Running 'mcmc.R' [168s]
  Running 'reml.R' [1s]
  Running 'step.R' [168s]
  Running 'zfileremoves.R' [170s]
Running the tests in 'tests/mcmc.R' failed.
Complete output:
  > ## BayesX MCMC testing
  > library("BayesXsrc")
  > mcmc <- run.bayesx("mcmc.prg", verbose = FALSE)
  > fx1 <- read.table("mcmc_f_x1_pspline.res", header = TRUE)
  > fx2 <- read.table("mcmc_f_x2_pspline.res", header = TRUE)
  > print(round(head(fx1), digits = 3))
    intnr     x1  pmean pqu2p5  pqu10   pmed  pqu90 pqu97p5 pcat95 pcat80
  1     1 -2.999 -0.244 -0.459 -0.386 -0.247 -0.091  -0.003     -1     -1
  2     2 -2.985 -0.251 -0.457 -0.388 -0.253 -0.103  -0.021     -1     -1
  3     3 -2.981 -0.253 -0.457 -0.388 -0.255 -0.108  -0.025     -1     -1
  4     4 -2.974 -0.257 -0.456 -0.389 -0.259 -0.115  -0.033     -1     -1
  5     5 -2.963 -0.263 -0.454 -0.391 -0.265 -0.126  -0.045     -1     -1
  6     6 -2.962 -0.263 -0.454 -0.391 -0.265 -0.126  -0.046     -1     -1
  > print(round(head(fx2), digits = 3))
    intnr    x2  pmean pqu2p5  pqu10   pmed  pqu90 pqu97p5 pcat95 pcat80
  1     1 0.001 -0.395 -0.550 -0.496 -0.394 -0.297  -0.241     -1     -1
  2     2 0.001 -0.395 -0.549 -0.496 -0.394 -0.297  -0.241     -1     -1
  3     3 0.002 -0.394 -0.546 -0.495 -0.393 -0.298  -0.242     -1     -1
  4     4 0.003 -0.394 -0.545 -0.494 -0.392 -0.298  -0.243     -1     -1
  5     5 0.003 -0.394 -0.544 -0.493 -0.392 -0.297  -0.243     -1     -1
  6     6 0.004 -0.393 -0.541 -0.492 -0.391 -0.297  -0.244     -1     -1
  > 
  > proc.time()
     user  system elapsed 
     0.20    0.07   13.65 
Running the tests in 'tests/step.R' failed.
Complete output:
  > ## BayesX STEP testing
  > library("BayesXsrc")
  > step <- run.bayesx("step.prg", verbose = FALSE)
  > print(step)
  $log
    [1] "> logopen using step.prg.log"                                                                                                                                                                                                                                                                
    [2] ""                                                                                                                                                                                                                                                                                            
    [3] "> stepwisereg b"                                                                                                                                                                                                                                                                             
    [4] ""                                                                                                                                                                                                                                                                                            
    [5] "> dataset d"                                                                                                                                                                                                                                                                                 
    [6] ""                                                                                                                                                                                                                                                                                            
    [7] "> d.infile using data.raw"                                                                                                                                                                                                                                                                   
    [8] ""                                                                                                                                                                                                                                                                                            
    [9] "NOTE: 7 variables with 1000 observations read from file"                                                                                                                                                                                                                                     
   [10] "data.raw"                                                                                                                                                                                                                                                                                    
   [11] ""                                                                                                                                                                                                                                                                                            
   [12] "> b.outfile = step"                                                                                                                                                                                                                                                                          
   [13] ""                                                                                                                                                                                                                                                                                            
   [14] "> b.regress y = x1(psplinerw2,nrknots=20,degree=3) + x2(psplinerw2,nrknots=20,degree=3) + x3(psplinerw2,nrknots=20,degree=3) + x4(psplinerw2,nrknots=20,degree=3), family=gaussian iterations=10000 burnin=2000 step=10 setseed=1298345438 algorithm=cdescent1 CI=MCMCselect predict using d"
   [15] ""                                                                                                                                                                                                                                                                                            
   [16] ""                                                                                                                                                                                                                                                                                            
   [17] "STEPWISE OBJECT b: stepwise procedure "                                                                                                                                                                                                                                                      
   [18] ""                                                                                                                                                                                                                                                                                            
   [19] "GENERAL OPTIONS: "                                                                                                                                                                                                                                                                           
   [20] ""                                                                                                                                                                                                                                                                                            
   [21] "  Performance criterion: AIC_imp "                                                                                                                                                                                                                                                           
   [22] "  Maximum number of iterations: 100"                                                                                                                                                                                                                                                         
   [23] ""                                                                                                                                                                                                                                                                                            
   [24] "  RESPONSE DISTRIBUTION: "                                                                                                                                                                                                                                                                   
   [25] ""                                                                                                                                                                                                                                                                                            
   [26] "  Family: Gaussian"                                                                                                                                                                                                                                                                          
   [27] "  Number of observations: 1000"                                                                                                                                                                                                                                                              
   [28] ""                                                                                                                                                                                                                                                                                            
   [29] "OPTIONS FOR STEPWISE PROCEDURE: "                                                                                                                                                                                                                                                            
   [30] ""                                                                                                                                                                                                                                                                                            
   [31] "  OPTIONS FOR NONPARAMETRIC TERM: x1"                                                                                                                                                                                                                                                        
   [32] ""                                                                                                                                                                                                                                                                                            
   [33] "  Minimum value for the smoothing parameter: 0.268834375"                                                                                                                                                                                                                                    
   [34] "  This is equivalent to degrees of freedom: approximately 16, exact 15.972"                                                                                                                                                                                                                  
   [35] "  Maximum value for the smoothing parameter: 5625"                                                                                                                                                                                                                                           
   [36] "  This is equivalent to degrees of freedom: approximately 2, exact 2.03204"                                                                                                                                                                                                                  
   [37] "  Number of different smoothing parameters with equidistant degrees of freedom: 20"                                                                                                                                                                                                          
   [38] "  Startvalue of the 1. startmodel is \"effect excluded\" "                                                                                                                                                                                                                                   
   [39] ""                                                                                                                                                                                                                                                                                            
   [40] "  OPTIONS FOR NONPARAMETRIC TERM: x2"                                                                                                                                                                                                                                                        
   [41] ""                                                                                                                                                                                                                                                                                            
   [42] "  Minimum value for the smoothing parameter: 0.268834375"                                                                                                                                                                                                                                    
   [43] "  This is equivalent to degrees of freedom: approximately 16, exact 16.0206"                                                                                                                                                                                                                 
   [44] "  Maximum value for the smoothing parameter: 5625"                                                                                                                                                                                                                                           
   [45] "  This is equivalent to degrees of freedom: approximately 2, exact 2.04161"                                                                                                                                                                                                                  
   [46] "  Number of different smoothing parameters with equidistant degrees of freedom: 20"                                                                                                                                                                                                          
   [47] "  Startvalue of the 1. startmodel is \"effect excluded\" "                                                                                                                                                                                                                                   
   [48] ""                                                                                                                                                                                                                                                                                            
   [49] "  OPTIONS FOR NONPARAMETRIC TERM: x3"                                                                                                                                                                                                                                                        
   [50] ""                                                                                                                                                                                                                                                                                            
   [51] "  Minimum value for the smoothing parameter: 0.28163125"                                                                                                                                                                                                                                     
   [52] "  This is equivalent to degrees of freedom: approximately 16, exact 15.9569"                                                                                                                                                                                                                 
   [53] "  Maximum value for the smoothing parameter: 6718.75"                                                                                                                                                                                                                                        
   [54] "  This is equivalent to degrees of freedom: approximately 2, exact 1.97392"                                                                                                                                                                                                                  
   [55] "  Number of different smoothing parameters with equidistant degrees of freedom: 20"                                                                                                                                                                                                          
   [56] "  Startvalue of the 1. startmodel is \"effect excluded\" "                                                                                                                                                                                                                                   
   [57] ""                                                                                                                                                                                                                                                                                            
   [58] "  OPTIONS FOR NONPARAMETRIC TERM: x4"                                                                                                                                                                                                                                                        
   [59] ""                                                                                                                                                                                                                                                                                            
   [60] "  Minimum value for the smoothing parameter: 0.268834375"                                                                                                                                                                                                                                    
   [61] "  This is equivalent to degrees of freedom: approximately 16, exact 16.0162"                                                                                                                                                                                                                 
   [62] "  Maximum value for the smoothing parameter: 5625"                                                                                                                                                                                                                                           
   [63] "  This is equivalent to degrees of freedom: approximately 2, exact 2.02573"                                                                                                                                                                                                                  
   [64] "  Number of different smoothing parameters with equidistant degrees of freedom: 20"                                                                                                                                                                                                          
   [65] "  Startvalue of the 1. startmodel is \"effect excluded\" "                                                                                                                                                                                                                                   
   [66] ""                                                                                                                                                                                                                                                                                            
   [67] ""                                                                                                                                                                                                                                                                                            
   [68] "STEPWISE PROCEDURE STARTED "                                                                                                                                                                                                                                                                 
   [69] ""                                                                                                                                                                                                                                                                                            
   [70] ""                                                                                                                                                                                                                                                                                            
   [71] ""                                                                                                                                                                                                                                                                                            
   [72] "  Startmodel:"                                                                                                                                                                                                                                                                               
   [73] ""                                                                                                                                                                                                                                                                                            
   [74] "  y = const"                                                                                                                                                                                                                                                                                 
   [75] " AIC_imp = -63.014288"                                                                                                                                                                                                                                                                       
   [76] ""                                                                                                                                                                                                                                                                                            
   [77] "  Startmodel:"                                                                                                                                                                                                                                                                               
   [78] ""                                                                                                                                                                                                                                                                                            
   [79] "  y = const + x2 + x1(psplinerw2,df=4.96172,(lambda=135.891)) + x4(psplinerw2,df=2.02573,(lambda=5625))"                                                                                                                                                                                     
   [80] " AIC_imp = -1009.2606"                                                                                                                                                                                                                                                                       
   [81] ""                                                                                                                                                                                                                                                                                            
   [82] "  Startmodel:"                                                                                                                                                                                                                                                                               
   [83] ""                                                                                                                                                                                                                                                                                            
   [84] "  y = const + x2 + x1(psplinerw2,df=6.0118,(lambda=58.3475)) + x4(psplinerw2,df=2.02573,(lambda=5625))"                                                                                                                                                                                      
   [85] " AIC_imp = -1010.5859"                                                                                                                                                                                                                                                                       
   [86] ""                                                                                                                                                                                                                                                                                            
   [87] "  Startmodel:"                                                                                                                                                                                                                                                                               
   [88] ""                                                                                                                                                                                                                                                                                            
   [89] "  y = const + x2 + x1(psplinerw2,df=6.0118,(lambda=58.3475)) + x4(psplinerw2,df=2.02573,(lambda=5625))"                                                                                                                                                                                      
   [90] " AIC_imp = -1010.5875"                                                                                                                                                                                                                                                                       
   [91] ""                                                                                                                                                                                                                                                                                            
   [92] "  Final Model:"                                                                                                                                                                                                                                                                              
   [93] ""                                                                                                                                                                                                                                                                                            
   [94] "  y = const + x2 + x1(psplinerw2,df=6.0118,(lambda=58.3475)) + x4(psplinerw2,df=2.02573,(lambda=5625))"                                                                                                                                                                                      
   [95] " AIC_imp = -1010.5875"                                                                                                                                                                                                                                                                       
   [96] "  Used number of iterations: 4"                                                                                                                                                                                                                                                              
   [97] ""                                                                                                                                                                                                                                                                                            
   [98] "  ------------------------------------------------------------------------ "                                                                                                                                                                                                                 
   [99] "  ------------------------------------------------------------------------ "                                                                                                                                                                                                                 
  [100] ""                                                                                                                                                                                                                                                                                            
  [101] ""                                                                                                                                                                                                                                                                                            
  [102] "  Final Model:"                                                                                                                                                                                                                                                                              
  [103] ""                                                                                                                                                                                                                                                                                            
  [104] "  y = const + x2 + x1(psplinerw2,df=6.0118,(lambda=58.3475)) + x4(psplinerw2,df=2.02573,(lambda=5625))"                                                                                                                                                                                      
  [105] " AIC_imp = -1010.5875"                                                                                                                                                                                                                                                                       
  [106] ""                                                                                                                                                                                                                                                                                            
  [107] ""                                                                                                                                                                                                                                                                                            
  [108] "CALCULATION OF CONFIDENCE INTERVALS STARTED:"                                                                                                                                                                                                                                                
  [109] ""                                                                                                                                                                                                                                                                                            
  [110] "  ITERATION: 1"                                                                                                                                                                                                                                                                              
  [111] ""                                                                                                                                                                                                                                                                                            
  [112] "  FixedEffects1"                                                                                                                                                                                                                                                                             
  [113] ""                                                                                                                                                                                                                                                                                            
  [114] "  Acceptance rate:    99.98 %"                                                                                                                                                                                                                                                               
  [115] ""                                                                                                                                                                                                                                                                                            
  [116] "  Relative Changes in  "                                                                                                                                                                                                                                                                     
  [117] ""                                                                                                                                                                                                                                                                                            
  [118] "  Mean:               0.0571208"                                                                                                                                                                                                                                                             
  [119] "  Variance:           1.79769e+308"                                                                                                                                                                                                                                                          
  [120] "  Minimum:            0.152805"                                                                                                                                                                                                                                                              
  [121] "  Maximum:            0.11311"                                                                                                                                                                                                                                                               
  [122] ""                                                                                                                                                                                                                                                                                            
  [123] ""                                                                                                                                                                                                                                                                                            
  [124] ""                                                                                                                                                                                                                                                                                            
  [125] "  f_x1"                                                                                                                                                                                                                                                                                      
  [126] ""                                                                                                                                                                                                                                                                                            
  [127] "  Acceptance rate:    100 %"                                                                                                                                                                                                                                                                 
  [128] ""                                                                                                                                                                                                                                                                                            
  [129] "  Relative Changes in  "                                                                                                                                                                                                                                                                     
  [130] ""                                                                                                                                                                                                                                                                                            
  [131] "  Mean:               0.120854"                                                                                                                                                                                                                                                              
  [132] "  Variance:           1.79769e+308"                                                                                                                                                                                                                                                          
  [133] "  Minimum:            0.372835"                                                                                                                                                                                                                                                              
  [134] "  Maximum:            0.394023"                                                                                                                                                                                                                                                              
  [135] ""                                                                                                                                                                                                                                                                                            
  [136] ""                                                                                                                                                                                                                                                                                            
  [137] ""                                                                                                                                                                                                                                                                                            
  [138] "  f_x4"                                                                                                                                                                                                                                                                                      
  [139] ""                                                                                                                                                                                                                                                                                            
  [140] "  Acceptance rate:    100 %"                                                                                                                                                                                                                                                                 
  [141] ""                                                                                                                                                                                                                                                                                            
  [142] "  Relative Changes in  "                                                                                                                                                                                                                                                                     
  [143] ""                                                                                                                                                                                                                                                                                            
  [144] "  Mean:               0.891349"                                                                                                                                                                                                                                                              
  [145] "  Variance:           1.79769e+308"                                                                                                                                                                                                                                                          
  [146] "  Minimum:            2.74173"                                                                                                                                                                                                                                                               
  [147] "  Maximum:            4.30506"                                                                                                                                                                                                                                                               
  [148] ""                                                                                                                                                                                                                                                                                            
  [149] ""                                                                                                                                                                                                                                                                                            
  [150] ""                                                                                                                                                                                                                                                                                            
  [151] "  FixedEffects1"                                                                                                                                                                                                                                                                             
  [152] ""                                                                                                                                                                                                                                                                                            
  [153] "  Acceptance rate:    99.99 %"                                                                                                                                                                                                                                                               
  [154] ""                                                                                                                                                                                                                                                                                            
  [155] "  Relative Changes in  "                                                                                                                                                                                                                                                                     
  [156] ""                                                                                                                                                                                                                                                                                            
  [157] "  Mean:               0.00252894"                                                                                                                                                                                                                                                            
  [158] "  Variance:           0.0533446"                                                                                                                                                                                                                                                             
  [159] "  Minimum:            0.0418556"                                                                                                                                                                                                                                                             
  [160] "  Maximum:            0.0040073"                                                                                                                                                                                                                                                             
  [161] ""                                                                                                                                                                                                                                                                                            
  [162] ""                                                                                                                                                                                                                                                                                            
  [163] ""                                                                                                                                                                                                                                                                                            
  [164] "  f_x1"                                                                                                                                                                                                                                                                                      
  [165] ""                                                                                                                                                                                                                                                                                            
  [166] "  Acceptance rate:    100 %"                                                                                                                                                                                                                                                                 
  [167] ""                                                                                                                                                                                                                                                                                            
  [168] "  Relative Changes in  "                                                                                                                                                                                                                                                                     
  [169] ""                                                                                                                                                                                                                                                                                            
  [170] "  Mean:               0.00779639"                                                                                                                                                                                                                                                            
  [171] "  Variance:           0.0593889"                                                                                                                                                                                                                                                             
  [172] "  Minimum:            0.0665339"                                                                                                                                                                                                                                                             
  [173] "  Maximum:            0.04175"                                                                                                                                                                                                                                                               
  [174] ""                                                                                                                                                                                                                                                                                            
  [175] ""                                                                                                                                                                                                                                                                                            
  [176] ""                                                                                                                                                                                                                                                                                            
  [177] "  f_x4"                                                                                                                                                                                                                                                                                      
  [178] ""                                                                                                                                                                                                                                                                                            
  [179] "  Acceptance rate:    100 %"                                                                                                                                                                                                                                                                 
  [180] ""                                                                                                                                                                                                                                                                                            
  [181] "  Relative Changes in  "                                                                                                                                                                                                                                                                     
  [182] ""                                                                                                                                                                                                                                                                                            
  [183] "  Mean:               0.0550975"                                                                                                                                                                                                                                                             
  [184] "  Variance:           0.0607946"                                                                                                                                                                                                                                                             
  [185] "  Minimum:            0.147113"                                                                                                                                                                                                                                                              
  [186] "  Maximum:            0.0493353"                                                                                                                                                                                                                                                             
  [187] ""                                                                                                                                                                                                                                                                                            
  [188] ""                                                                                                                                                                                                                                                                                            
  [189] ""                                                                                                                                                                                                                                                                                            
  [190] "  FixedEffects1"                                                                                                                                                                                                                                                                             
  [191] ""                                                                                                                                                                                                                                                                                            
  [192] "  Acceptance rate:    99.99 %"                                                                                                                                                                                                                                                               
  [193] ""                                                                                                                                                                                                                                                                                            
  [194] "  Relative Changes in  "                                                                                                                                                                                                                                                                     
  [195] ""                                                                                                                                                                                                                                                                                            
  [196] "  Mean:               0.000814076"                                                                                                                                                                                                                                                           
  [197] "  Variance:           0.0626436"                                                                                                                                                                                                                                                             
  [198] "  Minimum:            0.0137968"                                                                                                                                                                                                                                                             
  [199] "  Maximum:            0.00195948"                                                                                                                                                                                                                                                            
  [200] ""                                                                                                                                                                                                                                                                                            
  [201] ""                                                                                                                                                                                                                                                                                            
  [202] ""                                                                                                                                                                                                                                                                                            
  [203] "  f_x1"                                                                                                                                                                                                                                                                                      
  [204] ""                                                                                                                                                                                                                                                                                            
  [205] "  Acceptance rate:    100 %"                                                                                                                                                                                                                                                                 
  [206] ""                                                                                                                                                                                                                                                                                            
  [207] "  Relative Changes in  "                                                                                                                                                                                                                                                                     
  [208] ""                                                                                                                                                                                                                                                                                            
  [209] "  Mean:               0.00254165"                                                                                                                                                                                                                                                            
  [210] "  Variance:           0.0277323"                                                                                                                                                                                                                                                             
  [211] "  Minimum:            0.0148511"                                                                                                                                                                                                                                                             
  [212] "  Maximum:            0.0336116"                                                                                                                                                                                                                                                             
  [213] ""                                                                                                                                                                                                                                                                                            
  [214] ""                                                                                                                                                                                                                                                                                            
  [215] ""                                                                                                                                                                                                                                                                                            
  [216] "  f_x4"                                                                                                                                                                                                                                                                                      
  [217] ""                                                                                                                                                                                                                                                                                            
  [218] "  Acceptance rate:    100 %"                                                                                                                                                                                                                                                                 
  [219] ""                                                                                                                                                                                                                                                                                            
  [220] "  Relative Changes in  "                                                                                                                                                                                                                                                                     
  [221] ""                                                                                                                                                                                                                                                                                            
  [222] "  Mean:               0.0388739"                                                                                                                                                                                                                                                             
  [223] "  Variance:           0.0192119"                                                                                                                                                                                                                                                             
  [224] "  Minimum:            0.0778352"                                                                                                                                                                                                                                                             
  [225] "  Maximum:            0.0642008"                                                                                                                                                                                                                                                             
  [226] ""                                                                                                                                                                                                                                                                                            
  [227] ""                                                                                                                                                                                                                                                                                            
  [228] "  ITERATION: 10000"                                                                                                                                                                                                                                                                          
  [229] ""                                                                                                                                                                                                                                                                                            
  [230] "  FixedEffects1"                                                                                                                                                                                                                                                                             
  [231] ""                                                                                                                                                                                                                                                                                            
  [232] ""                                                                                                                                                                                                                                                                                            
  [233] "  Acceptance rate:    99.99 %"                                                                                                                                                                                                                                                               
  [234] ""                                                                                                                                                                                                                                                                                            
  [235] "> logclose"                                                                                                                                                                                                                                                                                  
  [236] ""                                                                                                                                                                                                                                                                                            
  [237] "NOTE: log-file step.prg.log closed"                                                                                                                                                                                                                                                          
  [238] ""                                                                                                                                                                                                                                                                                            
  
  $runtime
     user  system elapsed 
     0.00    0.01    1.35 
  
  > 
  > proc.time()
     user  system elapsed 
     0.14    0.10    1.56 
Running the tests in 'tests/zfileremoves.R' failed.
Complete output:
  > ## remove generated BayesX output files
  > testfiles <- c("mcmc.prg", "reml.prg", "step.prg",
  +   "mcmc.R", "reml.R", "step.R",
  +   "BayesX-tests.R", "data.raw")
  > files <- list.files()
  > files <- files[!files %in% testfiles]
  > files <- files[!grepl(".Rout", files)]
  > files <- files[!grepl(".save", files)]
  > file.remove(files)
   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE
  [25]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
  [37]  TRUE  TRUE  TRUE FALSE FALSE
  Warning messages:
  1: In file.remove(files) :
    cannot remove file 'output', reason 'Permission denied'
  2: In file.remove(files) :
    cannot remove file 'temp', reason 'Permission denied'
  3: In file.remove(files) :
    cannot remove file 'zfileremoves.R', reason 'Permission denied'
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.03    0.18