Errors in running code in vignettes:
when running code in 'OmicNavigatorAPI.Rnw'

> if (!interactive()) options(prompt = " ", continue = " ", 
+     width = 70)

> library(jsonlite)

> library(OmicNavigator)
OmicNavigator R package version: 1.4.3
The app is not installed. Install it with installApp()

> .tmplib <- tempfile()

> local({
+     dir.create(.tmplib)
+     .libPaths(c(.tmplib, .libPaths()))
+     abc <- OmicNavigator:::testStudy(name = "ABC")
+     plots <- OmicN .... [TRUNCATED] 
Installing study "ABC" in C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/OmicNavigator/tmp/RtmpkDJFlj/file31b4266264b
Exporting study "ABC" as an R package
Calculating pairwise overlaps. This may take a while...
Exported study to C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\OmicNavigator\tmp\RtmpkDJFlj/ONstudyABC
Success!

> studies <- listStudies(libraries = .tmplib)

> toJSON(studies, auto_unbox = TRUE, pretty = TRUE)
[
  {
    "name": "ABC",
    "package": {
      "Package": "ONstudyABC",
      "Title": "OmicNavigator study ABC",
      "Version": "0.0.0.9000",
      "Maintainer": "Unknown <unknown@unknown>",
      "Description": "The OmicNavigator data package for the study\n       \"ABC\"",
      "OmicNavigatorVersion": "1.4.3",
      "department": "immunology",
      "organism": "Mus musculus",
      "Imports": "ggplot2, graphics, rlang, stats",
      "Built": "R 4.2.0; ; 2021-09-21 23:09:51 UTC; windows",
      "description": "The OmicNavigator data package for the study\n       \"ABC\""
    },
    "results": [
      {
        "modelID": "model_01",
        "modelDisplay": "Model 1",
        "tests": [
          {
            "testID": "test_01",
            "testDisplay": "test 1"
          },
          {
            "testID": "test_02",
            "testDisplay": "test 2"
          }
        ]
      },
      {
        "modelID": "model_02",
        "modelDisplay": "Model 2",
        "tests": [
          {
            "testID": "test_01",
            "testDisplay": "test 1"
          },
          {
            "testID": "test_02",
            "testDisplay": "test 2"
          }
        ]
      },
      {
        "modelID": "model_03",
        "modelDisplay": "Model 3",
        "tests": [
          {
            "testID": "test_01",
            "testDisplay": "test 1"
          },
          {
            "testID": "test_02",
            "testDisplay": "test 2"
          }
        ]
      }
    ],
    "enrichments": [
      {
        "modelID": "model_01",
        "modelDisplay": "Model 1",
        "annotations": [
          {
            "annotationID": "annotation_01",
            "annotationDisplay": "Terms from annotation_01"
          },
          {
            "annotationID": "annotation_02",
            "annotationDisplay": "Terms from annotation_02"
          },
          {
            "annotationID": "annotation_03",
            "annotationDisplay": "Terms from annotation_03"
          }
        ]
      },
      {
        "modelID": "model_02",
        "modelDisplay": "Model 2",
        "annotations": [
          {
            "annotationID": "annotation_01",
            "annotationDisplay": "Terms from annotation_01"
          },
          {
            "annotationID": "annotation_02",
            "annotationDisplay": "Terms from annotation_02"
          },
          {
            "annotationID": "annotation_03",
            "annotationDisplay": "Terms from annotation_03"
          }
        ]
      },
      {
        "modelID": "model_03",
        "modelDisplay": "Model 3",
        "annotations": [
          {
            "annotationID": "annotation_01",
            "annotationDisplay": "Terms from annotation_01"
          },
          {
            "annotationID": "annotation_02",
            "annotationDisplay": "Terms from annotation_02"
          },
          {
            "annotationID": "annotation_03",
            "annotationDisplay": "Terms from annotation_03"
          }
        ]
      }
    ],
    "plots": [
      {
        "modelID": "model_01",
        "modelDisplay": "Model 1",
        "plots": [
          {
            "plotID": "plotBase",
            "plotDisplay": "Custom plot",
            "plotType": "singleFeature"
          },
          {
            "plotID": "plotMultiFeature",
            "plotDisplay": "PCA",
            "plotType": "multiFeature"
          }
        ]
      },
      {
        "modelID": "model_02",
        "modelDisplay": "Model 2",
        "plots": [
          {
            "plotID": "plotBase",
            "plotDisplay": "Custom plot",
            "plotType": "singleFeature"
          },
          {
            "plotID": "plotMultiFeature",
            "plotDisplay": "PCA",
            "plotType": "multiFeature"
          }
        ]
      },
      {
        "modelID": "model_03",
        "modelDisplay": "Model 3",
        "plots": [
          {
            "plotID": "plotGg",
            "plotDisplay": "Custom ggplot2 plot",
            "plotType": "singleFeature"
          }
        ]
      }
    ]
  }
] 

> resultsTable <- getResultsTable(study = "ABC", modelID = "model_01", 
+     testID = "test_01")

> toJSON(resultsTable[1:2, ], pretty = TRUE)
[
  {
    "customID": "feature_0060",
    "featureVarNumeric": "41",
    "featureVar01": "x",
    "featureVar02": "d",
    "featureVar03": "o",
    "beta": -3.5204,
    "beta_1": -0.9759,
    "p_val": 0.0001
  },
  {
    "customID": "feature_0084",
    "featureVarNumeric": "84",
    "featureVar01": "d",
    "featureVar02": "z",
    "featureVar03": "e",
    "beta": 3.7157,
    "beta_1": 1.6956,
    "p_val": 0.0002
  }
] 

> enrichmentsTable <- getEnrichmentsTable(study = "ABC", 
+     modelID = "model_01", annotationID = "annotation_01")

> toJSON(enrichmentsTable[1:2, ], pretty = TRUE)
[
  {
    "termID": "term_01",
    "description": "Description of term_01",
    "test_01": 0.03,
    "test_02": 0.03
  },
  {
    "termID": "term_02",
    "description": "Description of term_02",
    "test_01": 0.1,
    "test_02": 0.07
  }
] 

> enrichmentsTable <- getEnrichmentsTable(study = "ABC", 
+     modelID = "model_01", annotationID = "annotation_01", type = "adjusted")

> toJSON(enrichmentsTable[1:2, ], pretty = TRUE)
[
  {
    "termID": "term_01",
    "description": "Description of term_01",
    "test_01": 0.05,
    "test_02": 0.05
  },
  {
    "termID": "term_02",
    "description": "Description of term_02",
    "test_01": 0.12,
    "test_02": 0.09
  }
] 

> enrichmentsNetwork <- getEnrichmentsNetwork(study = "ABC", 
+     modelID = "model_01", annotationID = "annotation_01")

> enrichmentsNetworkMinimal <- list(tests = enrichmentsNetwork[["tests"]], 
+     nodes = enrichmentsNetwork[["nodes"]][1:3, ], links = enrichmentsNet .... [TRUNCATED] 

> toJSON(enrichmentsNetworkMinimal, auto_unbox = TRUE, 
+     pretty = TRUE)
{
  "tests": ["test_01", "test_02"],
  "nodes": [
    {
      "id": 1,
      "termID": "term_01",
      "description": "Description of term_01",
      "geneSetSize": 18,
      "nominal": [0.03, 0.03],
      "adjusted": [0.05, 0.05]
    },
    {
      "id": 2,
      "termID": "term_02",
      "description": "Description of term_02",
      "geneSetSize": 10,
      "nominal": [0.1, 0.07],
      "adjusted": [0.12, 0.09]
    },
    {
      "id": 3,
      "termID": "term_03",
      "description": "Description of term_03",
      "geneSetSize": 24,
      "nominal": [0.08, 0.1],
      "adjusted": [0.1, 0.12]
    }
  ],
  "links": [
    {
      "id": 1,
      "source": 1,
      "target": 3,
      "overlapSize": 6,
      "overlap": 0.3333,
      "jaccard": 0.1667
    },
    {
      "id": 2,
      "source": 1,
      "target": 4,
      "overlapSize": 3,
      "overlap": 0.2,
      "jaccard": 0.1
    },
    {
      "id": 3,
      "source": 1,
      "target": 6,
      "overlapSize": 3,
      "overlap": 0.2727,
      "jaccard": 0.1154
    }
  ]
} 

> nodeFeatures <- getNodeFeatures(study = "ABC", annotationID = "annotation_01", 
+     termID = "term_01")

> toJSON(nodeFeatures[1:4], pretty = TRUE)
["feature_0002", "feature_0010", "feature_0024", "feature_0032"] 

> linkFeatures <- getLinkFeatures(study = "ABC", annotationID = "annotation_01", 
+     termID1 = "term_01", termID2 = "term_03")

> toJSON(linkFeatures[1:4], pretty = TRUE)
["feature_0032", "feature_0038", "feature_0058", "feature_0075"] 

> plotStudy(study = "ABC", modelID = "model_01", featureID = "feature_0001", 
+     plotID = "plotBase")
Returning "default" plots for modelID "model_01"

> plotStudy(study = "ABC", modelID = "model_03", featureID = "feature_0001", 
+     plotID = "plotGg")
Temporarily attaching namespace "package:ggplot2" to the search path

> plotStudy(study = "ABC", modelID = "model_01", featureID = c("feature_0001", 
+     "feature_0002"), plotID = "plotMultiFeature")
Returning "default" plots for modelID "model_01"

> resultsIntersection <- getResultsIntersection(study = "ABC", 
+     modelID = "model_01", anchor = "test_01", mustTests = c("test_01", 
+         "t ..." ... [TRUNCATED] 
Returning "default" features for modelID "model_01"

> toJSON(resultsIntersection[1:2, ], pretty = TRUE)
[
  {
    "customID": "feature_0060",
    "featureVarNumeric": "41",
    "featureVar01": "x",
    "featureVar02": "d",
    "featureVar03": "o",
    "Set_Membership": "test_01 , test_02",
    "beta": -3.5204,
    "beta_1": -0.9759,
    "p_val": 0.0001
  },
  {
    "customID": "feature_0084",
    "featureVarNumeric": "84",
    "featureVar01": "d",
    "featureVar02": "z",
    "featureVar03": "e",
    "Set_Membership": "test_01 , test_02",
    "beta": 3.7157,
    "beta_1": 1.6956,
    "p_val": 0.0002
  }
] 

> enrichmentsIntersection <- getEnrichmentsIntersection(study = "ABC", 
+     modelID = "model_01", annotationID = "annotation_01", mustTests = c("tes ..." ... [TRUNCATED] 

> toJSON(enrichmentsIntersection[1:2, ], pretty = TRUE)
[
  {
    "termID": "term_01",
    "description": "Description of term_01",
    "test_01": 0.03,
    "test_02": 0.03
  },
  {
    "termID": "term_02",
    "description": "Description of term_02",
    "test_01": 0.1,
    "test_02": 0.07
  }
] 

> resultsUpset <- getResultsUpset(study = "ABC", modelID = "model_01", 
+     sigValue = 0.5, operator = "<", column = "p_val")

> enrichmentsUpset <- getEnrichmentsUpset(study = "ABC", 
+     modelID = "model_01", annotationID = "annotation_02", sigValue = 0.05, 
+     operator .... [TRUNCATED] 

> upsetCols <- getUpsetCols(study = "ABC", modelID = "model_01")

> toJSON(upsetCols, auto_unbox = TRUE, pretty = TRUE)
["beta", "p_val"] 

> metaFeaturesTable <- getMetaFeaturesTable(study = "ABC", 
+     modelID = "model_01", featureID = "feature_0001")
Returning "default" metaFeatures for modelID "model_01"

> toJSON(metaFeaturesTable[1:2, ], pretty = TRUE)
[
  {
    "metaFeatureID": "metaFeature_0001",
    "metaFeatureVarNumeric": "296",
    "metaFeatureVar01": "n",
    "metaFeatureVar02": "m",
    "metaFeatureVar03": "r"
  },
  {
    "metaFeatureID": "metaFeature_0101",
    "metaFeatureVarNumeric": "296",
    "metaFeatureVar01": "x",
    "metaFeatureVar02": "i",
    "metaFeatureVar03": "c"
  }
] 

> barcodeData <- getBarcodeData(study = "ABC", modelID = "model_01", 
+     testID = "test_01", annotationID = "annotation_02", termID = "term_05")
Returning "default" barcodes for modelID "model_01"

> toJSON(barcodeData, auto_unbox = TRUE, pretty = TRUE)
{
  "data": [
    {
      "featureID": "feature_0060",
      "featureEnrichment": "feature_0060",
      "featureDisplay": "feature_0060",
      "statistic": 3.5204,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0062",
      "featureEnrichment": "feature_0062",
      "featureDisplay": "feature_0062",
      "statistic": 2.0138,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0070",
      "featureEnrichment": "feature_0070",
      "featureDisplay": "feature_0070",
      "statistic": 1.9435,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0082",
      "featureEnrichment": "feature_0082",
      "featureDisplay": "feature_0082",
      "statistic": 1.5647,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0085",
      "featureEnrichment": "feature_0085",
      "featureDisplay": "feature_0085",
      "statistic": 1.4568,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0092",
      "featureEnrichment": "feature_0092",
      "featureDisplay": "feature_0092",
      "statistic": 1.2826,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0057",
      "featureEnrichment": "feature_0057",
      "featureDisplay": "feature_0057",
      "statistic": 1.0368,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0028",
      "featureEnrichment": "feature_0028",
      "featureDisplay": "feature_0028",
      "statistic": 0.9306,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0005",
      "featureEnrichment": "feature_0005",
      "featureDisplay": "feature_0005",
      "statistic": 0.9088,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0014",
      "featureEnrichment": "feature_0014",
      "featureDisplay": "feature_0014",
      "statistic": 0.7803,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0020",
      "featureEnrichment": "feature_0020",
      "featureDisplay": "feature_0020",
      "statistic": 0.4481,
      "logFoldChange": 0
    },
    {
      "featureID": "feature_0003",
      "featureEnrichment": "feature_0003",
      "featureDisplay": "feature_0003",
      "statistic": 0.164,
      "logFoldChange": 0
    }
  ],
  "highest": 4,
  "labelStat": "Beta coefficient",
  "labelLow": "Small effect size",
  "labelHigh": "Large effect size"
} 

> reportLink <- getReportLink(study = "ABC", modelID = "model_01")
Returning "default" reports for modelID "model_01"

> toJSON(reportLink, auto_unbox = TRUE, pretty = TRUE)
"https://www.domain.com/default.html" 

> reportLink <- getReportLink(study = "ABC", modelID = "model_02")

> toJSON(reportLink, auto_unbox = TRUE, pretty = TRUE)
"ONstudyABC/OmicNavigatorReports/model_02/report.html" 

> resultsLinkouts <- getResultsLinkouts(study = "ABC", 
+     modelID = "model_01")
Returning "default" resultsLinkouts for modelID "model_01"

> toJSON(resultsLinkouts, auto_unbox = TRUE, pretty = 2)
{
  "customID": [
    "https://ensembl.org/Homo_sapiens/Gene/Summary?g=",
    "https://www.targetvalidation.org/target/"
  ],
  "featureVar01": "https://www.ncbi.nlm.nih.gov/gene/"
}
 

> enrichmentsLinkouts <- getEnrichmentsLinkouts(study = "ABC", 
+     annotationID = "annotation_01")

> toJSON(enrichmentsLinkouts, auto_unbox = TRUE, pretty = 2)
[
  "http://amigo.geneontology.org/amigo/term/",
  "https://www.ebi.ac.uk/QuickGO/term/"
]
 

> enrichmentsLinkouts <- getEnrichmentsLinkouts(study = "ABC", 
+     annotationID = "annotation_03")

> toJSON(enrichmentsLinkouts, auto_unbox = TRUE, pretty = TRUE)
"https://reactome.org/content/detail/" 

> metaFeaturesLinkouts <- getMetaFeaturesLinkouts(study = "ABC", 
+     modelID = "model_01")
Returning "default" metaFeaturesLinkouts for modelID "model_01"

> toJSON(metaFeaturesLinkouts, auto_unbox = TRUE, pretty = 2)
{
  "metaFeatureVar01": [
    "https://ensembl.org/Homo_sapiens/Gene/Summary?g=",
    "https://www.targetvalidation.org/target/"
  ],
  "metaFeatureVar02": "https://www.ncbi.nlm.nih.gov/gene/"
}
 

> resultsFavicons <- getFavicons(linkouts = resultsLinkouts)

  When sourcing 'OmicNavigatorAPI.R':
Error: there is no package called 'faviconPlease'
Execution halted

  'OmicNavigatorAPI.Rnw' using 'UTF-8'... failed
  'OmicNavigatorUsersGuide.Rnw' using 'UTF-8'... OK