Running 'test_LINGAM.R' [5s]
  Running 'test_addBgKnowledge.R' [4s]
  Running 'test_adjustment.R' [5s]
  Running 'test_ages.R' [4s]
  Running 'test_amat2dag.R' [3s]
  Running 'test_arges.R' [3s]
  Running 'test_backdoor.R' [10s]
  Comparing 'test_backdoor.Rout' to 'test_backdoor.Rout.save' ...24,34c24,34
< 1  . 1 1 . 1 1 . . .  1  1  .
< 2  . . . . . . . . .  1  .  1
< 3  . . . . . . . 1 .  .  .  1
< 4  . . . . . . . . .  .  .  .
< 5  . . . . . . . 1 .  .  1  .
< 6  . . . . . . . . .  1  1  1
< 7  . . . . . . . 1 .  .  .  .
< 8  . . . . . . . . .  .  .  .
< 9  . . . . . . . . .  .  1  .
< 10 . . . . . . . . .  .  .  .
< 11 . . . . . . . . .  .  .  1
---
> 1  . . . 1 . 1 . . 1  1  1  1
> 2  . . . . . 1 . 1 .  .  1  .
> 3  . . . . . . . . 1  .  .  .
> 4  . . . . . . . . .  1  .  .
> 5  . . . . . . . . .  .  .  .
> 6  . . . . . . . . .  .  .  .
> 7  . . . . . . . . .  .  1  .
> 8  . . . . . . . . .  1  .  .
> 9  . . . . . . . . .  1  1  .
> 10 . . . . . . . . .  .  1  .
> 11 . . . . . . . . .  .  .  .
57,58c57,58
<   ..$ 4 : NULL
<   ..$ 5 : int(0) 
---
>   ..$ 4 : int(0) 
>   ..$ 5 : NULL
67,77c67,77
<   ..$ 1 : logi NA
<   ..$ 3 : int 1
<   ..$ 4 : NULL
<   ..$ 5 : int 1
<   ..$ 6 : int 1
<   ..$ 7 : int 1
<   ..$ 8 : int 1
<   ..$ 9 : int 1
<   ..$ 10: int 1
<   ..$ 11: int 1
<   ..$ 12: int 1
---
>   ..$ 1 : int(0) 
>   ..$ 3 : int(0) 
>   ..$ 4 : int(0) 
>   ..$ 5 : NULL
>   ..$ 6 : int(0) 
>   ..$ 7 : int(0) 
>   ..$ 8 : int(0) 
>   ..$ 9 : int(0) 
>   ..$ 10: int(0) 
>   ..$ 11: int(0) 
>   ..$ 12: int(0) 
78a79,90
>   ..$ 1 : int(0) 
>   ..$ 2 : int(0) 
>   ..$ 4 : int(0) 
>   ..$ 5 : NULL
>   ..$ 6 : int(0) 
>   ..$ 7 : int(0) 
>   ..$ 8 : int(0) 
>   ..$ 9 : int(0) 
>   ..$ 10: int(0) 
>   ..$ 11: int(0) 
>   ..$ 12: int(0) 
>  $ 4 :List of 11
81,82c93,94
<   ..$ 4 : NULL
<   ..$ 5 : int 1
---
>   ..$ 3 : int 1
>   ..$ 5 : NULL
90c102
<  $ 4 :List of 11
---
>  $ 5 :List of 11
94c106
<   ..$ 5 : NULL
---
>   ..$ 4 : NULL
102,113d113
<  $ 5 :List of 11
<   ..$ 1 : logi NA
<   ..$ 2 : int 1
<   ..$ 3 : int 1
<   ..$ 4 : NULL
<   ..$ 6 : int 1
<   ..$ 7 : int 1
<   ..$ 8 : int 1
<   ..$ 9 : int 1
<   ..$ 10: int 1
<   ..$ 11: int 1
<   ..$ 12: int 1
116,125c116,125
<   ..$ 2 : int 1
<   ..$ 3 : int 1
<   ..$ 4 : NULL
<   ..$ 5 : int 1
<   ..$ 7 : int 1
<   ..$ 8 : int 1
<   ..$ 9 : int 1
<   ..$ 10: int 1
<   ..$ 11: int 1
<   ..$ 12: int 1
---
>   ..$ 2 : logi NA
>   ..$ 3 : int [1:2] 1 2
>   ..$ 4 : int [1:2] 1 2
>   ..$ 5 : NULL
>   ..$ 7 : int [1:2] 1 2
>   ..$ 8 : int [1:2] 1 2
>   ..$ 9 : int [1:2] 1 2
>   ..$ 10: int [1:2] 1 2
>   ..$ 11: int [1:2] 1 2
>   ..$ 12: int [1:2] 1 2
130,131c130,131
<   ..$ 4 : NULL
<   ..$ 5 : int(0) 
---
>   ..$ 4 : int(0) 
>   ..$ 5 : NULL
139,149c139,149
<   ..$ 1 : int [1:3] 3 5 7
<   ..$ 2 : int [1:3] 3 5 7
<   ..$ 3 : logi NA
<   ..$ 4 : NULL
<   ..$ 5 : logi NA
<   ..$ 6 : int [1:3] 3 5 7
<   ..$ 7 : logi NA
<   ..$ 9 : int [1:3] 3 5 7
<   ..$ 10: int [1:3] 3 5 7
<   ..$ 11: int [1:3] 3 5 7
<   ..$ 12: int [1:3] 3 5 7
---
>   ..$ 1 : int 2
>   ..$ 2 : logi NA
>   ..$ 3 : int 2
>   ..$ 4 : int 2
>   ..$ 5 : NULL
>   ..$ 6 : int 2
>   ..$ 7 : int 2
>   ..$ 9 : int 2
>   ..$ 10: int 2
>   ..$ 11: int 2
>   ..$ 12: int 2
151,161c151,161
<   ..$ 1 : int(0) 
<   ..$ 2 : int(0) 
<   ..$ 3 : int(0) 
<   ..$ 4 : NULL
<   ..$ 5 : int(0) 
<   ..$ 6 : int(0) 
<   ..$ 7 : int(0) 
<   ..$ 8 : int(0) 
<   ..$ 10: int(0) 
<   ..$ 11: int(0) 
<   ..$ 12: int(0) 
---
>   ..$ 1 : logi NA
>   ..$ 2 : int [1:2] 1 3
>   ..$ 3 : logi NA
>   ..$ 4 : int [1:2] 1 3
>   ..$ 5 : NULL
>   ..$ 6 : int [1:2] 1 3
>   ..$ 7 : int [1:2] 1 3
>   ..$ 8 : int [1:2] 1 3
>   ..$ 10: int [1:2] 1 3
>   ..$ 11: int [1:2] 1 3
>   ..$ 12: int [1:2] 1 3
164,173c164,173
<   ..$ 2 : logi NA
<   ..$ 3 : int [1:3] 1 2 6
<   ..$ 4 : NULL
<   ..$ 5 : int [1:3] 1 2 6
<   ..$ 6 : logi NA
<   ..$ 7 : int [1:3] 1 2 6
<   ..$ 8 : int [1:3] 1 2 6
<   ..$ 9 : int [1:3] 1 2 6
<   ..$ 11: int [1:3] 1 2 6
<   ..$ 12: int [1:3] 1 2 6
---
>   ..$ 2 : int [1:4] 1 4 8 9
>   ..$ 3 : int [1:4] 1 4 8 9
>   ..$ 4 : logi NA
>   ..$ 5 : NULL
>   ..$ 6 : int [1:4] 1 4 8 9
>   ..$ 7 : int [1:4] 1 4 8 9
>   ..$ 8 : logi NA
>   ..$ 9 : logi NA
>   ..$ 11: int [1:4] 1 4 8 9
>   ..$ 12: int [1:4] 1 4 8 9
176,182c176,182
<   ..$ 2 : int [1:4] 1 5 6 9
<   ..$ 3 : int [1:4] 1 5 6 9
<   ..$ 4 : NULL
<   ..$ 5 : logi NA
<   ..$ 6 : logi NA
<   ..$ 7 : int [1:4] 1 5 6 9
<   ..$ 8 : int [1:4] 1 5 6 9
---
>   ..$ 2 : logi NA
>   ..$ 3 : int [1:5] 1 2 7 9 10
>   ..$ 4 : int [1:5] 1 2 7 9 10
>   ..$ 5 : NULL
>   ..$ 6 : int [1:5] 1 2 7 9 10
>   ..$ 7 : logi NA
>   ..$ 8 : int [1:5] 1 2 7 9 10
184,185c184,185
<   ..$ 10: int [1:4] 1 5 6 9
<   ..$ 12: int [1:4] 1 5 6 9
---
>   ..$ 10: logi NA
>   ..$ 12: int [1:5] 1 2 7 9 10
187,197c187,197
<   ..$ 1 : int [1:4] 2 3 6 11
<   ..$ 2 : logi NA
<   ..$ 3 : logi NA
<   ..$ 4 : NULL
<   ..$ 5 : int [1:4] 2 3 6 11
<   ..$ 6 : logi NA
<   ..$ 7 : int [1:4] 2 3 6 11
<   ..$ 8 : int [1:4] 2 3 6 11
<   ..$ 9 : int [1:4] 2 3 6 11
<   ..$ 10: int [1:4] 2 3 6 11
<   ..$ 11: logi NA
---
>   ..$ 1 : logi NA
>   ..$ 2 : int 1
>   ..$ 3 : int 1
>   ..$ 4 : int 1
>   ..$ 5 : NULL
>   ..$ 6 : int 1
>   ..$ 7 : int 1
>   ..$ 8 : int 1
>   ..$ 9 : int 1
>   ..$ 10: int 1
>   ..$ 11: int 1
216,220c216,220
<   ..$ 2 : logi NA
<   ..$ 3 : logi NA
<   ..$ 4 : NULL
<   ..$ 5 : logi NA
<   ..$ 6 : logi NA
---
>   ..$ 2 : int(0) 
>   ..$ 3 : int(0) 
>   ..$ 4 : logi NA
>   ..$ 5 : NULL
>   ..$ 6 : int(0) 
222c222
<   ..$ 8 : logi NA
---
>   ..$ 8 : int(0) 
228,232c228,232
<   ..$ 1 : logi NA
<   ..$ 3 : logi NA
<   ..$ 4 : NULL
<   ..$ 5 : logi NA
<   ..$ 6 : logi NA
---
>   ..$ 1 : int(0) 
>   ..$ 3 : int(0) 
>   ..$ 4 : int(0) 
>   ..$ 5 : NULL
>   ..$ 6 : int(0) 
238c238
<   ..$ 12: logi NA
---
>   ..$ 12: int(0) 
239a240,251
>   ..$ 1 : int(0) 
>   ..$ 2 : int(0) 
>   ..$ 4 : int(0) 
>   ..$ 5 : NULL
>   ..$ 6 : int(0) 
>   ..$ 7 : int(0) 
>   ..$ 8 : int(0) 
>   ..$ 9 : int(0) 
>   ..$ 10: int(0) 
>   ..$ 11: int(0) 
>   ..$ 12: int(0) 
>  $ 4 :List of 11
241,243c253,255
<   ..$ 2 : logi NA
<   ..$ 4 : NULL
<   ..$ 5 : logi NA
---
>   ..$ 2 : int(0) 
>   ..$ 3 : int(0) 
>   ..$ 5 : NULL
246,247c258,259
<   ..$ 8 : logi NA
<   ..$ 9 : int(0) 
---
>   ..$ 8 : int(0) 
>   ..$ 9 : logi NA
251c263
<  $ 4 :List of 11
---
>  $ 5 :List of 11
255c267
<   ..$ 5 : NULL
---
>   ..$ 4 : NULL
263,274d274
<  $ 5 :List of 11
<   ..$ 1 : logi NA
<   ..$ 2 : logi NA
<   ..$ 3 : logi NA
<   ..$ 4 : NULL
<   ..$ 6 : logi NA
<   ..$ 7 : int(0) 
<   ..$ 8 : logi NA
<   ..$ 9 : int(0) 
<   ..$ 10: logi NA
<   ..$ 11: logi NA
<   ..$ 12: logi NA
278,286c278,286
<   ..$ 3 : logi NA
<   ..$ 4 : NULL
<   ..$ 5 : logi NA
<   ..$ 7 : int(0) 
<   ..$ 8 : logi NA
<   ..$ 9 : int(0) 
<   ..$ 10: logi NA
<   ..$ 11: logi NA
<   ..$ 12: logi NA
---
>   ..$ 3 : int [1:2] 1 2
>   ..$ 4 : int [1:2] 1 2
>   ..$ 5 : NULL
>   ..$ 7 : int [1:2] 1 2
>   ..$ 8 : int [1:2] 1 2
>   ..$ 9 : int [1:2] 1 2
>   ..$ 10: int [1:2] 1 2
>   ..$ 11: int [1:2] 1 2
>   ..$ 12: int [1:2] 1 2
291,292c291,292
<   ..$ 4 : NULL
<   ..$ 5 : int(0) 
---
>   ..$ 4 : int(0) 
>   ..$ 5 : NULL
300,311d299
<   ..$ 1 : int [1:3] 3 5 7
<   ..$ 2 : int [1:3] 3 5 7
<   ..$ 3 : logi NA
<   ..$ 4 : NULL
<   ..$ 5 : logi NA
<   ..$ 6 : int [1:3] 3 5 7
<   ..$ 7 : logi NA
<   ..$ 9 : int [1:3] 3 5 7
<   ..$ 10: int [1:3] 3 5 7
<   ..$ 11: int [1:3] 3 5 7
<   ..$ 12: int [1:3] 3 5 7
<  $ 9 :List of 11
313c301
<   ..$ 2 : int(0) 
---
>   ..$ 2 : logi NA
315,317c303,305
<   ..$ 4 : NULL
<   ..$ 5 : int(0) 
<   ..$ 6 : int(0) 
---
>   ..$ 4 : int(0) 
>   ..$ 5 : NULL
>   ..$ 6 : logi NA
319c307
<   ..$ 8 : int(0) 
---
>   ..$ 9 : int(0) 
321c309
<   ..$ 11: int(0) 
---
>   ..$ 11: logi NA
322a311,322
>  $ 9 :List of 11
>   ..$ 1 : logi NA
>   ..$ 2 : int [1:2] 1 3
>   ..$ 3 : logi NA
>   ..$ 4 : int [1:2] 1 3
>   ..$ 5 : NULL
>   ..$ 6 : int [1:2] 1 3
>   ..$ 7 : int [1:2] 1 3
>   ..$ 8 : int [1:2] 1 3
>   ..$ 10: int [1:2] 1 3
>   ..$ 11: int [1:2] 1 3
>   ..$ 12: int [1:2] 1 3
325,334c325,334
<   ..$ 2 : logi NA
<   ..$ 3 : int [1:3] 1 2 6
<   ..$ 4 : NULL
<   ..$ 5 : int [1:3] 1 2 6
<   ..$ 6 : logi NA
<   ..$ 7 : int [1:3] 1 2 6
<   ..$ 8 : int [1:3] 1 2 6
<   ..$ 9 : int [1:3] 1 2 6
<   ..$ 11: int [1:3] 1 2 6
<   ..$ 12: int [1:3] 1 2 6
---
>   ..$ 2 : int [1:4] 1 4 8 9
>   ..$ 3 : int [1:4] 1 4 8 9
>   ..$ 4 : logi NA
>   ..$ 5 : NULL
>   ..$ 6 : int [1:4] 1 4 8 9
>   ..$ 7 : int [1:4] 1 4 8 9
>   ..$ 8 : logi NA
>   ..$ 9 : logi NA
>   ..$ 11: int [1:4] 1 4 8 9
>   ..$ 12: int [1:4] 1 4 8 9
337,343c337,343
<   ..$ 2 : int [1:4] 1 5 6 9
<   ..$ 3 : int [1:4] 1 5 6 9
<   ..$ 4 : NULL
<   ..$ 5 : logi NA
<   ..$ 6 : logi NA
<   ..$ 7 : int [1:4] 1 5 6 9
<   ..$ 8 : int [1:4] 1 5 6 9
---
>   ..$ 2 : logi NA
>   ..$ 3 : int [1:5] 1 2 7 9 10
>   ..$ 4 : int [1:5] 1 2 7 9 10
>   ..$ 5 : NULL
>   ..$ 6 : int [1:5] 1 2 7 9 10
>   ..$ 7 : logi NA
>   ..$ 8 : int [1:5] 1 2 7 9 10
345,346c345,346
<   ..$ 10: int [1:4] 1 5 6 9
<   ..$ 12: int [1:4] 1 5 6 9
---
>   ..$ 10: logi NA
>   ..$ 12: int [1:5] 1 2 7 9 10
348,352c348,352
<   ..$ 1 : int [1:4] 2 3 6 11
<   ..$ 2 : logi NA
<   ..$ 3 : logi NA
<   ..$ 4 : NULL
<   ..$ 5 : int [1:4] 2 3 6 11
---
>   ..$ 1 : logi NA
>   ..$ 2 : int(0) 
>   ..$ 3 : int(0) 
>   ..$ 4 : logi NA
>   ..$ 5 : NULL
354,357c354,357
<   ..$ 7 : int [1:4] 2 3 6 11
<   ..$ 8 : int [1:4] 2 3 6 11
<   ..$ 9 : int [1:4] 2 3 6 11
<   ..$ 10: int [1:4] 2 3 6 11
---
>   ..$ 7 : int(0) 
>   ..$ 8 : int(0) 
>   ..$ 9 : logi NA
>   ..$ 10: logi NA
389,391c389,391
<   ..$ 2 : logi NA
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
---
>   ..$ 2 : int(0) 
>   ..$ 3 : logi NA
>   ..$ 4 : NULL
393,394c393,394
<   ..$ 6 : logi NA
<   ..$ 7 : int(0) 
---
>   ..$ 6 : int(0) 
>   ..$ 7 : logi NA
400a401,412
>   ..$ 1 : int(0) 
>   ..$ 3 : int(0) 
>   ..$ 4 : NULL
>   ..$ 5 : int(0) 
>   ..$ 6 : int(0) 
>   ..$ 7 : logi NA
>   ..$ 8 : logi NA
>   ..$ 9 : logi NA
>   ..$ 10: int(0) 
>   ..$ 11: NULL
>   ..$ 12: NULL
>  $ 3 :List of 11
402,403c414,415
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
---
>   ..$ 2 : int(0) 
>   ..$ 4 : NULL
405,406c417,418
<   ..$ 6 : logi NA
<   ..$ 7 : int(0) 
---
>   ..$ 6 : int(0) 
>   ..$ 7 : logi NA
412c424
<  $ 3 :List of 11
---
>  $ 4 :List of 11
415c427
<   ..$ 4 : NULL
---
>   ..$ 3 : NULL
424,435d435
<  $ 4 :List of 11
<   ..$ 1 : logi NA
<   ..$ 2 : logi NA
<   ..$ 3 : NULL
<   ..$ 5 : int(0) 
<   ..$ 6 : logi NA
<   ..$ 7 : int(0) 
<   ..$ 8 : logi NA
<   ..$ 9 : logi NA
<   ..$ 10: logi NA
<   ..$ 11: NULL
<   ..$ 12: NULL
439,441c439,441
<   ..$ 3 : NULL
<   ..$ 4 : int(0) 
<   ..$ 6 : logi NA
---
>   ..$ 3 : int(0) 
>   ..$ 4 : NULL
>   ..$ 6 : int(0) 
444c444
<   ..$ 9 : int(0) 
---
>   ..$ 9 : logi NA
449,460d448
<   ..$ 1 : int [1:3] 2 4 5
<   ..$ 2 : logi NA
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
<   ..$ 5 : logi NA
<   ..$ 7 : int [1:3] 2 4 5
<   ..$ 8 : int [1:3] 2 4 5
<   ..$ 9 : int [1:3] 2 4 5
<   ..$ 10: int [1:3] 2 4 5
<   ..$ 11: NULL
<   ..$ 12: NULL
<  $ 7 :List of 11
463,464c451,452
<   ..$ 3 : NULL
<   ..$ 4 : int(0) 
---
>   ..$ 3 : int(0) 
>   ..$ 4 : NULL
466,467c454,455
<   ..$ 6 : int(0) 
<   ..$ 8 : int(0) 
---
>   ..$ 7 : int(0) 
>   ..$ 8 : logi NA
469c457
<   ..$ 10: logi NA
---
>   ..$ 10: int(0) 
472c460
<  $ 8 :List of 11
---
>  $ 7 :List of 11
475,477c463,477
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
<   ..$ 5 : int(0) 
---
>   ..$ 3 : int [1:2] 1 2
>   ..$ 4 : NULL
>   ..$ 5 : int [1:2] 1 2
>   ..$ 6 : int [1:2] 1 2
>   ..$ 8 : int [1:2] 1 2
>   ..$ 9 : int [1:2] 1 2
>   ..$ 10: int [1:2] 1 2
>   ..$ 11: NULL
>   ..$ 12: NULL
>  $ 8 :List of 11
>   ..$ 1 : logi NA
>   ..$ 2 : int [1:4] 1 3 6 7
>   ..$ 3 : logi NA
>   ..$ 4 : NULL
>   ..$ 5 : int [1:4] 1 3 6 7
479,481c479,481
<   ..$ 7 : int(0) 
<   ..$ 9 : logi NA
<   ..$ 10: logi NA
---
>   ..$ 7 : logi NA
>   ..$ 9 : int [1:4] 1 3 6 7
>   ..$ 10: int [1:4] 1 3 6 7
486,490c486,490
<   ..$ 2 : int [1:4] 1 4 7 8
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
<   ..$ 5 : int [1:4] 1 4 7 8
<   ..$ 6 : int [1:4] 1 4 7 8
---
>   ..$ 2 : int [1:5] 1 5 6 7 8
>   ..$ 3 : int [1:5] 1 5 6 7 8
>   ..$ 4 : NULL
>   ..$ 5 : logi NA
>   ..$ 6 : logi NA
493c493
<   ..$ 10: logi NA
---
>   ..$ 10: int [1:5] 1 5 6 7 8
498,502c498,502
<   ..$ 2 : logi NA
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
<   ..$ 5 : int [1:6] 1 2 4 7 8 9
<   ..$ 6 : int [1:6] 1 2 4 7 8 9
---
>   ..$ 2 : int(0) 
>   ..$ 3 : logi NA
>   ..$ 4 : NULL
>   ..$ 5 : int(0) 
>   ..$ 6 : int(0) 
540,549c540,549
< 1  0 2 0 3 0 0 0 2 2  2
< 2  3 0 0 0 0 2 0 0 0  2
< 3  0 0 0 0 0 0 0 0 0  0
< 4  2 0 0 0 0 2 0 0 2  2
< 5  0 0 0 0 0 2 0 0 0  0
< 6  0 3 0 3 3 0 0 0 0  0
< 7  0 0 0 0 0 0 0 0 2  2
< 8  3 0 0 0 0 0 0 0 2  2
< 9  3 0 0 3 0 0 3 3 0  2
< 10 3 3 0 3 0 0 3 3 3  0
---
> 1  0 0 2 0 0 0 2 2 2  3
> 2  0 0 0 0 0 0 2 0 0  0
> 3  3 0 0 0 0 0 0 2 0  0
> 4  0 0 0 0 0 0 0 0 0  0
> 5  0 0 0 0 0 0 0 0 2  0
> 6  0 0 0 0 0 0 0 2 2  0
> 7  3 3 0 0 0 0 0 2 2  0
> 8  3 0 3 0 0 3 3 0 2  0
> 9  3 0 0 0 3 3 3 3 0  0
> 10 2 0 0 0 0 0 0 0 0  0
562,569c562,569
<   ..$ 2 : int 4
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
<   ..$ 5 : int 4
<   ..$ 6 : int 4
<   ..$ 7 : int 4
<   ..$ 8 : int 4
<   ..$ 9 : logi NA
---
>   ..$ 2 : int 10
>   ..$ 3 : int 10
>   ..$ 4 : NULL
>   ..$ 5 : int 10
>   ..$ 6 : int 10
>   ..$ 7 : int 10
>   ..$ 8 : int 10
>   ..$ 9 : int 10
573a574,585
>   ..$ 1 : int(0) 
>   ..$ 3 : int(0) 
>   ..$ 4 : NULL
>   ..$ 5 : int(0) 
>   ..$ 6 : int(0) 
>   ..$ 7 : logi NA
>   ..$ 8 : logi NA
>   ..$ 9 : logi NA
>   ..$ 10: int(0) 
>   ..$ 11: NULL
>   ..$ 12: NULL
>  $ 3 :List of 11
575,576c587,588
<   ..$ 3 : NULL
<   ..$ 4 : int 1
---
>   ..$ 2 : int 1
>   ..$ 4 : NULL
580,582c592,594
<   ..$ 8 : int 1
<   ..$ 9 : int 1
<   ..$ 10: logi NA
---
>   ..$ 8 : logi NA
>   ..$ 9 : logi NA
>   ..$ 10: int 1
585c597
<  $ 3 :List of 11
---
>  $ 4 :List of 11
588c600
<   ..$ 4 : NULL
---
>   ..$ 3 : NULL
597,608d608
<  $ 4 :List of 11
<   ..$ 1 : logi NA
<   ..$ 2 : logi NA
<   ..$ 3 : NULL
<   ..$ 5 : int(0) 
<   ..$ 6 : logi NA
<   ..$ 7 : int(0) 
<   ..$ 8 : logi NA
<   ..$ 9 : logi NA
<   ..$ 10: logi NA
<   ..$ 11: NULL
<   ..$ 12: NULL
612,614c612,614
<   ..$ 3 : NULL
<   ..$ 4 : int(0) 
<   ..$ 6 : logi NA
---
>   ..$ 3 : int(0) 
>   ..$ 4 : NULL
>   ..$ 6 : int(0) 
617c617
<   ..$ 9 : int(0) 
---
>   ..$ 9 : logi NA
622,633d621
<   ..$ 1 : int [1:3] 2 4 5
<   ..$ 2 : logi NA
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
<   ..$ 5 : logi NA
<   ..$ 7 : int [1:3] 2 4 5
<   ..$ 8 : int [1:3] 2 4 5
<   ..$ 9 : int [1:3] 2 4 5
<   ..$ 10: int [1:3] 2 4 5
<   ..$ 11: NULL
<   ..$ 12: NULL
<  $ 7 :List of 11
636,637c624,625
<   ..$ 3 : NULL
<   ..$ 4 : int(0) 
---
>   ..$ 3 : int(0) 
>   ..$ 4 : NULL
639,640c627,628
<   ..$ 6 : int(0) 
<   ..$ 8 : int(0) 
---
>   ..$ 7 : int(0) 
>   ..$ 8 : logi NA
642c630,642
<   ..$ 10: logi NA
---
>   ..$ 10: int(0) 
>   ..$ 11: NULL
>   ..$ 12: NULL
>  $ 7 :List of 11
>   ..$ 1 : logi NA
>   ..$ 2 : logi NA
>   ..$ 3 : int [1:2] 1 2
>   ..$ 4 : NULL
>   ..$ 5 : int [1:2] 1 2
>   ..$ 6 : int [1:2] 1 2
>   ..$ 8 : int [1:2] 1 2
>   ..$ 9 : int [1:2] 1 2
>   ..$ 10: int [1:2] 1 2
647,654c647,654
<   ..$ 2 : int 1
<   ..$ 3 : NULL
<   ..$ 4 : int 1
<   ..$ 5 : int 1
<   ..$ 6 : int 1
<   ..$ 7 : int 1
<   ..$ 9 : logi NA
<   ..$ 10: logi NA
---
>   ..$ 2 : int [1:4] 1 3 6 7
>   ..$ 3 : logi NA
>   ..$ 4 : NULL
>   ..$ 5 : int [1:4] 1 3 6 7
>   ..$ 6 : logi NA
>   ..$ 7 : logi NA
>   ..$ 9 : int [1:4] 1 3 6 7
>   ..$ 10: int [1:4] 1 3 6 7
659,663c659,663
<   ..$ 2 : int [1:4] 1 4 7 8
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
<   ..$ 5 : int [1:4] 1 4 7 8
<   ..$ 6 : int [1:4] 1 4 7 8
---
>   ..$ 2 : int [1:5] 1 5 6 7 8
>   ..$ 3 : int [1:5] 1 5 6 7 8
>   ..$ 4 : NULL
>   ..$ 5 : logi NA
>   ..$ 6 : logi NA
666c666
<   ..$ 10: logi NA
---
>   ..$ 10: int [1:5] 1 5 6 7 8
671,675c671,675
<   ..$ 2 : logi NA
<   ..$ 3 : NULL
<   ..$ 4 : logi NA
<   ..$ 5 : int [1:6] 1 2 4 7 8 9
<   ..$ 6 : int [1:6] 1 2 4 7 8 9
---
>   ..$ 2 : int(0) 
>   ..$ 3 : logi NA
>   ..$ 4 : NULL
>   ..$ 5 : int(0) 
>   ..$ 6 : int(0) 
  Running 'test_bicscore.R' [4s]
  Running 'test_causalEffect.R' [3s]
  Running 'test_compareGraphs.R' [3s]
  Running 'test_dag2cpdag.R' [3s]
  Running 'test_dag2essgraph.R' [4s]
  Running 'test_displayAmat.R' [3s]
  Running 'test_dsep.R' [3s]
  Running 'test_fci.R' [3s]
  Running 'test_fciPlus.R' [6s]
  Running 'test_gSquareBin.R' [3s]
  Running 'test_gSquareDis.R' [5s]
  Running 'test_gac.R' [6s]
  Running 'test_getNextSet.R' [3s]
  Running 'test_gies.R' [9s]
  Running 'test_ida.R' [42m]
  Running 'test_idaFast.R' [7s]
  Running 'test_isValidGraph.R' [5s]
  Running 'test_jointIda.R' [4s]
  Running 'test_mat2targets.R' [3s]
  Running 'test_pc.R' [4s]
  Running 'test_pcSelect.R' [3s]
  Running 'test_pcalg2dagitty.R' [3s]
  Running 'test_pcorOrder.R' [4s]
  Running 'test_pdag2allDags.R' [3s]
  Running 'test_pdag2dag.R' [4s]
  Running 'test_possDeAn.R' [4s]
  Running 'test_randDAG.R' [3s]
  Running 'test_randomDAG.R' [3s]
  Running 'test_rfci.R' [5s]
  Running 'test_rmvDAG.R' [3s]
  Running 'test_shd.R' [3s]
  Running 'test_skeleton.R' [7s]
  Running 'test_udag2pag.R' [3s]
  Running 'test_udag2pdag.R' [6s]
  Running 'test_wgtMatrix.R' [3s]
Running the tests in 'tests/test_ages.R' failed.
Complete output:
  > ## Test file ages
  > library(pcalg)
  > (doExtras <- pcalg:::doExtras())
  [1] FALSE
  > 
  > ## Known example where ges and ages output a different result
  > bool3 <- TRUE
  > set.seed(77)
  > 
  > p <- 8
  > n <- 5000
  > ## true DAG:
  > vars <- c("Author", "Bar", "Ctrl", "Goal", paste0("V",5:8))
  > gGtrue <- randomDAG(p, prob = 0.3, V = vars)
  > data = rmvDAG(n, gGtrue)
  > 
  > ## Estimate the aggregated PDAG with ages
  > ages.fit <- ages(data = data)
  > 
  > 
  > ## Estimate the essential graph with ges
  > score <- new("GaussL0penObsScore", data)
  > ges.fit <- ges(score)
  > 
  > diff <- as(ges.fit$essgraph,"matrix") - as(ages.fit$essgraph,"matrix")
  > 
  > bool3 <- ( bool3 & (diff[6,2]==1) * (diff[8,2]==1) *(sum(abs( as(ges.fit$essgraph,"matrix") - as(ages.fit$essgraph,"matrix") ))==2) )
  > stopifnot(bool3)
  Error: bool3 is not TRUE
  Execution halted
Running the tests in 'tests/test_causalEffect.R' failed.
Complete output:
  > library(pcalg)
  > 
  > set.seed(34)
  > g <- randomDAG(5,0.8)
  > trMat <- matrix(0, 5,5)
  > trMat[1,5] <- 0.305
  > trMat[1,4] <- 0.863
  > trMat[1,2] <- 0.354
  > trMat[2,4] <- 0.392
  > trMat[2,5] <- 0.495
  > trMat[3,4] <- 0.278
  > 
  > 
  > ## eff 1->5: 0.305 + 0.354*0.495
  > trEff <- 0.305 + 0.354*0.495
  > estEff <- causalEffect(g, 5,1)
  > 
  > if (!(round(trEff,3) == round(estEff, 3))) {
  +   stop("Test in wgtMatrix: Weights have wrong value!")
  + }
  Error: Test in wgtMatrix: Weights have wrong value!
  Execution halted
Running the tests in 'tests/test_displayAmat.R' failed.
Complete output:
  > library(pcalg)
  > ##################################################
  > ## pcAlgo object
  > ##################################################
  > ## Load predefined data
  > data(gmG)
  > n <- nrow    (gmG8$x)
  > V <- colnames(gmG8$x)
  > 
  > ## define sufficient statistics
  > suffStat <- list(C = cor(gmG8$x), n = n)
  > ## estimate CPDAG
  > skel.fit <- skeleton(suffStat, indepTest = gaussCItest,
  +                      alpha = 0.01, labels = V)
  > (amSkel <- as(skel.fit, "amat"))
  Adjacency Matrix 'amat' (8 x 8) of type 'cpdag':
         Author Bar Ctrl Goal V5 V6 V7 V8
  Author      .   1    .    .  .  1  .  1
  Bar         1   .    1    .  1  .  .  .
  Ctrl        .   1    .    .  .  .  .  .
  Goal        .   .    .    .  .  .  .  .
  V5          .   1    .    .  .  1  .  1
  V6          1   .    .    .  1  .  1  .
  V7          .   .    .    .  .  1  .  .
  V8          1   .    .    .  1  .  .  .
  > str(amSkel)
   'amat' num [1:8, 1:8] 0 1 0 0 0 1 0 1 1 0 ...
   - attr(*, "dimnames")=List of 2
    ..$ : chr [1:8] "Author" "Bar" "Ctrl" "Goal" ...
    ..$ : chr [1:8] "Author" "Bar" "Ctrl" "Goal" ...
   - attr(*, "type")= chr "cpdag"
  > stopifnot(attr(amSkel, "type") == "cpdag",
  +           amSkel["Author", "Bar"] == 1,
  +           amSkel["Bar", "Author"] == 1,
  +           amSkel["Ctrl","Author"] == 0)
  > 
  > pc.fit <- pc(suffStat, indepTest = gaussCItest,
  +              alpha = 0.01, labels = V)
  > (amPC <- as(pc.fit, "amat"))
  Adjacency Matrix 'amat' (8 x 8) of type 'cpdag':
         Author Bar Ctrl Goal V5 V6 V7 V8
  Author      .   1    .    .  .  .  .  .
  Bar         1   .    1    .  .  .  .  .
  Ctrl        .   1    .    .  .  .  .  .
  Goal        .   .    .    .  .  .  .  .
  V5          .   1    .    .  .  .  .  .
  V6          1   .    .    .  1  .  .  .
  V7          .   .    .    .  .  1  .  .
  V8          1   .    .    .  1  .  .  .
  > stopifnot(attr(amPC, "type") == "cpdag",
  +           amPC["V5", "V8"] == 0,
  +           amPC["V8", "V5"] == 1,
  +           amPC["Goal","Author"] == 0)
  > 
  > ##################################################
  > ## fciAlgo object
  > ##################################################
  > set.seed(42)
  > p <- 7
  > ## generate and draw random DAG :
  > myDAG <- randomDAG(p, prob = 0.4)
  > 
  > ## find PAG using the FCI algorithm
  > myC <- cov2cor(trueCov(myDAG))
  > suffStat <- list(C = myC, n = 10^9)
  > V <- LETTERS[1:p] ## labels of nodes
  > 
  > fmFCI <- fci(suffStat, indepTest=gaussCItest, labels = V,
  +              alpha = 0.9999, doPdsep = FALSE)
  > (amFCI <- as(fmFCI, "amat"))
  Adjacency Matrix 'amat' (7 x 7) of type 'pag':
    A B C D E F G
  A . 1 1 . . 2 1
  B 1 . 1 . . 2 1
  C 1 1 . . . 2 1
  D . . . . . . .
  E . . . . . 2 .
  F 1 1 1 . 1 . .
  G 1 1 1 . . . .
  > stopifnot(attr(amFCI, "type") == "pag",
  +           amFCI["B","E"] == 2,
  +           amFCI["C","D"] == 1,
  +           amFCI["G","A"] == 3)
  Error: amFCI["B", "E"] == 2 is not TRUE
  Execution halted
Running the tests in 'tests/test_ida.R' failed.
Complete output:
  > library(pcalg)
  > 
  > set.seed(123)
  > nreps <- 100
  > res <- logical(nreps)
  > all.eff.true <- res
  > Rnd <- function(e) round(e, 14)## get 14 digits accuracy, as we use true (DAG, cov)
  > for (i in 1:nreps) {
  +   p <- 2 + rpois(1, lambda = 8) # ==>  p >= 2, E[p] = 10
  +   ## generate and draw random DAG :
  +   myDAG <- randomDAG(p, prob = 0.2)
  +   myCPDAG <- dag2cpdag(myDAG)
  +   mcov <- trueCov(myDAG)
  +   
  +   ## x != y  in {1,2,...p} ;
  +   xy <- sample.int(p, 2); x <- xy[1]; y <- xy[2]
  +   
  +   ## plot(myCPDAG)
  +   eff.true <- Rnd(causalEffect(myDAG, y, x))
  +   all.eff.true[i] <- eff.true
  +   ## cat("x=",x," y=",y," eff=",eff.true,"\n")
  +   
  +   eff.est <- Rnd(ida(x,y, mcov, myCPDAG, method="local"))
  +   res[i] <- (eff.true %in% eff.est)
  + }
  > cat('Time elapsed: ', (.pt <- proc.time()),"\n")
  Time elapsed:  5.67 0.37 6.34 NA NA 
  > 
  > stem(all.eff.true)
  
    The decimal point is 1 digit(s) to the left of the |
  
    0 | 00000000000000000000000000000000000000000000000000000000000000000000+6
    1 | 778
    2 | 9
    3 | 
    4 | 2
    5 | 338
    6 | 124
    7 | 08
    8 | 
    9 | 6
  
  > if (!all(res)) stop("Test ida: True effects were not recovered!")
  > 
  > ## *one* test for  method="global" :
  > eff.g.est <- Rnd(ida(x,y, mcov, myCPDAG, method="global", verbose=TRUE))
  Fit - y: 8 x: 4 |b.hat= 0 
  Fit - y: 8 x: 4 |b.hat= 0 
  Fit - y: 8 x: 4 |b.hat= 0 
  Fit - y: 8 x: 4 |b.hat= 0 
  Fit - y: 8 x: 4 |b.hat= 0 
  Fit - y: 8 x: 4 |b.hat= 0 
  Fit - y: 8 x: 4 |b.hat= 0 
  Fit - y: 8 x: 4 |b.hat= 0 
  Fit - y: 8 x: 4 |b.hat= 0 
  Fit - y: 8 x: 4 |b.hat= 0 
  > stopifnot(eff.est == eff.g.est)
  > 
  > cat('Time elapsed additionally: ', proc.time() - .pt,"\n")
  Time elapsed additionally:  2483.29 0.45 2498.17 NA NA 
  > 
  > ## another special case (from Raphael Gervais)
  > set.seed(123)
  > p <- 7
  > myDAG <- randomDAG(p, prob = 0.2) ## true DAG
  > amatT <- as(myDAG, "matrix") # weighted adjacency matrix of true DAG
  > effT <- Rnd(amatT[2,3]*amatT[3,5]) # Causal effect of 2 on 5 from true DAG weighted matrix
  > myCPDAG <- dag2cpdag(myDAG) ## true CPDAG
  > covTrue <- trueCov(myDAG) ## true covariance matrix
  > effG <- Rnd(ida(2,5, covTrue,myCPDAG,method = "global"))
  > 
  > if (!(effT %in% effG)) stop("Test ida special case: True effects were not recovered!")
  Error: Test ida special case: True effects were not recovered!
  Execution halted
Running the tests in 'tests/test_idaFast.R' failed.
Complete output:
  > library(pcalg)
  > 
  > set.seed(43)
  > nreps <- 50
  > res <- matrix(FALSE, 3, nreps)
  > resF <- rep(FALSE, nreps)
  > 
  > for (i in 1:nreps) {
  +   if (i%%100 == 0) cat("i=",i,"\n")
  +   set.seed(i)
  +   p <- 10
  +   ## generate and draw random DAG :
  +   myDAG <- randomDAG(p, prob = 0.4)
  +   myCPDAG <- dag2cpdag(myDAG)
  +   mcov <- trueCov(myDAG)
  + 
  +   x <- sample(1:10,1)
  +   y1 <- sample(setdiff(1:10,x),1)
  +   y2 <- sample(setdiff(1:10,c(x,y1)),1)
  +   y3 <- sample(setdiff(1:10,c(x,y1,y2)),1)
  +   ## plot(myCPDAG)
  +   eff.true1 <- round(causalEffect(myDAG, y1, x),14)
  +   eff.true2 <- round(causalEffect(myDAG, y2, x),14)
  +   eff.true3 <- round(causalEffect(myDAG, y3, x),14)
  +   ## cat("x=",x," y1=",y1," eff=",eff.true1,"\n")
  +   ## cat("x=",x," y1=",y2," eff=",eff.true2,"\n")
  + 
  +   (eff.est1 <- round(ida(x,y1,mcov,myCPDAG,method="local",verbose=FALSE),14))
  +   (eff.est2 <- round(ida(x,y2,mcov,myCPDAG,method="local",verbose=FALSE),14))
  +   (eff.est3 <- round(ida(x,y3,mcov,myCPDAG,method="local",verbose=FALSE),14))
  +   (eff.estF <- round(idaFast(x,c(y1,y2,y3),mcov,myCPDAG),14))
  + 
  +   res[1,i] <- (eff.true1 %in% eff.est1)
  +   res[2,i] <- (eff.true2 %in% eff.est2)
  +   res[3,i] <- (eff.true3 %in% eff.est3)
  + 
  +   resF[i] <- all(eff.estF == rbind(eff.est1,eff.est2,eff.est3))
  + }
  > 
  > if (!all(res)) stop("Test idaFast: True effects were not recovered!")
  Error: Test idaFast: True effects were not recovered!
  Execution halted
Running the tests in 'tests/test_pcSelect.R' failed.
Complete output:
  > #### Testing  pcSelect()  _and_  (its main helper) mcor()
  > ####          ~~~~~~~~                             ~~~~
  > 
  > library(pcalg)
  > 
  > p <- 10
  > n <- 1000
  > 
  > set.seed(101)
  > myDAG <- randomDAG(p, prob = 0.2)
  > d.mat <- rmvDAG(n, myDAG, errDist = "normal")
  > y <- d.mat[,10]
  > dm <- d.mat[,-10]
  > res1 <- pcSelect(y,dm, alpha=0.05)
  > if (!all(res1$G == 1:9 %in% c(4,5,6)))
  +   stop("Test of pcSelect: Consistency problem 101")
  Error: Test of pcSelect: Consistency problem 101
  Execution halted
Running the tests in 'tests/test_pcalg2dagitty.R' failed.
Complete output:
  > ## Translate amat as describes in amatType to dagitty object
  > 
  > library(pcalg)
  > library(dagitty)
  
  Attaching package: 'dagitty'
  
  The following object is masked from 'package:pcalg':
  
      randomDAG
  
  > doExtras <- pcalg:::doExtras()
  > 
  > res <- rep(FALSE, 10)
  > ####################
  > ## Test DAG 1
  > ####################
  > data(gmG)
  > n <- nrow    (gmG8$x)
  > V <- colnames(gmG8$x) # labels aka node names
  > 
  > amat <- wgtMatrix(gmG8$g)
  > amat[amat != 0] <- 1
  > dagitty_dag1 <- pcalg2dagitty(amat,V,type="dag")
  > ## Use dagitty:::graphLayout instead of just graphLayout
  > ## because Rgraphviz package that R uses has a function w the same name
  > ## par(mfrow=c(1,2))
  > ## plot(gmG8$g, main = "True DAG")
  > ## plot(dagitty:::graphLayout(dagitty_dag1))
  > 
  > res[1] <- (dagitty_dag1 == "dag {\nAuthor\nBar\nCtrl\nGoal\nV5\nV6\nV7\nV8\nAuthor -> Bar\nAuthor -> V6\nAuthor -> V8\nBar -> Ctrl\nBar -> V5\nV5 -> V6\nV5 -> V8\nV6 -> V7\n}\n")
  > 
  > #############
  > ## Test DAG 2
  > #############
  > set.seed(123)
  > p <- 10
  > V <- sample(LETTERS, p)
  > g <- pcalg::randomDAG(p,prob=0.3, V = V)
  > 
  > amat <- wgtMatrix(g)
  > amat[amat != 0] <- 1
  > dagitty_dag2 <- pcalg2dagitty(amat,V,type="dag")
  > ## Use dagitty:::graphLayout instead of just graphLayout
  > ## because Rgraphviz package that R uses has a function w the same name
  > ## par(mfrow=c(1,2))
  > ## plot(g, main = "True DAG")
  > ## plot(dagitty:::graphLayout(dagitty_dag2))
  > 
  > res[2] <- (dagitty_dag2 == "dag {\nA\nH\nJ\nK\nQ\nT\nU\nW\nX\nZ\nA -> Q\nH -> A\nH -> K\nH -> Q\nH -> T\nH -> Z\nJ -> W\nT -> A\nT -> Q\nT -> X\nU -> Q\nU -> W\nU -> X\nW -> K\n}\n")
  > 
  > ###############
  > ## Test CPDAG 1
  > ###############
  > data(gmG)
  > n <- nrow(gmG8$ x)
  > V <- colnames(gmG8$ x) # labels aka node names
  > 
  > ## estimate CPDAG
  > pc.fit <- pc(suffStat = list(C = cor(gmG8$x), n = n),
  +              indepTest = gaussCItest, ## indep.test: partial correlations
  +              alpha=0.01, labels = V, verbose = FALSE)
  > amat <- as(pc.fit, "amat")
  > dagitty_cpdag1 <- pcalg2dagitty(amat,V,type="cpdag")
  > ## Use dagitty:::graphLayout instead of just graphLayout
  > ## because Rgraphviz package that R uses has a function w the same name
  > ## par(mfrow = c(1,2))
  > ## plot(pc.fit)
  > ## plot(dagitty:::graphLayout(dagitty_cpdag1))
  > 
  > res[3] <- (dagitty_cpdag1 == "pdag {\nAuthor\nBar\nCtrl\nGoal\nV5\nV6\nV7\nV8\nAuthor -- Bar\nAuthor -> V6\nAuthor -> V8\nBar -- Ctrl\nBar -> V5\nV5 -> V6\nV5 -> V8\nV6 -> V7\n}\n")
  > 
  > stopifnot(all(res[1:3]))
  Error: all(res[1:3]) is not TRUE
  Execution halted
Running the tests in 'tests/test_randDAG.R' failed.
Complete output:
  > library(pcalg)
  > ## setwd("/sfs/u/kalischm/research/packages/unifDAGs/")
  > ## source("aux_general.R")
  > ## source("randDAG.R")
  > 
  > ### Check all methods: ----------------------------------------------
  > 
  > ## MM hack: extract them from the randDAG() function definition
  > body. <- body(randDAG)
  > is.switch <- function(P) !is.symbol(P) && identical(as.symbol("switch"), P[[1]])
  > switchCall <- body.[vapply(body., is.switch, NA)][[1]]
  > stopifnot(identical(as.symbol("switch"), switchCall[[1]]))
  > (rDAGmeths <- names(switchCall)[-c(1:2, length(switchCall))])
  [1] "er"        "regular"   "watts"     "bipartite" "barabasi"  "geometric"
  [7] "power"     "interEr"  
  > rDAGall <- function(n, d, ...)
  +     sapply(rDAGmeths, function(meth) randDAG(n,d, method=meth, ...),
  +            simplify=FALSE)
  > set.seed(37)
  > rD.10.4 <- rDAGall(10, 4)
  > ## with a low-level warning
  > rD.10.4 # looks ok
  $er
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 21 
  
  $regular
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 20 
  
  $watts
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 20 
  
  $bipartite
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 21 
  
  $barabasi
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 19 
  
  $geometric
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 23 
  
  $power
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 23 
  
  $interEr
  A graphNEL graph with directed edges
  Number of Nodes = 10 
  Number of Edges = 21 
  
  > 
  > ok <- suppressPackageStartupMessages(
  +     require("graph"))
  > stopifnot(ok)
  > 
  > stopifnot(vapply(rD.10.4, isDirected, NA))
  > 
  > stopifnot(identical(
  +     lapply(rD.10.4, leaves, "out"),
  +     list(er = "3", regular = c("1", "5", "6"), watts = c("3", "4", "6"),
  +          bipartite = c("1", "2", "5"), barabasi = c("4", "8"),
  +          geometric = c("4", "7"), power = c("4", "5", "9"),
  +          interEr = c("3", "7"))
  + ))
  Error: identical(lapply(rD.10.4, leaves, "out"), list(er = "3", regular = c("1",  .... is not TRUE
  Execution halted
Running the tests in 'tests/test_rmvDAG.R' failed.
Complete output:
  > library(pcalg)
  > 
  > set.seed(100)
  > 
  > wmat <- rbind(c(0,1,0,0,0),
  +               c(0,0,0,1,0),
  +               c(0,0,0,1,0),
  +               c(0,0,0,0,1),
  +               c(0,0,0,0,0))
  > colnames(wmat) <- rownames(wmat) <- c("1","2","3","4","5")
  > print.table(wmat, zero.print=".")
    1 2 3 4 5
  1 . 1 . . .
  2 . . . 1 .
  3 . . . 1 .
  4 . . . . 1
  5 . . . . .
  > 
  > g <- as(wmat,"graphNEL")
  > 
  > e.true <- 0
  > var.true <- 5
  > 
  > dat <- rmvDAG(1000,g)
  > x5 <- dat[,5]
  > 
  > ## test mean
  > if (t.test(x5,alternative="two.sided")$p.value<0.05) {
  +   stop("Test of rmvDAG: Mean not correct!")
  + }
  > 
  > ## test variance
  > if (var.test(x5,rnorm(1000,0,sqrt(5)),ratio=1,
  +              alternative="two.sided")$p.value<0.05) {
  +   stop("Test of rmvDAG: Variance not correct!")
  + }
  > 
  > ###----- Check  gmG  generation: ---> ../man/gmG.Rd
  > 
  > ## Used to generate "gmG"
  > set.seed(40)
  > p <- 8
  > n <- 5000
  > ## true DAG:
  > vars <- c("Author", "Bar", "Ctrl", "Goal", paste0("V",5:8))
  > gGtrue <- randomDAG(p, prob = 0.3, V = vars)
  > x <- rmvDAG(n, gGtrue, back.compatible=TRUE)
  > 
  > data(gmG)
  > 
  > ## gmG, gmI were produced on 64-bit -> very small difference even in weights:
  > stopifnot(all.equal(gGtrue, gmG$g,  tol=6e-16),
  +           all.equal(x,      gmG$ x, tol=1e-15))
  Error: gGtrue and gmG$g are not equal:
    Attributes: < Component "edgeData": Names: 7 string mismatches >
    Attributes: < Component "edgeData": Attributes: < Component "data": Names: 7 string mismatches > >
    Attributes: < Component "edgeData": Attributes: < Component "data": Component "Author|V8": Component "weight": Mean relative difference: 0.4651165 > >
    ....
  Execution halted
Running the tests in 'tests/test_shd.R' failed.
Complete output:
  > library(pcalg)
  > 
  > set.seed(123)
  > 
  > ## expl 1
  > g1 <- randomDAG(5,0.5)
  > g2 <- randomDAG(5,0.5)
  > res1 <- (shd(g1,g2)==4)
  > 
  > ## expl 2
  > g3 <- dag2cpdag(g1)
  > res2 <- (shd(g3,g1)==3)
  > 
  > if(!all(c(res1,res2))) {
  +   stop("Test of shd: Theoretical value not matched!")
  + }
  Error: Test of shd: Theoretical value not matched!
  Execution halted
Running the tests in 'tests/test_udag2pdag.R' failed.
Complete output:
  > library(pcalg)
  > 
  > .libPaths()
  [1] "D:/temp/Rtmp0apqhB/RLIBS_12e40244c77f5"
  [2] "D:/RCompile/recent/R/library"          
  > ## acyclic graphs
  > 
  > nreps <- 30
  > p <- 8
  > n <- 1000
  > 
  > for(u2pd in c("rand", "retry", "relaxed")) {
  +     cat("\n u2pd =", u2pd, "\n ------------\n")
  +     cyc.res <- logical(nreps)
  +     for (i in 1:nreps) {
  +         set.seed(i)
  +         myDAG <- randomDAG(p, prob = 0.2)
  +         d.mat <- rmvDAG(n, myDAG, errDist = "normal")
  +         res <- suppressWarnings(pcAlgo(d.mat, alpha = 0.05, directed=TRUE, u2pd = u2pd))
  +         ##                      ------ directed;  u2pd = "rand" --> udag2pdag()
  +         res.A <- wgtMatrix(res@graph)
  +         res.A[res.A!=0] <- 1
  +         undir.A <- res.A + t(res.A)
  +         undir.A[undir.A==1] <- 0
  +         undir.A[undir.A==2] <- 1
  +         res.dir <- res.A - undir.A
  +         cyc.res[i] <- ggm::isAcyclic(res.dir)
  +     }
  +     if (!all(cyc.res)) stop("Test of pcAlgo(*, directed): Cyclic part in PDAG!")
  + } ## for(u2pd ...)
  
   u2pd = rand 
   ------------
  
   u2pd = retry 
   ------------
  
   u2pd = relaxed 
   ------------
  Error: Test of pcAlgo(*, directed): Cyclic part in PDAG!
  Execution halted
Running the tests in 'tests/test_wgtMatrix.R' failed.
Complete output:
  > library(pcalg)
  > 
  > set.seed(42)
  > 
  > ## wmat_ij is edge from j to i
  > g <- randomDAG(3,0.4)
  > wmat <- wgtMatrix(g)
  > if (!(wmat[2,1]!=0 & wmat[1,2]==0 & wmat[3,1]!=0 & wmat[3,2]==0)) {
  +   stop("Test of wgtMatrix: Something with orientation of edges is wrong!")
  + }
  > 
  > ## test weird parameters
  > g <- randomDAG(3,0)
  > wmat <- wgtMatrix(g)
  > if (!all(wmat==matrix(0,3,3))) {
  +   stop("Test of wgtMatrix: Problem when used on empty graph!")
  + }
  > 
  > ## test if weight parameters are correct
  > set.seed(34)
  > g <- randomDAG(5,0.8)
  > trMat <- matrix(0, 5,5)
  > trMat[1,5] <- 0.305
  > trMat[1,4] <- 0.863
  > trMat[1,2] <- 0.354
  > trMat[2,4] <- 0.392
  > trMat[2,5] <- 0.495
  > trMat[3,4] <- 0.278
  > 
  > if (!all(round(wgtMatrix(g),3) == t(trMat))) {
  +   stop("Test in wgtMatrix: Weights have wrong value!")
  + }
  Error: Test in wgtMatrix: Weights have wrong value!
  Execution halted