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: 1.4.2
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/RtmpeGxa2e/file3a8033936a8e
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\RtmpeGxa2e/ONstudyABC

  When sourcing 'OmicNavigatorAPI.R':
Error: (converted from warning) installation of package 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/OmicNavigator/tmp/RtmpeGxa2e/ONstudyABC' had non-zero exit status
Execution halted
when running code in 'OmicNavigatorUsersGuide.Rnw'

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

> local({
+     .tmplib <- tempfile()
+     dir.create(.tmplib)
+     .libPaths(c(.tmplib, .libPaths()))
+ })

> data("RNAseq123", package = "OmicNavigator")

> ls()
[1] "Mm.c2"         "basal.vs.lp"   "basal.vs.ml"   "cam.BasalvsLP"
[5] "cam.BasalvsML" "group"         "lane"          "lcpm"         
[9] "samplenames"  

> library(OmicNavigator)
OmicNavigator R package version: 1.4.2
The app is not installed. Install it with installApp()

> study <- createStudy(name = "vignetteExample", description = "Bioc workflow package RNAseq123")

> head(basal.vs.lp)
      ENTREZID SYMBOL TXCHROM     logFC   AveExpr         t
19216    19216 Ptger1    chr8 -2.401062  4.263219 -8.911887
57811    57811    Rgr   chr14 -5.048202 -1.579505 -7.777238
22068    22068  Trpc6    chr9 -4.202937  3.413562 -7.506933
12767    12767  Cxcr4    chr1 -3.631749  5.049865 -6.255800
16439    16439  Itpr2    chr6 -1.957691  6.412740 -5.533072
20866    20866  Stim1    chr7  1.842699  6.663871  5.377393
           P.Value    adj.P.Val
19216 7.535233e-06 0.0001299437
57811 2.197986e-05 0.0002819392
22068 2.797665e-05 0.0003377516
12767 1.031838e-04 0.0009651739
16439 2.368098e-04 0.0018990476
20866 2.866392e-04 0.0022225231

> basal.vs.lp.on <- basal.vs.lp[, -2:-3]

> basal.vs.ml.on <- basal.vs.ml[, -2:-3]

> head(basal.vs.ml.on)
      ENTREZID     logFC   AveExpr          t      P.Value
22068    22068 -6.361321  3.413562 -12.828451 4.675483e-07
19216    19216 -2.323077  4.263219  -8.459881 1.119083e-05
21390    21390  2.415695 -1.790873   3.339258 4.828374e-03
22065    22065  2.538410 -3.098852   3.192573 6.057918e-03
16440    16440 -1.393191  7.836093  -3.019645 7.878121e-03
57811    57811 -2.656060 -1.579505  -3.024537 7.882325e-03
         adj.P.Val
22068 1.774549e-05
19216 1.549012e-04
21390 2.323210e-02
22065 2.839212e-02
16440 3.577325e-02
57811 3.578257e-02

> results <- list(main = list(basal.vs.lp = basal.vs.lp.on, 
+     basal.vs.ml = basal.vs.ml.on))

> study <- addResults(study, results)

> head(cam.BasalvsLP)
                                           NGenes Direction    PValue
REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS      8      Down 0.2761301
REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION        4      Down 0.6700697
REACTOME_PROSTANOID_LIGAND_RECEPTORS            7      Down 0.6978828
REACTOME_OPSINS                                 5      Down 0.7317891
                                                 FDR
REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS 0.5914291
REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION   0.8722180
REACTOME_PROSTANOID_LIGAND_RECEPTORS       0.8871448
REACTOME_OPSINS                            0.9006782

> cam.BasalvsLP.on <- data.frame(termID = row.names(cam.BasalvsLP), 
+     description = gsub("_", " ", tolower(row.names(cam.BasalvsLP))), 
+     nom .... [TRUNCATED] 

> cam.BasalvsML.on <- data.frame(termID = row.names(cam.BasalvsML), 
+     description = gsub("_", " ", tolower(row.names(cam.BasalvsML))), 
+     nom .... [TRUNCATED] 

> head(cam.BasalvsML.on)
                                      termID
1 REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS
2       REACTOME_PROSTANOID_LIGAND_RECEPTORS
3   REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION
4                            REACTOME_OPSINS
                                 description   nominal  adjusted
1 reactome elevation of cytosolic ca2 levels 0.4119939 0.6745223
2       reactome prostanoid ligand receptors 0.4630303 0.7124122
3   reactome binding and entry of hiv virion 0.6426407 0.8298654
4                            reactome opsins 0.6629803 0.8411875

> enrichments <- list(main = list(c2 = list(basal.vs.lp = cam.BasalvsLP.on, 
+     basal.vs.ml = cam.BasalvsML.on)))

> study <- addEnrichments(study, enrichments)

> models <- list(main = "limma+voom model of RNA-seq experiment of mouse mammary glands")

> study <- addModels(study, models)

> tests <- list(main = list(basal.vs.lp = "Which genes are DE between Basal and LP cells?", 
+     basal.vs.ml = "Which genes are DE between Basal and ..." ... [TRUNCATED] 

> study <- addTests(study, tests)

> basal.vs.lp[1:2, 1:6]
      ENTREZID SYMBOL TXCHROM     logFC   AveExpr         t
19216    19216 Ptger1    chr8 -2.401062  4.263219 -8.911887
57811    57811    Rgr   chr14 -5.048202 -1.579505 -7.777238

> features <- list(main = basal.vs.lp[, 1:3])

> study <- addFeatures(study, features)

> Mm.c2
$REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS
[1] "109305" "16438"  "16439"  "16440"  "18436"  "20866"  "22065" 
[8] "22068"  "26946" 

$REACTOME_PROSTANOID_LIGAND_RECEPTORS
[1] "14764" "19214" "19216" "19217" "19218" "19219" "19220" "19222"
[9] "21390"

$REACTOME_OPSINS
[1] "12057"  "13603"  "14539"  "20132"  "212541" "30044"  "353344"
[8] "57811" 

$REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION
[1] "105675" "12504"  "12767"  "12772"  "12774"  "19034"  "268373"
[8] "382096"


> annotations <- list(c2 = list(terms = Mm.c2, description = "Broad Institute's MSigDB c2 collection", 
+     featureID = "ENTREZID"))

> study <- addAnnotations(study, annotations)

> head(basal.vs.lp.on)
      ENTREZID     logFC   AveExpr         t      P.Value
19216    19216 -2.401062  4.263219 -8.911887 7.535233e-06
57811    57811 -5.048202 -1.579505 -7.777238 2.197986e-05
22068    22068 -4.202937  3.413562 -7.506933 2.797665e-05
12767    12767 -3.631749  5.049865 -6.255800 1.031838e-04
16439    16439 -1.957691  6.412740 -5.533072 2.368098e-04
20866    20866  1.842699  6.663871  5.377393 2.866392e-04
         adj.P.Val
19216 0.0001299437
57811 0.0002819392
22068 0.0003377516
12767 0.0009651739
16439 0.0018990476
20866 0.0022225231

> barcodes <- list(main = list(statistic = "t", logFoldChange = "logFC", 
+     labelStat = "abs(t)", featureDisplay = "SYMBOL"))

> study <- addBarcodes(study, barcodes)

> installStudy(study)
Installing study "vignetteExample" in C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/OmicNavigator/tmp/RtmpodqyWa/file2e883b426435
Exporting study "vignetteExample" 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\RtmpodqyWa/ONstudyvignetteExample
Success!

> head(samplenames)
[1] "10_6_5_11" "9_6_5_11"  "purep53"   "JMS8-2"    "JMS8-3"   
[6] "JMS8-4"   

> table(group)
group
Basal    LP    ML 
    3     3     3 

> table(lane)
lane
L004 L006 L008 
   3    4    2 

> samplesTable <- data.frame(name = samplenames, group, 
+     lane)

> head(samplesTable)
       name group lane
1 10_6_5_11    LP L004
2  9_6_5_11    ML L004
3   purep53 Basal L004
4    JMS8-2 Basal L006
5    JMS8-3    ML L006
6    JMS8-4    LP L006

> samples <- list(main = samplesTable)

> study <- addSamples(study, samples)

> lcpm[1:3, 1:3]
       Samples
Tags    10_6_5_11  9_6_5_11    purep53
  12767  7.552094  5.086721  3.0429773
  13603  2.679699  1.816975  1.5133290
  21390 -1.825453 -2.457757 -0.4876709

> assays <- list(main = as.data.frame(lcpm))

> study <- addAssays(study, assays)

> plottingData <- getPlottingData(study, modelID = "main", 
+     featureID = "12767")

> plottingData
$assays
      10_6_5_11 9_6_5_11  purep53   JMS8-2   JMS8-3   JMS8-4   JMS8-5
12767  7.552094 5.086721 3.042977 4.308618 4.635581 6.410611 2.968442
      JMS9-P7c JMS9-P8c
12767 4.275112 7.189941

$samples
       name group lane
1 10_6_5_11    LP L004
2  9_6_5_11    ML L004
3   purep53 Basal L004
4    JMS8-2 Basal L006
5    JMS8-3    ML L006
6    JMS8-4    LP L006
7    JMS8-5 Basal L006
8  JMS9-P7c    ML L008
9  JMS9-P8c    LP L008

$features
  ENTREZID SYMBOL TXCHROM
1    12767  Cxcr4    chr1


> boxplot(as.numeric(plottingData$assays[1, ]) ~ plottingData$samples$group, 
+     col = c("pink", "purple", "gold"), xlab = "Cell type", ylab = "Gen ..." ... [TRUNCATED] 

> cellTypeBox <- function(plottingData) {
+     boxplot(as.numeric(plottingData$assays[1, ]) ~ plottingData$samples$group, 
+         col = c("pink",  .... [TRUNCATED] 

> library(ggplot2)

  When sourcing 'OmicNavigatorUsersGuide.R':
Error: there is no package called 'ggplot2'
Execution halted

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