Package: akc
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: easycsv
Check: examples
New result: ERROR
  Running examples in ‘easycsv-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: fread_zip
  > ### Title: read multiple csv files into named data frames
  > ### Aliases: fread_zip
  > ### Keywords: ~utilities ~misc
  > 
  > ### ** Examples
  > 
  > 
  >   require(easycsv)
  >   filezip <- system.file("exampleZips", "example_tables.zip", package="easycsv")
  >   fread_zip(filezip)
  Error in data.table::fread(input = tbl, sep = sep, nrows = nrows, header = header,  : 
    'autostart' is deprecated. Consider skip='string' or skip=n. This argument will be removed in the next release.
  Calls: fread_zip -> <Anonymous> -> stopf -> raise_condition -> signal
  Execution halted

Package: hilldiv
Check: examples
New result: ERROR
  Running examples in ‘hilldiv-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: div_profile_plot
  > ### Title: Diversity profile plot
  > ### Aliases: div_profile_plot
  > ### Keywords: alpha beta gamma hill
  > 
  > ### ** Examples
  > 
  > data(bat.diet.otutable)
  > data(bat.diet.hierarchy)
  > #One sample example
  > bat.diet.sample <- bat.diet.otutable[,1]
  > profile.onesample <- div_profile(count=bat.diet.sample,qvalues=seq(from = 0, to = 5, by = (0.1)))
  > div_profile_plot(profile.onesample)
  > #Multiple samples
  > profile.multiplesamples <- div_profile(bat.diet.otutable)
  > div_profile_plot(profile.multiplesamples)
  Error in melt.default(profile) : 
    The melt generic in data.table has been passed a matrix and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both packages are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(profile). In the next version, this warning will become an error.
  Calls: div_profile_plot ... melt -> melt.default -> stopf -> raise_condition -> signal
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
  div_profile 5.637  0.071   5.709

Package: ICAMS
Check: Rd cross-references
New result: NOTE
  Found the following Rd file(s) with Rd \link{} targets missing package
  anchors:
    AnnotateDBSVCF.Rd: BSgenome
    AnnotateSBSVCF.Rd: BSgenome
    GeneExpressionData.Rd: data.table
    ICAMS.Rd: BSgenome
    MutectVCFFilesToCatalog.Rd: BSgenome
    MutectVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
    MutectVCFFilesToZipFile.Rd: BSgenome
    NormalizeGenomeArg.Rd: BSgenome
    PlotTransBiasGeneExp.Rd: data.table
    PlotTransBiasGeneExpToPdf.Rd: data.table
    StrelkaSBSVCFFilesToCatalog.Rd: BSgenome
    StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
    StrelkaSBSVCFFilesToZipFile.Rd: BSgenome
    VCFsToCatalogs.Rd: BSgenome
    VCFsToCatalogsAndPlotToPdf.Rd: BSgenome
    VCFsToDBSCatalogs.Rd: BSgenome
    VCFsToSBSCatalogs.Rd: BSgenome
    VCFsToZipFile.Rd: BSgenome
    revc.Rd: reverseComplement
  Please provide package anchors for all Rd \link{} targets not in the
  package itself and the base packages.

Package: kibior
Check: Rd cross-references
New result: NOTE
  Found the following Rd file(s) with Rd \link{} targets missing package
  anchors:
    kibior.Rd: R6Class, count
  Please provide package anchors for all Rd \link{} targets not in the
  package itself and the base packages.

Package: phenofit
Check: tests
New result: ERROR
    Running ‘testthat.R’ [63s/63s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(phenofit)
    > 
    > test_check("phenofit")
    List of 5
     $ AG    : tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
     $ Beck  : tibble [6 × 7] (S3: tbl_df/tbl/data.frame)
     $ Elmore: tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
     $ Gu    : tibble [6 × 10] (S3: tbl_df/tbl/data.frame)
     $ Zhang : tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
    NULL
    # A tibble: 6 × 8
      flag      t0    mn    mx     rsp    a3     rau    a5
      <chr>  <dbl> <dbl> <dbl>   <dbl> <dbl>   <dbl> <dbl>
    1 1999_1 -135. 0.201 0.636 0.00932  2.85 0.00852  2   
    2 2000_1  189. 0.238 0.635 0.0126   2.47 0.00801  3.21
    3 2001_1  569. 0.252 0.626 0.0108   2.96 0.00950  2.96
    4 2002_1  892. 0.253 0.614 0.0159   2    0.00724  3.08
    5 2003_1 1268. 0.236 0.577 0.0121   2.88 0.00723  2.88
    6 2004_1 1677. 0.202 0.576 0.00832  2.84 0.00990  3.48
         meth        R2       NSE         R         RMSE        pvalue n_sim
       <char>     <num>     <num>     <num>        <num>         <num> <num>
    1:     AG 0.9986908 0.9985845 0.9993452 9.940385e-03  4.489925e-65    46
    2:   Beck 1.0000000 1.0000000 1.0000000 1.389780e-09  0.000000e+00    46
    3: Elmore 1.0000000 1.0000000 1.0000000 4.161813e-10  0.000000e+00    46
    4:     Gu 1.0000000 1.0000000 1.0000000 4.891365e-11  0.000000e+00    46
    5:  Zhang 1.0000000 1.0000000 1.0000000 5.529073e-06 8.043461e-208    46
    $AG
     formula:	mn + (mx - mn) * exp(-((t0 - t) * rsp)^a3)
      formula:	mn + (mx - mn) * exp(-((t - t0) * rau)^a5)
    pars:
                 t0        mn        mx         rsp a3         rau a5
    nlminb 149.8926 0.1020656 0.7095242 0.009389263  6 0.009367765  6
    
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.19427e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.03034e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.08395e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.36432e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 6.97437e-18); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 6.04329e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
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    warning: solve(): system is singular; attempting approx solution
    
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    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
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    warning: solve(): system is singular (rcond: 1.94249e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
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    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.84957e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
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    warning: solve(): system is singular (rcond: 8.58712e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.09346e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.82199e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38705e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.88785e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 7.40149e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 6.20634e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 4.38854e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.00786e-16); attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.46031e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 5.02097e-17); attempting approx solution
    
    warning: solve(): system is singular (rcond: 1.25524e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular; attempting approx solution
    
    warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution
    [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-curvefit.R:18:5'): curvefit works ────────────────────────────
    all.equal(p1, p2, tolerance = 1e-06) is not TRUE
    
    `actual` is a character vector ('Component "Elmore": Component "mn": Mean relative difference: 1.990404e-06')
    `expected` is a logical vector (TRUE)
    
    [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ]
    Error: Test failures
    Execution halted

Package: simDAG
Check: tests
New result: ERROR
    Running ‘testthat.R’ [29s/33s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(simDAG)
    > library(testthat)
    > library(data.table)
    > library(igraph)
    
    Attaching package: 'igraph'
    
    The following object is masked from 'package:testthat':
    
        compare
    
    The following objects are masked from 'package:stats':
    
        decompose, spectrum
    
    The following object is masked from 'package:base':
    
        union
    
    > 
    > data.table::setDTthreads(1)
    > 
    > test_check("simDAG")
    Loading required namespace: MASS
    Loading required namespace: ggplot2
    Loading required namespace: ggforce
    t = 1 node = sickness2
    t = 1 node = sickness1
    t = 2 node = sickness2
    t = 2 node = sickness1
    t = 3 node = sickness2
    t = 3 node = sickness1
    t = 4 node = sickness2
    t = 4 node = sickness1
    t = 5 node = sickness2
    t = 5 node = sickness1
    Loading required namespace: Rfast
    Loading required namespace: doSNOW
    Loading required namespace: doRNG
    starting worker pid=1963931 on localhost:11293 at 11:49:31.352
    starting worker pid=1963933 on localhost:11293 at 11:49:31.397
    
      |                                                                            
      |                                                                      |   0%Loading required package: simDAG
    loaded simDAG and set parent environment
    Loading required package: foreach
    Loading required package: rngtools
    Loading required package: simDAG
    loaded simDAG and set parent environment
    Loading required package: foreach
    Loading required package: rngtools
    
      |                                                                            
      |=======                                                               |  10%
      |                                                                            
      |==============                                                        |  20%
      |                                                                            
      |=====================                                                 |  30%
      |                                                                            
      |============================                                          |  40%
      |                                                                            
      |===================================                                   |  50%
      |                                                                            
      |==========================================                            |  60%
      |                                                                            
      |=================================================                     |  70%
      |                                                                            
      |========================================================              |  80%
      |                                                                            
      |===============================================================       |  90%
      |                                                                            
      |======================================================================| 100%starting worker pid=1964095 on localhost:11293 at 11:49:32.252
    starting worker pid=1964094 on localhost:11293 at 11:49:32.255
    Loading required package: simDAG
    loaded simDAG and set parent environment
    Loading required package: foreach
    Loading required package: rngtools
    Loading required package: simDAG
    loaded simDAG and set parent environment
    Loading required package: foreach
    Loading required package: rngtools
    starting worker pid=1964390 on localhost:11293 at 11:49:34.018
    starting worker pid=1964389 on localhost:11293 at 11:49:34.018
    Loading required package: simDAG
    loaded simDAG and set parent environment
    Loading required package: foreach
    Loading required package: rngtools
    Loading required package: simDAG
    loaded simDAG and set parent environment
    Loading required package: foreach
    Loading required package: rngtools
    [ FAIL 2 | WARN 14 | SKIP 43 | PASS 611 ]
    
    ══ Skipped tests (43) ══════════════════════════════════════════════════════════
    • On CRAN (43): 'test_DAG.node_S3.r:6:3', 'test_DAG.node_S3.r:11:3',
      'test_DAG.node_S3.r:16:3', 'test_DAG.node_S3.r:21:3',
      'test_DAG.node_S3.r:27:3', 'test_DAG.node_S3.r:34:3',
      'test_DAG.node_S3.r:39:3', 'test_DAG.node_S3.r:44:3',
      'test_DAG.node_S3.r:49:3', 'test_DAG.node_S3.r:55:3', 'test_dag.r:17:3',
      'test_dag.r:30:3', 'test_dag.r:37:3', 'test_dag.r:50:3', 'test_dag.r:66:3',
      'test_node.r:519:3', 'test_plot.DAG.r:12:3', 'test_plot.DAG.r:16:3',
      'test_plot.DAG.r:20:3', 'test_plot.DAG.r:24:3', 'test_plot.DAG.r:28:3',
      'test_plot.DAG.r:32:3', 'test_plot.DAG.r:36:3', 'test_plot.DAG.r:41:3',
      'test_plot.DAG.r:45:3', 'test_plot.DAG.r:53:3', 'test_plot.DAG.r:60:3',
      'test_plot.DAG.r:65:3', 'test_plot.DAG.r:70:3', 'test_plot.DAG.r:101:3',
      'test_plot.DAG.r:105:3', 'test_plot.DAG.r:109:3', 'test_plot.simDT.r:25:3',
      'test_plot.simDT.r:29:3', 'test_plot.simDT.r:33:3', 'test_plot.simDT.r:37:3',
      'test_plot.simDT.r:41:3', 'test_plot.simDT.r:49:3', 'test_plot.simDT.r:57:3',
      'test_simDT_S3.r:12:3', 'test_simDT_S3.r:17:3', 'test_simDT_S3.r:22:3',
      'test_simDT_S3.r:26:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_sim_discrete_time.r:290:3'): helpful error message formula error ──
    Error: An error occured when interpreting the formula of node 'B'. The message was:
    Error: Error in `[.data.table`(mod_mat, , args$parents, with = FALSE): columns not found: [A, C]
    This error may occur when one of the terms in a supplied formula does not match any variables in the generated data.
     Please check whether all terms in your supplied formula occur in the data generated up to this point.
     The variables currently available in data are:
    (Intercept), ATRUE, B, .id
    
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test_sim_discrete_time.r:290:3
      2. │ └─testthat:::expect_condition_matching(...)
      3. │   └─testthat:::quasi_capture(...)
      4. │     ├─testthat (local) .capture(...)
      5. │     │ └─base::withCallingHandlers(...)
      6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      7. └─simDAG::sim_discrete_time(dag, n_sim = 100, max_t = 3)
      8.   └─base::tryCatch(...)
      9.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11.         └─value[[3L]](cond)
    ── Error ('test_sim_from_dag.r:102:3'): helpful error message formula error ────
    Error: An error occured when interpreting the formula of node 'B'. The message was:
    Error: Error in `[.data.table`(mod_mat, , args$parents, with = FALSE): columns not found: [A, C]
    This error may occur when one of the terms in a supplied formula does not match any variables in the generated data.
     Please check whether all terms in your supplied formula occur in the data generated up to this point.
     The variables currently available in data are:
    (Intercept), ATRUE
    
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test_sim_from_dag.r:102:3
      2. │ └─testthat:::expect_condition_matching(...)
      3. │   └─testthat:::quasi_capture(...)
      4. │     ├─testthat (local) .capture(...)
      5. │     │ └─base::withCallingHandlers(...)
      6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      7. └─simDAG::sim_from_dag(dag, n_sim = 100)
      8.   └─base::tryCatch(...)
      9.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11.         └─value[[3L]](cond)
    
    [ FAIL 2 | WARN 14 | SKIP 43 | PASS 611 ]
    Error: Test failures
    Execution halted

Package: TrialEmulation
Check: tests
New result: ERROR
    Running ‘testthat.R’ [191s/178s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(TrialEmulation)
    > 
    > data.table::setDTthreads(2)
    > test_check("TrialEmulation")
    Starting data manipulation
    Starting data extension
    Summary of extended data:
    Number of observations: 1939053
    ------------------------------------------------------------
    
    Starting data manipulation
    P(treatment = 1 | previous treatment = 0) for denominator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept) -3.84325    0.04785  -80.31   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 4329.7  on 21263  degrees of freedom
    Residual deviance: 4329.7  on 21263  degrees of freedom
    AIC: 4331.7
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 0) for numerator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept) -3.84325    0.04785  -80.31   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 4329.7  on 21263  degrees of freedom
    Residual deviance: 4329.7  on 21263  degrees of freedom
    AIC: 4331.7
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 1) for denominator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)  4.37616    0.06815   64.21   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 2346.7  on 17555  degrees of freedom
    Residual deviance: 2346.7  on 17555  degrees of freedom
    AIC: 2348.7
    
    Number of Fisher Scoring iterations: 7
    
    P(treatment = 1 | previous treatment = 1) for numerator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)  4.37616    0.06815   64.21   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 2346.7  on 17555  degrees of freedom
    Residual deviance: 2346.7  on 17555  degrees of freedom
    AIC: 2348.7
    
    Number of Fisher Scoring iterations: 7
    
    Starting data extension
    Summary of extended data:
    Number of observations: 963883
    ------------------------------------------------------------
    
    Starting data manipulation
    P(treatment = 1 | previous treatment = 0) for denominator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept) -3.32517    0.03599   -92.4   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 6948.7  on 23042  degrees of freedom
    Residual deviance: 6948.7  on 23042  degrees of freedom
    AIC: 6950.7
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 0) for numerator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept) -3.32517    0.03599   -92.4   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 6948.7  on 23042  degrees of freedom
    Residual deviance: 6948.7  on 23042  degrees of freedom
    AIC: 6950.7
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 1) for denominator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)   3.9124     0.0453   86.37   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 4892.8  on 25356  degrees of freedom
    Residual deviance: 4892.8  on 25356  degrees of freedom
    AIC: 4894.8
    
    Number of Fisher Scoring iterations: 6
    
    P(treatment = 1 | previous treatment = 1) for numerator
    
    Call:
    glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)   3.9124     0.0453   86.37   <2e-16 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 4892.8  on 25356  degrees of freedom
    Residual deviance: 4892.8  on 25356  degrees of freedom
    AIC: 4894.8
    
    Number of Fisher Scoring iterations: 6
    
    Starting data extension
    Summary of extended data:
    Number of observations: 1939053
    ------------------------------------------------------------
    
    Starting data manipulation
    P(treatment = 1 | previous treatment = 0) for denominator
    
    Call:
    glm(formula = treatment ~ age_s + x4 + x2 + x1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept) -0.13699    0.25792  -0.531   0.5953    
    age_s       -0.04014    0.19890  -0.202   0.8401    
    x4           1.09583    0.21355   5.131 2.88e-07 ***
    x2           0.09687    0.19430   0.499   0.6181    
    x1           0.61385    0.36325   1.690   0.0911 .  
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 232.27  on 169  degrees of freedom
    Residual deviance: 185.41  on 165  degrees of freedom
    AIC: 195.41
    
    Number of Fisher Scoring iterations: 4
    
    P(treatment = 1 | previous treatment = 0) for numerator
    
    Call:
    glm(formula = treatment ~ age_s + x4, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)  0.12031    0.20308   0.592    0.554    
    age_s        0.01215    0.19512   0.062    0.950    
    x4           1.10863    0.21415   5.177 2.26e-07 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 232.27  on 169  degrees of freedom
    Residual deviance: 188.62  on 167  degrees of freedom
    AIC: 194.62
    
    Number of Fisher Scoring iterations: 4
    
    P(treatment = 1 | previous treatment = 1) for denominator
    
    Call:
    glm(formula = treatment ~ age_s + x4 + x2 + x1, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)   0.6783     0.2797   2.425 0.015318 *  
    age_s        -0.1924     0.2115  -0.910 0.362887    
    x4            0.8536     0.2218   3.849 0.000119 ***
    x2            0.3246     0.1963   1.653 0.098252 .  
    x1            0.7923     0.4914   1.612 0.106867    
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 188.83  on 150  degrees of freedom
    Residual deviance: 164.85  on 146  degrees of freedom
    AIC: 174.85
    
    Number of Fisher Scoring iterations: 4
    
    P(treatment = 1 | previous treatment = 1) for numerator
    
    Call:
    glm(formula = treatment ~ age_s + x4, family = binomial(link = "logit"), 
        data = data)
    
    Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
    (Intercept)   0.7476     0.2520   2.967 0.003011 ** 
    age_s        -0.1686     0.2081  -0.810 0.417888    
    x4            0.7935     0.2163   3.669 0.000244 ***
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    (Dispersion parameter for binomial family taken to be 1)
    
        Null deviance: 188.83  on 150  degrees of freedom
    Residual deviance: 170.78  on 148  degrees of freedom
    AIC: 176.78
    
    Number of Fisher Scoring iterations: 4
    
    Starting data extension
    Summary of extended data:
    Number of observations: 500
    ------------------------------------------------------------
    
    [ FAIL 10 | WARN 1 | SKIP 33 | PASS 429 ]
    
    ══ Skipped tests (33) ══════════════════════════════════════════════════════════
    • On CRAN (33): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
      'test-data_utils.R:131:3', 'test-generics.R:25:3', 'test-generics.R:66:3',
      'test-generics.R:95:3', 'test-modelling.R:99:3', 'test-modelling.R:154:3',
      'test-modelling.R:175:3', 'test-modelling.R:205:3', 'test-modelling.R:229:3',
      'test-modelling.R:266:3', 'test-modelling.R:290:3', 'test-modelling.R:314:3',
      'test-modelling.R:357:3', 'test-modelling.R:431:3', 'test-predict.R:26:3',
      'test-predict.R:51:3', 'test-predict.R:108:3', 'test-predict.R:171:3',
      'test-sampling.R:5:3', 'test-sampling.R:15:3', 'test-sampling.R:34:3',
      'test-sampling.R:54:3', 'test-sampling.R:86:3', 'test-sampling.R:103:3',
      'test-sampling.R:180:3', 'test-te_weights.R:20:3', 'test-te_weights.R:62:3',
      'test-trial_sequence.R:41:3', 'test-trial_sequence.R:45:3',
      'test-trial_sequence.R:49:3', 'test-trial_sequence.R:56:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-te_datastore_duckdb.R:73:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──
    sort(sc_01@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).
    
      `actual`: 7  9    14 15 21 21    29 32 and 32 more...
    `expected`: 1 10 13 14 15    21 27 29 32            ...
    ── Failure ('test-te_datastore_duckdb.R:83:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──
    sc_02@outcome_data@n_rows (`actual`) not equal to 756 (`expected`).
    
      `actual`: 761.0
    `expected`: 756.0
    ── Failure ('test-te_datastore_duckdb.R:101:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──
    sort(sc_01@outcome_data@data$sample_weight) (`actual`) not equal to c(rep(1, 14), rep(100, 17)) (`expected`).
    
      `actual[29:33]`: 100 100 100 100 100
    `expected[29:31]`: 100 100 100        
    ── Failure ('test-te_datastore_duckdb.R:102:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──
    sort(sc_02@outcome_data@data$sample_weight) (`actual`) not equal to c(rep(1, 14), rep(2, 742)) (`expected`).
    
      `actual[754:761]`: 2 2 2 2 2 2 2 2
    `expected[754:756]`: 2 2 2          
    ── Failure ('test-te_datastore_duckdb.R:112:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──
    sort(sc_04@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).
    
      `actual`: 16.0 20.0 44.0 44.0 44.0 44.0 44.0 49.0 53.0 53.0 and 18 more...
    `expected`:  2.0 14.0 16.0 33.0 34.0 44.0 44.0 44.0 44.0 44.0            ...
    ── Failure ('test-te_datastore_duckdb.R:152:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──
    sort(sc_01@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).
    
      `actual`: 7  9    14 15 21 21    29 32 and 32 more...
    `expected`: 1 10 13 14 15    21 27 29 32            ...
    ── Failure ('test-te_datastore_duckdb.R:162:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──
    sc_02@outcome_data@n_rows (`actual`) not equal to 756 (`expected`).
    
      `actual`: 761.0
    `expected`: 756.0
    ── Failure ('test-te_datastore_duckdb.R:182:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──
    sort(sc_01@outcome_data@data$sample_weight) (`actual`) not equal to c(rep(1, 14), rep(100, 17)) (`expected`).
    
      `actual[29:33]`: 100 100 100 100 100
    `expected[29:31]`: 100 100 100        
    ── Failure ('test-te_datastore_duckdb.R:183:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──
    sort(sc_02@outcome_data@data$sample_weight) (`actual`) not equal to c(rep(1, 14), rep(2, 742)) (`expected`).
    
      `actual[754:761]`: 2 2 2 2 2 2 2 2
    `expected[754:756]`: 2 2 2          
    ── Failure ('test-te_datastore_duckdb.R:193:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──
    sort(sc_04@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).
    
      `actual`: 16.0 20.0 44.0 44.0 44.0 44.0 44.0 49.0 53.0 53.0 and 18 more...
    `expected`:  2.0 14.0 16.0 33.0 34.0 44.0 44.0 44.0 44.0 44.0            ...
    
    [ FAIL 10 | WARN 1 | SKIP 33 | PASS 429 ]
    Error: Test failures
    Execution halted

Package: wxgenR
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Vignette_BlacksburgVA.Rmd’ using rmarkdown
  ** Processing: /home/hornik/tmp/CRAN_recheck/wxgenR.Rcheck/vign_test/wxgenR/vignettes/Vignette_BlacksburgVA_files/figure-html/unnamed-chunk-9-1.png
  768x768 pixels, 3x8 bits/pixel, RGB
  Input IDAT size = 207244 bytes
  Input file size = 207622 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0
    zc = 9  zm = 8  zs = 1  f = 0
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 201168
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 201168
  
  Output IDAT size = 201168 bytes (6076 bytes decrease)
  Output file size = 201246 bytes (6376 bytes = 3.07% decrease)
  
  ** Processing: /home/hornik/tmp/CRAN_recheck/wxgenR.Rcheck/vign_test/wxgenR/vignettes/Vignette_BlacksburgVA_files/figure-html/unnamed-chunk-10-1.png
  768x768 pixels, 3x8 bits/pixel, RGB
  Input IDAT size = 237414 bytes
  Input file size = 237828 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0
    zc = 9  zm = 8  zs = 1  f = 0
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 231658
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 231658
  
  Output IDAT size = 231658 bytes (5756 bytes decrease)
  Output file size = 231736 bytes (6092 bytes = 2.56% decrease)
  
  ** Processing: /home/hornik/tmp/CRAN_recheck/wxgenR.Rcheck/vign_test/wxgenR/vignettes/Vignette_BlacksburgVA_files/figure-html/unnamed-chunk-12-1.png
  768x768 pixels, 3x8 bits/pixel, RGB
  Input IDAT size = 96682 bytes
  Input file size = 96892 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 80526
    zc = 9  zm = 8  zs = 1  f = 0
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 80526
  
  Output IDAT size = 80526 bytes (16156 bytes decrease)
  Output file size = 80604 bytes (16288 bytes = 16.81% decrease)
  
  ** Processing: /home/hornik/tmp/CRAN_recheck/wxgenR.Rcheck/vign_test/wxgenR/vignettes/Vignette_BlacksburgVA_files/figure-html/unnamed-chunk-13-1.png
  768x768 pixels, 3x8 bits/pixel, RGB
  Input IDAT size = 90268 bytes
  Input file size = 90478 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 73896
    zc = 9  zm = 8  zs = 1  f = 0
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 73896
  
  Output IDAT size = 73896 bytes (16372 bytes decrease)
  Output file size = 73974 bytes (16504 bytes = 18.24% decrease)
  
  --- finished re-building ‘Vignette_BlacksburgVA.Rmd’
  
  --- re-building ‘Vignette_LowerSantaCruzRiverBasinAZ.Rmd’ using rmarkdown
  
  Quitting from lines 198-201 [unnamed-chunk-6] (Vignette_LowerSantaCruzRiverBasinAZ.Rmd)
  Error: processing vignette 'Vignette_LowerSantaCruzRiverBasinAZ.Rmd' failed with diagnostics:
  The melt generic in data.table has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both packages are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(.). In the next version, this warning will become an error.
  --- failed re-building ‘Vignette_LowerSantaCruzRiverBasinAZ.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Vignette_LowerSantaCruzRiverBasinAZ.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted