20080925 Use pygobject 2.4 if needed (e.g on CentOS 4).
# 4.22 20080925 Handle typename in pygobject.h for CentOS4.
# 4.23 20081007 Don't build python if python is not passed as arg.
# 4.24 20081007 Back to version 2.5.1 that compiles on bragg3, 2.5.2 does not
# (port 8080 already in use).
# 4.25 20081008 Migrate to CCP4 version 6.0.2 for testing in York.
# 4.26 20081014 Use Python 2.6
# 4.27 20081105 Adjust clipper configuration. Remove clipper-new-ccp4-install
# usage, it is no longer needed, it seems. Remove configure
# argument --enable-mmdbold
# 4.28 20081110 Upgrade to mmdb-1.19, get it from EBI.
# 4.29 20081118 Use the ccp4 libs underlay.
# 4.30 20081119 Use -O not -O2 to compile coot on 64 bit machine
# 4.31 20081121 Swig 1.3.34 is OK for 32 bit, I think.
# 4.32 20081122 Use clipper-2.1
# 4.33 20081122 Use clipper-2.1, extra tweaks.
# 4.34 20081122 Add a second test, make a holding directory for tar file before
# second test is run.
# 4.35 20081124 test for greg using full path to guile.
# 4.36 20081130 Bump the gmp version to 4.2.4 (Does that fix the gmp.h on
# intrepid problem?)
# 4.37 20090220 Fix up guile-gui, post-neil-jerram patch added.
# 4.38 20090423 Fix up PYTHONPATH when starting greg tests.
# 4.39 20090427 Remove python and its config from bin in slimmed dir
# 4.40 20090506 Upgrade to mmdb 1.21
# 4.41 20090508 add density-score-by-residue to tar ball.
# 4.42 20090517 Remove standard error redirections.
# 4.43 20090522 Update to guile-1.8.6 on the advice of Ed Podharski.
# 4.44 20090523 Add some build info to the mmdb and clipper logs.
# 4.45 20090523 build status results now go to $build_type-build-status
# (not gtk2-build-status)
# 4.46 20090613 Add coot revision info to build status line.
# 4.47 20090617 Make a file (and transfer it if neeeded) type-binary-xxx.txt
# containing the $coot_version of the just-built binary. Used
# in the update-binary mechanism to find if there is a newer
# version than this binary (that we are running).
# 4.48 20090624 Make pre_release_server_dir be biop.ox
# 4.49 20090628 On my_exit, remove the test-status file, not the build-status
# file.
# 4.50 20090628 Change the GSL version to 1.12
# 4.51 20090703 check exit status of wget for coot source tar file.
# 4.52 20090704 mmdb-1.21 from York.
# 4.53 20090706 check build dependencies when on ubuntu
# 4.54 20090722 fix coot_revision typo for build status.
# 4.55 20090724 make compilers_dir depend on build_type (python build logs
# split out)
# 4.56 20090727 Add a date for build-in-progress status
# 4.57 20090728 gtk2 -> $build_type fixups for status
# 4.58 20090730 remove swig from package list tested on ubuntu.
# 4.59 20090913 Add a date to the fail status message
# 4.60 20091001 comment out the deletion of the coot_wrap files.
# 4.61 20091117 update the version of clipper.
# 4.62 20091203 release server is now in oxford.
# 4.63 20091208 Add curl to the build system
# 4.64 20091209 Fix typo in untaring curl tar file.
# 4.65 20091209 Add libidn to build (for curl).
# 4.66 20091209 Test for holding dir in making tar file.
# 4.67 20091209 Add LDFLAGS to args for libcurl configure.
# 4.68 20091210 Add post-process-libcurl logic.
# 4.69 20091216 Don't delete bin/curl, we need it for updates. (20100120 Not any more)
# 4.70 20100120 debugging added to curl build (problems on bragg3).
# 4.71 20100203 Remove goosh.
# 4.72 20100203 Update clipper version.
# 4.73 20100205 only download mmdb once.
# 4.74 20100304 Fix install_top_dir typos.
# 4.75 20101102 Dependency check for gtkglext patch (compatibility with gtk+ version).
# 4.76 20101102 Correct directory for previoius patch.
# 4.77 20110505 switch to new style Refmac library.
# 4.78 20110507 Refmac mon lib to 5.29
# 4.79 20110610 biop -> lmb.bioch
# 4.80 20110707 also make holding directory for stable builds.
# 4.81 20110725 Add goocanvas.
# 4.82 20110725 Add test for gtk and cairo before going ahead with compiling and using
# goocanvas.
# 4.83 20110805 On 64 bit redhat 4, building freeglut, we need to use /usr/X11R6/lib64,
# not /usr/X11R6/lib, edit configure.
# 4.84 20110821 Hack in a solution the the new clipper problem (new clipper with cif
# tools needs new libtools/configure new ccp4 libs (underlay-2).
# 4.85 20111021 Update python to 2.6, guile to 1.8.8, add guile patch.
# 4.86 20111214 Update to mmdb 1.24 (new) which has working LINKRs.
# 4.87 20120108 Use make not MAKE for guile-gtk.
# 4.88 20120120 Don't use -j $nproc for make if we don't have memory.
# 4.89 20120223 Use libccp4c-5.0.2-ysbl-3.tar.gz, that has libccp4c_la_LIBADD.
# 4.90 20120713 debug $coot_dir_name link usage.
# 4.91 20120808 update to handle version of debian in /etc/issue.
# 4.92 20120820 Debian /etc/issue handling for wheezy.
# 4.93 20120921 Update mmdb to version 1.24.2
# 4.94 20130123 Move pre-release and release server-dir to Cambridge.
# 4.95 20130128 Refmac dictionary to 5.39
# 4.96 20130228 New mmdb version - 1.25.0
# 4.97 20130424 Rework (fix typo) for python include directory slimming.
# 4.98 20130424 Remove ssh copying
# 4.99 20130424 swig 1.3.29 is broken no matter what the architecture.
# 5.00 20130425 CXX testing updates (for ubuntu).
# 5.01 20130429 mmdb version bump 1.25.2
# 5.02 20130502 better diagnostic for goocanvas compile
# 5.03 20130503 Remove SWIG version test (now it is not needed to build source)
# 5.04 20130514 Add COOT_BUILD_INFO_STRING.
# 5.05 20130604 For Release 0.7.1, change release vs pre-release logic
# (MRC server).
# 5.06 20130612 More tinkering to get the correct version for release from the server.
# 5.07 20130707 Adjustment to build stable logic.
# 5.08 20130716 Move source server to personal/pemsley.
# 5.09 20130818 Use ssm-1.3
# 5.10 20130824 debugging publish
# 5.11 20130826 Allow build without guile; name directory for building.
# 5.12 20130909 LD_LIBRARY_PATH changes/fixup.
# 5.13 20130910 Force -O usage for guile compilation.
# 5.14 20130920 Publish logs.
# 5.15 20140408 New version of Python.
# 5.16 20140817 Python version to 2.7.8
# 5.17 20140911 SSM updates.
# 5.18 20141128 Add hack bin for debian awk
# 5.19 20141128 Use dist_name for debian (not systype)
# 5.20 20141203 More/better Debian awk hack.
# 5.21 20141203 Unset some build environment variables (including LD_LIBRARY_PATH)
# 5.22 20141210 More LD_LIBRARY_PATH hacking for debian
# 5.23 20141210 libreadline needs to be linked with -lcurses (on Debian)
# 5.25 20141212
# 5.26 20150215 Use /opt/X11 and COOT_CCP4_PACKAGES for dependences on Darwin.
# 5.27 20170925 bump libccp4 version to 6.5.1 - this has libccp4.pc for pkg-config
# 5.28 20170925 Fixes for clipper and guile and gmp version update (gcc-7.2)
# 5.29 20171006 Test for libgnomecanvas devel (now not available in system for Redhat 7.3)
# 5.30 20180109 Update python version.
# 6.00 20200812 include glm
# 6.01 20210430 pkg-config tweak and no remove rdkit libs for coot configure
# 6.02 20220417 add ffi into Python setup.py
# 6.03 20220704 work on GLIB and python modules
# 6.04 20220705 Python still doesn't build (on cluster) - add debugging
# 6.05 20220706 Use https:: instead of ftp::
# 6.06 20220707 try export LD_LIBRARY_PATH=$install_top_dir/lib in Coot section
# 6.07 20220710 libffi fixes for python
# 6.08 20220803-PE pygobject cleanups
# 6.09 20220907-PE meson adjustment for compiling glib (what a pain)
# 6.10 20230603-PE remove goocanvas
# 6.11 20231113-PE print out the script_version
# 6.12 20240105-PE link $HOME/data/greg-data for the testing step
# 6.13 20240216-PE Install Darwin OpenSSL in $install_top_dir
# 6.14 20240220-PE Set the C++ flags for Catch2 (needed for macOS/clang) and build with CMake
# 6.15 20240220-PE OpenSSL and python apiflags and boost bjam updates
# 6.16 20240228-PE Add status of FFTW building
# 6.17 20240229-PE Portentious day. Adding in gettext for libintl for python and rdkit
# 6.18 20240304-PE Remove the --pydebug from Python's configuration
# 6.19 20240306-PE Don't build gettext on anything other than Darwin
# 6.20 20240326-PE Add cairo
# 6.21 20240327-PE Reposition the cairo build (after ninja)
# 6.22 20240427-PE Fix-ups for building on fedora (partial)
script_version=6.22
echo ==================================================== add test for SWIG version
echo ==================================================== add test for CMake version
echo this is script version $script_version
# :: NOTE::
# this "strange" construction of variable names: x=${x:=thing} sets the
# variable x only if it has not previously been defined.
#
# So, the idea is that you write a wrapper for this script (defining typically
# AUTOBUILD_INSTALLED, AUTOBUILD_BUILD, LOGS and build_coot_prerelease) then
# source this file. That means that you (probably) don't have to edit your
# version of build-it every time it changes.
# ENABLE_PYTHON_COOT: if ENABLE_PYTHON_COOT is set to 0 or "no" then
# python coot is not enable (guile coot is enabled). if
# ENABLE_PYTHON_COOT is set, but not set to 0 or no then python coot
# is enabled. If ENABLE_PYTHON_COOT is not set, the guile-coot is
# enabled (python coot is not enabled).
# Pythonizing coot makes non-transferable binararies (why?). Let
# the pythonness be controlled on the command line:
#
# At the moment, if you build with Gtk2, you build with python, hence $build_type
# is the same thing.
#
# Set the host and the OS.
# Fairly fundamental.
#
# arch needs inetutils for hostname
OS=$(uname)
HOST=$(hostname)
# Do we need to use a proxy server to get documents from the web? (set
# to 1 if we do)
use_proxy=${use_proxy:=}
# if we do need a proxy then we should give the proxy host and port too:
proxy_host=${proxy_host:=myproxy.com}
proxy_port=${proxy_port:=800}
no_proxy=${no_proxy:=".corp.net.com"}
# set this to true if you want to run the test suite and make binary
# bundles (needs test data and the CCP4 suite):
#
run_tests=${run_tests:=false}
# run the second test? Almost always passes and takes up lots of
# disk space
#
run_second_test=${run_second_test:=true}
# This is where the compiled binaries/libraries/data get installed:
# Note that the directory name must NOT end in a /
#
AUTOBUILD_INSTALLED=${AUTOBUILD_INSTALLED:=${HOME}/autobuild/${OS}-${HOST}}
if test x$GITHUB_ENV = x ; then
: # we are not in a hithub actions build
else
if [ "$CHAPI_ONLY" = true ] ; then
if [ $OS = Darwin ] ; then
AUTOBUILD_INSTALLED=$HOME/install/chapi-Darwin-macos
else
AUTOBUILD_INSTALLED=$HOME/install/chapi-Linux-ubuntu
fi
else
AUTOBUILD_INSTALLED=$HOME/install/coot-Linux-ubuntu
fi
fi
# or perhaps, for the adventurous:
#AUTOBUILD_INSTALLED=$CCP4_MASTER
# This is where the actual build (compilation) master directory is:
# a temporary or scratch directory would be sensible.
#
# AUTOBUILD_BUILD=${HOME}/autobuild
# I'm putting my build on "scratch space"
AUTOBUILD_BUILD=${AUTOBUILD_BUILD:=$HOME/autobuild/building}
# This is where the build logs go:
# suggested value:
# LOGS=$AUTOBUILD_BUILD/logs
# but I want to put my log file on the web, so I put them here:
LOGS=${LOGS:=$HOME/public_html/build-logs/${OS}-${HOST}}
# set this to "no" if you don't want to compile the pre-release code.
# build_coot_prerelease=
build_coot_prerelease=${build_coot_prerelease:=1}
# get build specials, e.g. change the compiler or the compiler options
# (e.g build for debugging), extra libraries etc setup LD_LIBRARY_PATH
# (or whatever) to include the autobuild library dir so that
# intermediate (configure compile) programs run and the addition to
# the path of GNU make and wget.
#
# use this to specify config_extras
#
# options are: GL_prefix, e.g. SunOS has Mesa Graphics - this is
# where to find them:
# glut_prefix, optionally can use freeglut
#
# Suggested value: comment out this line
specs=${specs:=$HOME/autobuild/build-scripts/${HOST}-specials}
# if we are not in chapi mode, we ask
# where has gtk been installed if this is Mac OS?
# (this was from when gtk3 could be installed on macOS).
# I should add /usr/local of course these days
if test "$CHAPI_ONLY" = true ; then
:
else
if test "$OS" = "Darwin" ; then
if test -n "$gtk" ; then
if test -d "$gtk" ; then
: # pass, good
else
echo gtk variable must point to the directory where gtk has been installed
fi
else
# gtk was not set, let's try to guess
testdir=$HOME/gtk/inst
if test -d $testdir ; then
gtk=$HOME/gtk/inst
else
echo this build script needs to know where gtk has been installed
echo \(at the moment\)
echo set gtk to point to the directory where gtk has been installed
exit 2
fi
fi
fi
fi
# Make nightly binary tarballs?
# You probably don't want to do this, so recommended is do_nightlies=0
do_nightlies=${do_nightlies:=1}
# if you do want to build them where should they go?
# NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD
NIGHTLY_DEST_DIR=${NIGHTLY_DEST_DIR:=${HOME}/public_html/software/binaries/nightlies/pre-release}
# if we are not building a nightly/pre-release, i.e. this is a binary
# for a stable release, they go somewhere else:
#
STABLE_DEST_DIR=${STABLE_DEST_DIR:=${HOME}/public_html/software/binaries/stable}
# this is given args: arg1(dir) arg2(file-name)
# how do we transfer the file on the build host to the web server?
# Some systems we can simply copy the files. For others, we now have
# this "publish" mechanism (to be overwritten as needed)
publish=${publish:=:}
publish_logs=${publish_logs:=:}
# if umask was not set, then use 0022
# umask 0022
if [ -z "$umask" ] ; then
umask 0022
else
umask "$umask"
fi
# When we fail to extract the correct tar file from the web site, what
# shall we build instead?
#
fallback_coot_version=coot-0.4
# ----------------------------------------------------------------
# End of tinkering with parameters.
# ----------------------------------------------------------------
# First, check that this is bash.
#
if [ "$BASH" = "" ] ; then
echo this shell is not bash\!
echo this script must be run with bash\!
exit
fi
# now the functions:
function mkdir_maybe {
dir=$1
if [ ! -e "$dir" ] ; then
mkdir "$dir"
fi
}
# Give args: prefix-dir and (based on is-static-flag) either
# "clear-static" or "clear-dynamic"
#
function post_install_slim {
echo we are slimming directory "$1"
fat_dir="$1"
cleaned_dir="$2"
clear_type="$3"
echo fat_dir is "$fat_dir"
echo clear_type is "$clear_type"
echo cleaned_dir is "$cleaned_dir"
mkdir_maybe "$cleaned_dir"
mkdir_maybe "$cleaned_dir"/bin
mkdir_maybe "$cleaned_dir"/lib
# and this for pyconfig.h
if [ "$ENABLE_PYTHON_COOT" = yes ] ; then
mkdir_maybe "$cleaned_dir"/include
mkdir_maybe "$cleaned_dir"/include/$python_version
fi
lib_sos=`cd $fat_dir && ls -1 lib/lib*.so*`
lib_as=`cd $fat_dir && ls -1 lib/lib*.a`
if [ "$clear_type" = "clear-dynamic" ] ; then
keep_lib_archs="$lib_as"
fi
if [ "$clear_type" = "clear-static" ] ; then
keep_lib_archs="$lib_sos"
fi
file_list="etc info man share libexec \
libexec/coot-bin \
libexec/findwaters-bin \
libexec/findligand-bin \
libexec/mini-rsr-bin \
libexec/density-score-by-residue-bin \
bin/coot \
bin/findwaters \
bin/findligand \
bin/guile \
bin/coot-density-score-by-residue \
bin/coot-available-comp-id \
bin/coot-compare-dictionaries \
bin/coot-make-shelx-restraints \
bin/coot-dictionary-bond-distributions \
bin/lidia \
bin/curl \
$keep_lib_archs"
if [ "$ENABLE_PYTHON_COOT" = yes ] ; then
# 20090427 remove python and python config from bin dir (as it
# interfers with system python)
file_list="$file_list html \
lib/$python_version include/$python_version"
fi
echo rsyncing...
for file in $file_list ;
do
dn=$(dirname $file)
if [ -e $fat_dir/$file ] ; then
# echo rsync -axr $fat_dir/$file $cleaned_dir/$dn
rsync -axr $fat_dir/$file $cleaned_dir/$dn
else
echo $fat_dir/$file does not exist
fi
done
echo done rsyncing.
}
function make_tar {
echo in make_tar args: $1 $2
echo in make_tar: in dir: $PWD
tar_dir=$1
tar_file_name=$2
cd $install_top_dir/..
if [ -e $tar_dir ] ; then
echo taring nightly... from $tar_dir to $tar_file_name
tar czf $tar_file_name $tar_dir
status=$?
if [ "$status" != 0 ] ; then
echo ERROR:: tar czf $tar_file_name $tar_dir failed.
echo ERROR:: while in directory $(pwd)
echo ERROR:: tar failed > $tar_file_name.md5sum
rm $tar_file_name
else
md5sum $tar_file_name > $tar_file_name.md5sum
/bin/ls -l $tar_file_name >> $tar_file_name.md5sum
echo done tar successfully.
fi
else
echo ERROR:: tar target directory $tar_dir does not exist.
fi
}
function setup_ccp4 {
# we have access to $OS and $arch.
if test "$OS" = Linux ; then
setup_file=/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/include/ccp4.setup-sh
if test -e $setup_file ; then
. $setup_file
else
if [ "$systype" = x86_64-centos-6 ] ; then
setup_file=/home/emsley/ccp4/setup-scripts/sh/ccp4.setup
else
if [ "$systype" = x86_64-centos-5 ] ; then
setup_file=/home/emsley/ccp4/ccp4-6.2.0/include/ccp4.setup-sh
else
setup_file=setup-ccp4
fi
fi
if test -e $setup_file ; then
echo evaluating $setup_file
. $setup_file
else
echo WARNING:: ccp4 setup file $setup_file does not exist.
fi
fi
fi
if test "$OS" = Darwin ; then
. /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh
fi
}
# exit
function my_exit {
exit_arg=$1
shift
extra_args=$*
# echo fail-build $extra_args > $LOGS/$build-status
if [ -e $LOGS/$test-status ] ; then
rm $LOGS/$test-status
fi
exit $exit_arg
}
# Return 0 on success, 1 on failure (or not tested)
#
#
# This can only be run when the coot tar file and greg tests have been
# untared (in this particular build)
#
# we should be in the directory where coot was untarred for building
# when this function was called.
#
function test_coot {
echo testing with greg
echo testing with greg >&2
echo currently we are here:
pwd
date
if [ "$1" != "" ] ; then
coot_binary=$1
else
coot_binary=$install_top_dir/libexec/coot-bin
fi
if test "$run_tests" = true ; then
# let's test our new coot
# for python build we need to set COOT_PYTHON_DIR and COOT_HOME
# as well as PYTHONPATH things now, because we do a "proper"
# import * from coot, which needs to find coot.py the
# conventional/pythonic way. If pythonic coot doesn't start properly,
# the greg tests fail.
COOT_PYTHON_DIR=$install_top_dir/share/coot/python
PYTHONPATH=$COOT_PYTHON_DIR
PYTHONHOME=$install_top_dir
export COOT_PYTHON_DIR
export PYTHONPATH
export PYTHONHOME
# the greg tests are where the coot source code was untarred.
#
# if it's not there, then let's link it.
if [ ! -d greg-tests ] ; then
echo greg-tests dir missing in this directory:
pwd
echo trying to link
if [ -d ~/data/greg-data ] ; then
ln -s ~/data/greg-data .
else
echo $HOME/data/greg-data data files are not in place
fi
return 1
fi
setup_ccp4
cat <<EOF > command-line-greg.scm
(use-modules (ice-9 greg))
(set! greg-tools (list "greg-tests"))
(set! greg-debug #t)
(set! greg-verbose 5)
(let ((r (greg-test-run)))
(if r
(coot-real-exit 0)
(coot-real-exit 1)))
EOF
echo $install_top_dir/bin/coot --no-graphics --script command-line-greg.scm
$install_top_dir/bin/coot --no-graphics --script command-line-greg.scm
status=$?
if [ $status = 0 ] ; then
echo test_coot: coot test passed
return 0
else
echo test_coot: coot test failed
return 1
fi
else
echo run_tests is not true, not testing.
return 1
fi
}
# Return 0 on success, 1 on failure (or not tested)
#
# we should be in the directory where coot was untarred for building
# when this function was called.
#
function test_coot_python {
echo testing with python unittest
echo testing with python unittest >&2
echo currently we are here:
pwd
if test "$run_tests" = true ; then
# let's test our new coot
# for python build we need to set COOT_PYTHON_DIR and COOT_HOME
# as well as PYTHONPATH things now
COOT_PYTHON_DIR=$install_top_dir/share/coot/python
PYTHONPATH=$COOT_PYTHON_DIR
PYTHONHOME=$install_top_dir
export COOT_PYTHON_DIR
export PYTHONPATH
export PYTHONHOME
echo $install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py
$install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py
status=$?
if [ $status = 0 ] ; then
echo test_coot_python: coot test passed
return 0
else
echo test_coot_python: coot test failed
return 1
fi
else
return 1
fi
}
function fixup_libcurl {
sed s,-L/usr/lib,, curl-config > curl-config.tmp
mv curl-config.tmp curl-config
sed s,-L/usr/lib,, lib/libcurl.la > lib/libcurl.la.tmp
mv lib/libcurl.la.tmp lib/libcurl.la
}
# now we can set the gtk version
gtk_version=${gtk_version:=4}
build_type=gtk$gtk_version # python is implicit - we will do guile when we can
# now on to some code!
if [ "$use_proxy" = 1 ] ; then
# establish proxy settings
printf "Proxy user: "
read proxy_user
printf "Proxy password: "
read -s proxy_pass
printf "\n"
http_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
https_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
ftp_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
ssl_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
export http_proxy https_proxy ftp_proxy ssl_proxy no_proxy
fi
# use the right (GNU) tar and provide the path to wget (needed
# for downloads) and to GNU make - (which is necesary for python
# at least).
#
# So that python and the *-configs are found when it is installed:
# A bit of a kludge because we do testing for pre-release later.
# It's a logical mess.
#
if test "$build_coot_prerelease" = 1 ; then
PATH=${AUTOBUILD_INSTALLED}-pre-release-$build_type/bin:$PATH
else
PATH=$AUTOBUILD_INSTALLED-$build_type/bin:$PATH
fi
PATH=$PATH:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin:
PATH=$PATH:/etc:/usr/etc
#
# This is where the sources downloaded from network go:
AUTOBUILD_SOURCES=${AUTOBUILD_BUILD}/sources
if (! test -d ${AUTOBUILD_SOURCES}) ; then
mkdir -p ${AUTOBUILD_SOURCES}
fi
export PATH
echo PATH is now: $PATH
echo LOGS is $LOGS
echo AUTOBUILD_SOURCES is $AUTOBUILD_SOURCES
echo AUTOBUILD_BUILD is $AUTOBUILD_BUILD
echo AUTOBUILD_INSTALLED is $AUTOBUILD_INSTALLED
echo GITHUB_ENV $GITHUB_ENV
echo GITHUB_WORKSPACE $GITHUB_WORKSPACE
# now make the build logs directory
mkdir -p $LOGS
shared_static_flag="--disable-shared" # huh?
shared_static_flag="--disable-static"
shared_lib_ext=so
systype=unknown
# malloc.h business, Darwin does not have malloc.h
# used in the gtk_canvas build
have_malloc=1
if test "$OS" = "Darwin" ; then
have_malloc=0
fix_ulong=1
update_libtool=1
update_config_guess_sub=1
shared_static_flag="--disable-static"
shared_lib_ext=dylib
# what happens if I do this?
# need_readline_patch=1
# uname -a gives processor type in last field on Darwin
processor=$(uname -a | awk '{print $(NF)}')
need_gtk_imlib_libtool_fix=1
if test "$processor" = "i386" ; then
need_glib_getpwuid_fix=1
need_glib_poll_fix=1
fi
osversion=$(sw_vers -productVersion)
systype=MacOSX-${osversion}-${processor}
fi
# redirect the output.
#
# exec 2>&1 > $LOGS/$HOST.log
# Try not to redirect standard out so that it goes to
# the sub-shell log? (testing)
if [ -n "$TEE_STDOUT" ]; then
echo INFO:: std output will be both printed here and written to $LOGS/build-gtk4.log
exec > >(tee $LOGS/build-gtk4.log)
else
echo INFO:: redirecting std output to $LOGS/build-gtk4.log
exec > $LOGS/build-gtk4.log
fi