-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathconfig.log
1051 lines (1026 loc) · 45.9 KB
/
config.log
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
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by DiscovarDeNovo configure 52488, which was
generated by GNU Autoconf 2.63. Invocation command line was
$ ./configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/home/zackcohen/.linuxbrew/Cellar/discovardenovo/52488
## --------- ##
## Platform. ##
## --------- ##
hostname = shasta
uname -m = x86_64
uname -r = 4.4.0-31-generic
uname -s = Linux
uname -v = #50-Ubuntu SMP Wed Jul 13 00:07:12 UTC 2016
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /home/zackcohen/.linuxbrew/bin
PATH: /home/zackcohen/bin
PATH: /home/zackcohen/.local/bin
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games
PATH: /usr/local/games
PATH: /snap/bin
PATH: /usr/bin/java
PATH: /home/zackcohen/.linuxbrew/Library/Homebrew/shims/scm
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2094: checking for a BSD-compatible install
configure:2162: result: /usr/bin/install -c
configure:2173: checking whether build environment is sane
configure:2233: result: yes
configure:2374: checking for a thread-safe mkdir -p
configure:2413: result: /bin/mkdir -p
configure:2426: checking for gawk
configure:2442: found /usr/bin/gawk
configure:2453: result: gawk
configure:2464: checking whether make sets $(MAKE)
configure:2486: result: yes
configure:2599: checking build system type
configure:2617: result: x86_64-unknown-linux-gnu
configure:2639: checking host system type
configure:2654: result: x86_64-unknown-linux-gnu
configure:2688: checking for style of include used by make
configure:2716: result: GNU
configure:2786: checking for gcc
configure:2813: result: /usr/bin/gcc
configure:3045: checking for C compiler version
configure:3053: /usr/bin/gcc --version >&5
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.1) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3057: $? = 0
configure:3064: /usr/bin/gcc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.1' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.1)
configure:3068: $? = 0
configure:3075: /usr/bin/gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3079: $? = 1
configure:3102: checking for C compiler default output file name
configure:3124: /usr/bin/gcc -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
configure:3128: $? = 0
configure:3166: result: a.out
configure:3185: checking whether the C compiler works
configure:3195: ./a.out
configure:3199: $? = 0
configure:3218: result: yes
configure:3225: checking whether we are cross compiling
configure:3227: result: no
configure:3230: checking for suffix of executables
configure:3237: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
configure:3241: $? = 0
configure:3267: result:
configure:3273: checking for suffix of object files
configure:3299: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:3303: $? = 0
configure:3328: result: o
configure:3332: checking whether we are using the GNU C compiler
configure:3361: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:3368: $? = 0
configure:3385: result: yes
configure:3394: checking whether /usr/bin/gcc accepts -g
configure:3424: /usr/bin/gcc -c -g -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:3431: $? = 0
configure:3532: result: yes
configure:3549: checking for /usr/bin/gcc option to accept ISO C89
configure:3623: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:3630: $? = 0
configure:3653: result: none needed
configure:3673: checking dependency style of /usr/bin/gcc
configure:3783: result: none
configure:3798: checking for a sed that does not truncate output
configure:3864: result: /bin/sed
configure:3882: checking for grep that handles long lines and -e
configure:3942: result: /bin/grep
configure:3947: checking for egrep
configure:4011: result: /bin/grep -E
configure:4016: checking for fgrep
configure:4080: result: /bin/grep -F
configure:4115: checking for ld used by /usr/bin/gcc
configure:4182: result: /usr/bin/ld
configure:4191: checking if the linker (/usr/bin/ld) is GNU ld
configure:4206: result: yes
configure:4218: checking for BSD- or MS-compatible name lister (nm)
configure:4267: result: /usr/bin/nm -B
configure:4385: checking the name lister (/usr/bin/nm -B) interface
configure:4392: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:4395: /usr/bin/nm -B "conftest.o"
configure:4398: output
0000000000000000 B some_variable
configure:4405: result: BSD nm
configure:4408: checking whether ln -s works
configure:4412: result: yes
configure:4420: checking the maximum length of command line arguments
configure:4540: result: 1572864
configure:4557: checking whether the shell understands some XSI constructs
configure:4567: result: yes
configure:4571: checking whether the shell understands "+="
configure:4577: result: yes
configure:4612: checking for /usr/bin/ld option to reload object files
configure:4619: result: -r
configure:4688: checking for objdump
configure:4704: found /usr/bin/objdump
configure:4715: result: objdump
configure:4747: checking how to recognize dependent libraries
configure:4943: result: pass_all
configure:5003: checking for ar
configure:5019: found /usr/bin/ar
configure:5030: result: ar
configure:5108: checking for strip
configure:5124: found /usr/bin/strip
configure:5135: result: strip
configure:5207: checking for ranlib
configure:5223: found /usr/bin/ranlib
configure:5234: result: ranlib
configure:5324: checking command to parse /usr/bin/nm -B output from /usr/bin/gcc object
configure:5442: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:5445: $? = 0
configure:5449: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
configure:5452: $? = 0
configure:5506: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c conftstm.o >&5
configure:5509: $? = 0
configure:5547: result: ok
configure:5643: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:5646: $? = 0
configure:6414: checking how to run the C preprocessor
configure:6454: /usr/bin/gcc -E -isystem/home/zackcohen/.linuxbrew/include conftest.c
configure:6461: $? = 0
configure:6492: /usr/bin/gcc -E -isystem/home/zackcohen/.linuxbrew/include conftest.c
conftest.c:10:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6499: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:6532: result: /usr/bin/gcc -E
configure:6561: /usr/bin/gcc -E -isystem/home/zackcohen/.linuxbrew/include conftest.c
configure:6568: $? = 0
configure:6599: /usr/bin/gcc -E -isystem/home/zackcohen/.linuxbrew/include conftest.c
conftest.c:10:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6606: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:6646: checking for ANSI C header files
configure:6676: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6683: $? = 0
configure:6782: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
configure:6786: $? = 0
configure:6792: ./conftest
configure:6796: $? = 0
configure:6814: result: yes
configure:6838: checking for sys/types.h
configure:6859: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6866: $? = 0
configure:6883: result: yes
configure:6838: checking for sys/stat.h
configure:6859: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6866: $? = 0
configure:6883: result: yes
configure:6838: checking for stdlib.h
configure:6859: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6866: $? = 0
configure:6883: result: yes
configure:6838: checking for string.h
configure:6859: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6866: $? = 0
configure:6883: result: yes
configure:6838: checking for memory.h
configure:6859: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6866: $? = 0
configure:6883: result: yes
configure:6838: checking for strings.h
configure:6859: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6866: $? = 0
configure:6883: result: yes
configure:6838: checking for inttypes.h
configure:6859: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6866: $? = 0
configure:6883: result: yes
configure:6838: checking for stdint.h
configure:6859: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6866: $? = 0
configure:6883: result: yes
configure:6838: checking for unistd.h
configure:6859: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6866: $? = 0
configure:6883: result: yes
configure:6901: checking for dlfcn.h
configure:6922: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:6929: $? = 0
configure:6946: result: yes
configure:7131: checking for objdir
configure:7146: result: .libs
configure:7442: checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions
configure:7460: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -fno-rtti -fno-exceptions conftest.c >&5
configure:7464: $? = 0
configure:7477: result: yes
configure:7497: checking for /usr/bin/gcc option to produce PIC
configure:7769: result: -fPIC -DPIC
configure:7781: checking if /usr/bin/gcc PIC flag -fPIC -DPIC works
configure:7799: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -fPIC -DPIC -DPIC conftest.c >&5
configure:7803: $? = 0
configure:7816: result: yes
configure:7840: checking if /usr/bin/gcc static flag -static works
configure:7868: result: yes
configure:7883: checking if /usr/bin/gcc supports -c -o file.o
configure:7904: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -o out/conftest2.o conftest.c >&5
configure:7908: $? = 0
configure:7930: result: yes
configure:7938: checking if /usr/bin/gcc supports -c -o file.o
configure:7985: result: yes
configure:8018: checking whether the /usr/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:9092: result: yes
configure:9331: checking dynamic linker characteristics
configure:9774: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib -Wl,-rpath -Wl,/foo conftest.c >&5
configure:9781: $? = 0
configure:10017: result: GNU/Linux ld.so
configure:10119: checking how to hardcode library paths into programs
configure:10144: result: immediate
configure:10977: checking whether stripping libraries is possible
configure:10982: result: yes
configure:11017: checking if libtool supports shared libraries
configure:11019: result: yes
configure:11022: checking whether to build shared libraries
configure:11043: result: no
configure:11046: checking whether to build static libraries
configure:11050: result: yes
configure:11197: checking for C++ compiler version
configure:11205: /usr/bin/g++ --version >&5
g++ (Ubuntu 5.4.0-6ubuntu1~16.04.1) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:11209: $? = 0
configure:11216: /usr/bin/g++ -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.1' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.1)
configure:11220: $? = 0
configure:11227: /usr/bin/g++ -V >&5
g++: error: unrecognized command line option '-V'
g++: fatal error: no input files
compilation terminated.
configure:11231: $? = 1
configure:11234: checking whether we are using the GNU C++ compiler
configure:11263: /usr/bin/g++ -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.cpp >&5
configure:11270: $? = 0
configure:11287: result: yes
configure:11296: checking whether /usr/bin/g++ accepts -g
configure:11326: /usr/bin/g++ -c -g -isystem/home/zackcohen/.linuxbrew/include conftest.cpp >&5
configure:11333: $? = 0
configure:11434: result: yes
configure:11459: checking dependency style of /usr/bin/g++
configure:11569: result: none
configure:11697: checking for C++ compiler version
configure:11705: /usr/bin/g++ --version >&5
g++ (Ubuntu 5.4.0-6ubuntu1~16.04.1) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:11709: $? = 0
configure:11716: /usr/bin/g++ -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.1' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.1)
configure:11720: $? = 0
configure:11727: /usr/bin/g++ -V >&5
g++: error: unrecognized command line option '-V'
g++: fatal error: no input files
compilation terminated.
configure:11731: $? = 1
configure:11734: checking whether we are using the GNU C++ compiler
configure:11787: result: yes
configure:11796: checking whether /usr/bin/g++ accepts -g
configure:11934: result: yes
configure:11959: checking dependency style of /usr/bin/g++
configure:12069: result: none
configure:12092: checking how to run the C++ preprocessor
configure:12128: /usr/bin/g++ -E -isystem/home/zackcohen/.linuxbrew/include conftest.cpp
configure:12135: $? = 0
configure:12166: /usr/bin/g++ -E -isystem/home/zackcohen/.linuxbrew/include conftest.cpp
conftest.cpp:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:12173: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:12206: result: /usr/bin/g++ -E
configure:12235: /usr/bin/g++ -E -isystem/home/zackcohen/.linuxbrew/include conftest.cpp
configure:12242: $? = 0
configure:12273: /usr/bin/g++ -E -isystem/home/zackcohen/.linuxbrew/include conftest.cpp
conftest.cpp:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:12280: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:12456: checking for ld used by /usr/bin/g++
configure:12523: result: /usr/bin/ld -m elf_x86_64
configure:12532: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld
configure:12547: result: yes
configure:12602: checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:13577: result: yes
configure:13605: /usr/bin/g++ -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.cpp >&5
configure:13608: $? = 0
configure:13790: checking for /usr/bin/g++ option to produce PIC
configure:14107: result: -fPIC -DPIC
configure:14116: checking if /usr/bin/g++ PIC flag -fPIC -DPIC works
configure:14134: /usr/bin/g++ -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -fPIC -DPIC -DPIC conftest.cpp >&5
configure:14138: $? = 0
configure:14151: result: yes
configure:14172: checking if /usr/bin/g++ static flag -static works
configure:14200: result: yes
configure:14212: checking if /usr/bin/g++ supports -c -o file.o
configure:14233: /usr/bin/g++ -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -o out/conftest2.o conftest.cpp >&5
configure:14237: $? = 0
configure:14259: result: yes
configure:14264: checking if /usr/bin/g++ supports -c -o file.o
configure:14311: result: yes
configure:14341: checking whether the /usr/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:14367: result: yes
configure:14504: checking dynamic linker characteristics
configure:14895: /usr/bin/g++ -o conftest -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib -Wl,-rpath -Wl,/foo conftest.cpp >&5
configure:14902: $? = 0
configure:15138: result: GNU/Linux ld.so
configure:15189: checking how to hardcode library paths into programs
configure:15214: result: immediate
configure:15261: checking whether byte ordering is bigendian
configure:15286: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
conftest.c:23:9: error: unknown type name 'not'
not a universal capable compiler
^
conftest.c:23:15: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'universal'
not a universal capable compiler
^
conftest.c:23:15: error: unknown type name 'universal'
configure:15293: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #ifndef __APPLE_CC__
| not a universal capable compiler
| #endif
| typedef int dummy;
|
configure:15343: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
configure:15350: $? = 0
configure:15382: /usr/bin/gcc -c -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:29:4: error: unknown type name 'not'
not big endian
^
conftest.c:29:12: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'endian'
not big endian
^
configure:15389: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <sys/types.h>
| #include <sys/param.h>
|
| int
| main ()
| {
| #if BYTE_ORDER != BIG_ENDIAN
| not big endian
| #endif
|
| ;
| return 0;
| }
configure:15641: result: no
configure:15756: result: g++ version is >= 4.7... yes
configure:15979: checking for the pthreads library -lpthreads
configure:16027: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c -lpthreads >&5
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
configure:16034: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void* a) {a=0;}
| static void* start_routine(void* a) {return a;}
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_create(&th,0,start_routine,0);
| pthread_cleanup_pop(0);
| ;
| return 0;
| }
configure:16057: result: no
configure:15924: checking whether pthreads work without any flags
configure:16027: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
/tmp/ccMC6bvl.o: In function `main':
conftest.c:(.text.startup+0x21): undefined reference to `pthread_join'
conftest.c:(.text.startup+0x56): undefined reference to `__pthread_register_cancel'
conftest.c:(.text.startup+0x67): undefined reference to `pthread_create'
conftest.c:(.text.startup+0x71): undefined reference to `__pthread_unregister_cancel'
collect2: error: ld returned 1 exit status
configure:16034: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void* a) {a=0;}
| static void* start_routine(void* a) {return a;}
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_create(&th,0,start_routine,0);
| pthread_cleanup_pop(0);
| ;
| return 0;
| }
configure:16057: result: no
configure:15929: checking whether pthreads work with -Kthread
configure:16027: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -Kthread -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
gcc: error: unrecognized command line option '-Kthread'
configure:16034: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void* a) {a=0;}
| static void* start_routine(void* a) {return a;}
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_create(&th,0,start_routine,0);
| pthread_cleanup_pop(0);
| ;
| return 0;
| }
configure:16057: result: no
configure:15929: checking whether pthreads work with -kthread
configure:16027: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -kthread -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
gcc: error: unrecognized command line option '-kthread'
configure:16034: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void* a) {a=0;}
| static void* start_routine(void* a) {return a;}
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_create(&th,0,start_routine,0);
| pthread_cleanup_pop(0);
| ;
| return 0;
| }
configure:16057: result: no
configure:15979: checking for the pthreads library -llthread
configure:16027: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c -llthread >&5
/usr/bin/ld: cannot find -llthread
collect2: error: ld returned 1 exit status
configure:16034: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "DiscovarDeNovo"
| #define PACKAGE_TARNAME "discovardenovo"
| #define PACKAGE_VERSION "52488"
| #define PACKAGE_STRING "DiscovarDeNovo 52488"
| #define PACKAGE_BUGREPORT "[email protected]"
| #define PACKAGE "discovardenovo"
| #define VERSION "52488"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <pthread.h>
| static void routine(void* a) {a=0;}
| static void* start_routine(void* a) {return a;}
| int
| main ()
| {
| pthread_t th; pthread_attr_t attr;
| pthread_join(th, 0);
| pthread_attr_init(&attr);
| pthread_cleanup_push(routine, 0);
| pthread_create(&th,0,start_routine,0);
| pthread_cleanup_pop(0);
| ;
| return 0;
| }
configure:16057: result: no
configure:15929: checking whether pthreads work with -pthread
configure:16027: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -pthread -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
configure:16034: $? = 0
configure:16057: result: yes
configure:16076: checking for joinable pthread attribute
configure:16101: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -pthread -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
configure:16108: $? = 0
configure:16128: result: PTHREAD_CREATE_JOINABLE
configure:16138: checking if more special flags are required for pthreads
configure:16145: result: no
configure:16261: checking for /usr/bin/gcc option to support OpenMP
configure:16281: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
conftest.c:3:2: error: unknown type name 'choke'
choke me
^
In file included from conftest.c:5:0:
/usr/lib/gcc/x86_64-linux-gnu/5/include/omp.h:35:1: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'typedef'
typedef struct
^
configure:16288: $? = 1
configure: failed program was:
|
| #ifndef _OPENMP
| choke me
| #endif
| #include <omp.h>
| int main () { return omp_get_num_threads (); }
|
configure:16320: /usr/bin/gcc -o conftest -Os -w -pipe -march=native -fpermissive -fopenmp -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
configure:16327: $? = 0
configure:16357: result: -fopenmp
configure:16373: checking validity of OpenMP configuation.
configure:16388: /usr/bin/gcc -o conftest -fopenmp -Os -w -pipe -march=native -fpermissive -isystem/home/zackcohen/.linuxbrew/include -L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib conftest.c >&5
configure:16395: $? = 0
configure:16646: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by DiscovarDeNovo config.status 52488, which was
generated by GNU Autoconf 2.63. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on shasta
config.status:976: creating Makefile
config.status:976: creating src/Makefile
config.status:1187: executing depfiles commands
config.status:1187: executing libtool commands
configure:18935: WARNING: unrecognized options: --disable-debug, --disable-silent-rules
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_c_bigendian=no
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=/usr/bin/gcc
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-Os -w -pipe -march=native -fpermissive'
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=-isystem/home/zackcohen/.linuxbrew/include
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=set
ac_cv_env_CXXFLAGS_value='-Os -w -pipe -march=native -fpermissive'
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=/usr/bin/g++
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib'
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_header_dlfcn_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_FGREP='/bin/grep -F'
ac_cv_path_GREP=/bin/grep
ac_cv_path_SED=/bin/sed
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='/usr/bin/gcc -E'
ac_cv_prog_CXXCPP='/usr/bin/g++ -E'
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_CC=/usr/bin/gcc
ac_cv_prog_ac_ct_OBJDUMP=objdump
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_c_openmp=-fopenmp
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
am_cv_CC_dependencies_compiler_type=none
am_cv_CXX_dependencies_compiler_type=none
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_nm_interface='BSD nm'
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/bin/ld
lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64'
lt_cv_path_NM='/usr/bin/nm -B'
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_c_o_CXX=yes
lt_cv_prog_compiler_pic_works=yes
lt_cv_prog_compiler_pic_works_CXX=yes
lt_cv_prog_compiler_rtti_exceptions=yes
lt_cv_prog_compiler_static_works=yes
lt_cv_prog_compiler_static_works_CXX=yes
lt_cv_prog_gnu_ld=yes
lt_cv_prog_gnu_ldcxx=yes
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_max_cmd_len=1572864
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /tmp/discovardenovo-20160805-10035-fv5rf1/discovardenovo-52488/missing --run aclocal-1.11'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE='#'
AMTAR='${SHELL} /tmp/discovardenovo-20160805-10035-fv5rf1/discovardenovo-52488/missing --run tar'
AR='ar'
AUTOCONF='${SHELL} /tmp/discovardenovo-20160805-10035-fv5rf1/discovardenovo-52488/missing --run autoconf'
AUTOHEADER='${SHELL} /tmp/discovardenovo-20160805-10035-fv5rf1/discovardenovo-52488/missing --run autoheader'
AUTOMAKE='${SHELL} /tmp/discovardenovo-20160805-10035-fv5rf1/discovardenovo-52488/missing --run automake-1.11'
AWK='gawk'
CC='/usr/bin/gcc'
CCDEPMODE='depmode=none'
CFLAGS='-Os -w -pipe -march=native -fpermissive'
CPP='/usr/bin/gcc -E'
CPPFLAGS='-isystem/home/zackcohen/.linuxbrew/include'
CXX='/usr/bin/g++'
CXXCPP='/usr/bin/g++ -E'
CXXDEPMODE='depmode=none'
CXXFLAGS='-Os -w -pipe -march=native -fpermissive -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG'
CYGPATH_W='echo'
DEFS='-DPACKAGE_NAME=\"DiscovarDeNovo\" -DPACKAGE_TARNAME=\"discovardenovo\" -DPACKAGE_VERSION=\"52488\" -DPACKAGE_STRING=\"DiscovarDeNovo\ 52488\" -DPACKAGE_BUGREPORT=\"[email protected]\" -DPACKAGE=\"discovardenovo\" -DVERSION=\"52488\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_PTHREAD=1'
DEPDIR='.deps'
DSYMUTIL=''
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
FGREP='/bin/grep -F'
GREP='/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
JEMALLOC_LIB='-ljemalloc'
LD='/usr/bin/ld -m elf_x86_64'
LDFLAGS='-L/home/zackcohen/.linuxbrew/lib -Wl,--dynamic-linker=/home/zackcohen/.linuxbrew/lib/ld.so -Wl,-rpath,/home/zackcohen/.linuxbrew/lib'
LIBOBJS=''
LIBS=''
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LIBZ_LIB='-lz'
LIPO=''
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /tmp/discovardenovo-20160805-10035-fv5rf1/discovardenovo-52488/missing --run makeinfo'
MKDIR_P='/bin/mkdir -p'
NM='/usr/bin/nm -B'
NMEDIT=''
OBJDUMP='objdump'
OBJEXT='o'
OPENMP_CFLAGS='-fopenmp'
OS_RELEASE='4.4.0-31-generic'
OTOOL64=''
OTOOL=''
PACKAGE='discovardenovo'
PACKAGE_BUGREPORT='[email protected]'
PACKAGE_NAME='DiscovarDeNovo'
PACKAGE_STRING='DiscovarDeNovo 52488'
PACKAGE_TARNAME='discovardenovo'
PACKAGE_VERSION='52488'
PATH_SEPARATOR=':'
PTHREAD_CC='/usr/bin/gcc'
PTHREAD_CFLAGS='-pthread'
PTHREAD_LIBS=''
RANLIB='ranlib'
SED='/bin/sed'
SET_MAKE=''
SHELL='/bin/bash'
STRIP='strip'
VERSION='52488'
ac_ct_CC='/usr/bin/gcc'
ac_ct_CXX=''
ac_ct_DUMPBIN=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE='#'
am__fastdepCXX_FALSE=''
am__fastdepCXX_TRUE='#'
am__include='include'
am__isrc=''
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
ax_pthread_config=''
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-unknown-linux-gnu'