* using log directory 'd:/Rcompile/CRANpkg/local/3.2/umx.Rcheck'
* using R version 3.2.5 (2016-04-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'umx/DESCRIPTION' ... OK
* this is package 'umx' version '1.7.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'umx' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'umx-Ex.R' failed
The error most likely occurred in:

> ### Name: umx_make_TwinData
> ### Title: Simulate twin data with control over A, C, E, and moderation
> ### Aliases: umx_make_TwinData
> 
> ### ** Examples
> 
> # =====================================================================
> # = Basic Example, with all elements of std univariate data specified =
> # =====================================================================
> tmp = umx_make_TwinData(nMZpairs = 100, nDZpairs = 100, AA = .36, CC = .04, EE = .60)
  AA   CC   EE 
0.36 0.04 0.60 
   a    c    e 
0.60 0.20 0.77 
> # Show list of 2 data sets
> str(tmp)
List of 2
 $ mzData:'data.frame':	100 obs. of  2 variables:
  ..$ var_T1: num [1:100] -0.184 0.131 -0.2 1.248 0.634 ...
  ..$ var_T2: num [1:100] -0.8639 0.1767 -1.1981 1.4213 -0.0828 ...
 $ dzData:'data.frame':	100 obs. of  2 variables:
  ..$ var_T1: num [1:100] -0.23835 1.97309 0.00807 -0.01887 -2.81784 ...
  ..$ var_T2: num [1:100] 0.878 0.665 2.47 -0.498 -0.752 ...
> # = How to consume the built datasets =
> mzData = tmp[[1]];
> dzData = tmp[[2]];
> cov(mzData); cov(dzData)
          var_T1    var_T2
var_T1 0.8407772 0.2894738
var_T2 0.2894738 0.8392091
          var_T1    var_T2
var_T1 0.9252151 0.2689865
var_T2 0.2689865 1.1468924
> str(mzData); str(dzData); 
'data.frame':	100 obs. of  2 variables:
 $ var_T1: num  -0.184 0.131 -0.2 1.248 0.634 ...
 $ var_T2: num  -0.8639 0.1767 -1.1981 1.4213 -0.0828 ...
'data.frame':	100 obs. of  2 variables:
 $ var_T1: num  -0.23835 1.97309 0.00807 -0.01887 -2.81784 ...
 $ var_T2: num  0.878 0.665 2.47 -0.498 -0.752 ...
> 
> # Prefer to work in path coefficient values? (little a?)
> tmp = umx_make_TwinData(200, AA = .6^2, CC = .2^2)
  AA   CC   EE 
0.36 0.04 0.60 
   a    c    e 
0.60 0.20 0.77 
> # Check the correlations
> umxAPA(tmp[[1]]); umxAPA(tmp[[2]])


|          |var_T1      |var_T2       |
|:---------|:-----------|:------------|
|var_T1    |1           |             |
|var_T2    |0.38        |1            |
|Mean (SD) |0.02 (1.09) |-0.09 (1.06) |


|          |var_T1      |var_T2       |
|:---------|:-----------|:------------|
|var_T1    |1           |             |
|var_T2    |0.28        |1            |
|Mean (SD) |0.06 (1.08) |-0.05 (1.01) |
> 
> # =============
> # = Shortcuts =
> # =============
> 
> # Omit nDZpairs (equal numbers of both by default)
> tmp = umx_make_TwinData(nMZpairs = 100, nDZpairs = 100, AA = .36, CC = .04, EE = .60)
  AA   CC   EE 
0.36 0.04 0.60 
   a    c    e 
0.60 0.20 0.77 
> tmp = umx_make_TwinData(100, AA = 0.5, CC = 0.3) # omit any one of A, C, or E (sums to 1)
 AA  CC  EE 
0.5 0.3 0.2 
   a    c    e 
0.71 0.55 0.45 
> cov(tmp[[1]])
          var_T1    var_T2
var_T1 0.9449795 0.7491375
var_T2 0.7491375 1.1086902
> # Not limited to unit variance
> tmp = umx_make_TwinData(100, AA = 3, CC = 2, EE = 3, sum2one = FALSE) 
AA CC EE 
 3  2  3 
   a    c    e 
1.73 1.41 1.73 
> cov(tmp[[1]])
         var_T1   var_T2
var_T1 9.073327 5.406647
var_T2 5.406647 8.999746
> 
> # =====================
> # = Moderator Example =
> # =====================
> 
> x = umx_make_TwinData(100, AA = c(avg = .7, min = 0, max = 1), CC = .55, EE = .63)
         [,1]     [,2]
[1,] 1.817612 1.187612
[2,] 1.187612 1.817612
         [,1]     [,2]
[1,] 2.045892 1.415892
[2,] 1.415892 2.045892
         [,1]     [,2]
[1,] 1.897024 1.267024
[2,] 1.267024 1.897024
         [,1]     [,2]
[1,] 2.127157 1.497157
[2,] 1.497157 2.127157
         [,1]     [,2]
[1,] 1.973341 1.343341
[2,] 1.343341 1.973341
         [,1]     [,2]
[1,] 1.903742 1.273742
[2,] 1.273742 1.903742
         [,1]     [,2]
[1,] 2.184945 1.554945
[2,] 1.554945 2.184945
       [,1]   [,2]
[1,] 1.9664 1.3364
[2,] 1.3364 1.9664
         [,1]     [,2]
[1,] 1.995312 1.365312
[2,] 1.365312 1.995312
         [,1]     [,2]
[1,] 1.884668 1.254668
[2,] 1.254668 1.884668
         [,1]     [,2]
[1,] 1.852492 1.222492
[2,] 1.222492 1.852492
         [,1]     [,2]
[1,] 1.759827 1.129827
[2,] 1.129827 1.759827
         [,1]     [,2]
[1,] 1.666362 1.036362
[2,] 1.036362 1.666362
         [,1]     [,2]
[1,] 1.842859 1.212859
[2,] 1.212859 1.842859
         [,1]     [,2]
[1,] 1.884553 1.254553
[2,] 1.254553 1.884553
         [,1]     [,2]
[1,] 2.184605 1.554605
[2,] 1.554605 2.184605
         [,1]     [,2]
[1,] 2.076402 1.446402
[2,] 1.446402 2.076402
         [,1]     [,2]
[1,] 1.820615 1.190615
[2,] 1.190615 1.820615
         [,1]     [,2]
[1,] 2.035632 1.405632
[2,] 1.405632 2.035632
        [,1]    [,2]
[1,] 1.69911 1.06911
[2,] 1.06911 1.69911
         [,1]     [,2]
[1,] 1.899968 1.269968
[2,] 1.269968 1.899968
         [,1]     [,2]
[1,] 1.958627 1.328627
[2,] 1.328627 1.958627
          [,1]      [,2]
[1,] 1.5971019 0.9671019
[2,] 0.9671019 1.5971019
         [,1]     [,2]
[1,] 2.078784 1.448784
[2,] 1.448784 2.078784
         [,1]     [,2]
[1,] 1.765367 1.135367
[2,] 1.135367 1.765367
          [,1]      [,2]
[1,] 1.5782573 0.9482573
[2,] 0.9482573 1.5782573
         [,1]     [,2]
[1,] 1.672884 1.042884
[2,] 1.042884 1.672884
          [,1]      [,2]
[1,] 1.5515408 0.9215408
[2,] 0.9215408 1.5515408
         [,1]     [,2]
[1,] 1.811327 1.181327
[2,] 1.181327 1.811327
         [,1]     [,2]
[1,] 2.017634 1.387634
[2,] 1.387634 2.017634
         [,1]     [,2]
[1,] 1.786407 1.156407
[2,] 1.156407 1.786407
        [,1]    [,2]
[1,] 1.67553 1.04553
[2,] 1.04553 1.67553
         [,1]     [,2]
[1,] 1.824403 1.194403
[2,] 1.194403 1.824403
         [,1]     [,2]
[1,] 1.881029 1.251029
[2,] 1.251029 1.881029
         [,1]     [,2]
[1,] 1.921093 1.291093
[2,] 1.291093 1.921093
         [,1]     [,2]
[1,] 1.954595 1.324595
[2,] 1.324595 1.954595
         [,1]     [,2]
[1,] 1.839164 1.209164
[2,] 1.209164 1.839164
         [,1]     [,2]
[1,] 1.867261 1.237261
[2,] 1.237261 1.867261
         [,1]     [,2]
[1,] 2.067175 1.437175
[2,] 1.437175 2.067175
         [,1]     [,2]
[1,] 2.143458 1.513458
[2,] 1.513458 2.143458
         [,1]     [,2]
[1,] 1.742023 1.112023
[2,] 1.112023 1.742023
         [,1]     [,2]
[1,] 1.961869 1.331869
[2,] 1.331869 1.961869
         [,1]     [,2]
[1,] 1.883096 1.253096
[2,] 1.253096 1.883096
         [,1]     [,2]
[1,] 2.100158 1.470158
[2,] 1.470158 2.100158
         [,1]     [,2]
[1,] 2.035038 1.405038
[2,] 1.405038 2.035038
         [,1]     [,2]
[1,] 2.059369 1.429369
[2,] 1.429369 2.059369
         [,1]     [,2]
[1,] 1.829955 1.199955
[2,] 1.199955 1.829955
         [,1]     [,2]
[1,] 2.054123 1.424123
[2,] 1.424123 2.054123
        [,1]    [,2]
[1,] 1.99819 1.36819
[2,] 1.36819 1.99819
         [,1]     [,2]
[1,] 1.668432 1.038432
[2,] 1.038432 1.668432
         [,1]     [,2]
[1,] 1.724652 1.094652
[2,] 1.094652 1.724652
         [,1]     [,2]
[1,] 2.108935 1.478935
[2,] 1.478935 2.108935
         [,1]     [,2]
[1,] 1.803158 1.173158
[2,] 1.173158 1.803158
         [,1]     [,2]
[1,] 2.099283 1.469283
[2,] 1.469283 2.099283
         [,1]     [,2]
[1,] 1.989822 1.359822
[2,] 1.359822 1.989822
         [,1]     [,2]
[1,] 1.701502 1.071502
[2,] 1.071502 1.701502
         [,1]     [,2]
[1,] 1.790169 1.160169
[2,] 1.160169 1.790169
         [,1]     [,2]
[1,] 1.663769 1.033769
[2,] 1.033769 1.663769
         [,1]     [,2]
[1,] 1.911706 1.281706
[2,] 1.281706 1.911706
         [,1]     [,2]
[1,] 1.290069 0.660069
[2,] 0.660069 1.290069
       [,1]   [,2]
[1,] 2.0819 1.4519
[2,] 1.4519 2.0819
         [,1]     [,2]
[1,] 1.928481 1.298481
[2,] 1.298481 1.928481
         [,1]     [,2]
[1,] 2.015795 1.385795
[2,] 1.385795 2.015795
         [,1]     [,2]
[1,] 1.842943 1.212943
[2,] 1.212943 1.842943
         [,1]     [,2]
[1,] 2.119138 1.489138
[2,] 1.489138 2.119138
         [,1]     [,2]
[1,] 1.911602 1.281602
[2,] 1.281602 1.911602
         [,1]     [,2]
[1,] 1.716402 1.086402
[2,] 1.086402 1.716402
        [,1]    [,2]
[1,] 1.86695 1.23695
[2,] 1.23695 1.86695
         [,1]     [,2]
[1,] 2.030124 1.400124
[2,] 1.400124 2.030124
         [,1]     [,2]
[1,] 1.638983 1.008983
[2,] 1.008983 1.638983
         [,1]     [,2]
[1,] 1.868087 1.238087
[2,] 1.238087 1.868087
         [,1]     [,2]
[1,] 1.747309 1.117309
[2,] 1.117309 1.747309
          [,1]      [,2]
[1,] 1.6224268 0.9924268
[2,] 0.9924268 1.6224268
         [,1]     [,2]
[1,] 2.229367 1.599367
[2,] 1.599367 2.229367
         [,1]     [,2]
[1,] 1.907891 1.277891
[2,] 1.277891 1.907891
         [,1]     [,2]
[1,] 1.965683 1.335683
[2,] 1.335683 1.965683
         [,1]     [,2]
[1,] 1.900899 1.270899
[2,] 1.270899 1.900899
          [,1]      [,2]
[1,] 1.6164587 0.9864587
[2,] 0.9864587 1.6164587
         [,1]     [,2]
[1,] 1.892173 1.262173
[2,] 1.262173 1.892173
         [,1]     [,2]
[1,] 2.104616 1.474616
[2,] 1.474616 2.104616
         [,1]     [,2]
[1,] 2.109233 1.479233
[2,] 1.479233 2.109233
        [,1]    [,2]
[1,] 1.79382 1.16382
[2,] 1.16382 1.79382
         [,1]     [,2]
[1,] 2.132638 1.502638
[2,] 1.502638 2.132638
         [,1]     [,2]
[1,] 2.129854 1.499854
[2,] 1.499854 2.129854
         [,1]     [,2]
[1,] 2.015763 1.385763
[2,] 1.385763 2.015763
         [,1]     [,2]
[1,] 2.157608 1.527608
[2,] 1.527608 2.157608
         [,1]     [,2]
[1,] 2.049161 1.419161
[2,] 1.419161 2.049161
         [,1]     [,2]
[1,] 1.967859 1.337859
[2,] 1.337859 1.967859
         [,1]     [,2]
[1,] 1.555844 0.925844
[2,] 0.925844 1.555844
         [,1]     [,2]
[1,] 1.994718 1.364718
[2,] 1.364718 1.994718
         [,1]     [,2]
[1,] 1.892722 1.262722
[2,] 1.262722 1.892722
         [,1]     [,2]
[1,] 1.740417 1.110417
[2,] 1.110417 1.740417
         [,1]     [,2]
[1,] 1.854969 1.224969
[2,] 1.224969 1.854969
         [,1]     [,2]
[1,] 1.713964 1.083964
[2,] 1.083964 1.713964
         [,1]     [,2]
[1,] 2.082767 1.452767
[2,] 1.452767 2.082767
         [,1]     [,2]
[1,] 1.851361 1.221361
[2,] 1.221361 1.851361
         [,1]     [,2]
[1,] 1.657673 1.027673
[2,] 1.027673 1.657673
         [,1]     [,2]
[1,] 1.903593 1.273593
[2,] 1.273593 1.903593
         [,1]     [,2]
[1,] 1.664765 1.034765
[2,] 1.034765 1.664765
         [,1]     [,2]
[1,] 1.657919 1.027919
[2,] 1.027919 1.657919
> str(x)
List of 2
 $ mzData:'data.frame':	100 obs. of  4 variables:
  ..$ var_T1: num [1:100] -1.833 -1.199 -1.402 -1.275 -0.569 ...
  ..$ var_T2: num [1:100] -2.5937 -0.0461 -0.1004 -2.3143 -2.1981 ...
  ..$ M_T1  : num [1:100] -0.374 0.995 0.102 1.483 0.56 ...
  ..$ M_T2  : num [1:100] -0.374 0.995 0.102 1.483 0.56 ...
 $ dzData:'data.frame':	100 obs. of  4 variables:
  ..$ var_T1: num [1:100] -2.377 2.161 1.599 0.304 -2.47 ...
  ..$ var_T2: num [1:100] -2.493 -0.228 0.105 0.302 -0.152 ...
  ..$ M_T1  : num [1:100] -0.405 1.941 0.485 -0.202 -1.17 ...
  ..$ M_T2  : num [1:100] -0.405 1.941 0.485 -0.202 -1.17 ...
> 
> # =====================
> # = Threshold Example =
> # =====================
> tmp = umx_make_TwinData(100, AA = .6, CC = .2, nThresh = 3)
 AA  CC  EE 
0.6 0.2 0.2 
   a    c    e 
0.77 0.45 0.45 
> str(tmp)
List of 2
 $ mzData:'data.frame':	100 obs. of  2 variables:
  ..$ var_T1: Ord.factor w/ 4 levels "quantile1"<"quantile2"<..: 3 3 3 1 1 3 4 3 4 4 ...
  .. ..- attr(*, "mxFactor")= logi TRUE
  ..$ var_T2: Ord.factor w/ 4 levels "quantile1"<"quantile2"<..: 3 3 4 1 1 4 4 2 4 4 ...
  .. ..- attr(*, "mxFactor")= logi TRUE
 $ dzData:'data.frame':	100 obs. of  2 variables:
  ..$ var_T1: Ord.factor w/ 4 levels "quantile1"<"quantile2"<..: 3 4 2 4 4 2 1 3 2 4 ...
  .. ..- attr(*, "mxFactor")= logi TRUE
  ..$ var_T2: Ord.factor w/ 4 levels "quantile1"<"quantile2"<..: 2 3 2 4 4 1 1 4 4 2 ...
  .. ..- attr(*, "mxFactor")= logi TRUE
> umxAPA(tmp[[1]]); umxAPA(tmp[[2]])
Error: could not find function "pmvnorm"
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [9s] OK
  Running 'testthat.R' [9s]
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR