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BUG (_R_CHECK_LENGTH_1_LOGIC2_): Error in .dpOrDefault(GdObject, ".__hasAnno", FALSE) && !is.null(bartext) && : 'length(x) = 3 > 1' in coercion to 'logical(1)' #23

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HenrikBengtsson opened this issue Feb 16, 2020 · 2 comments
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BUG (_R_CHECK_LENGTH_1_LOGIC2_): Error in .dpOrDefault(GdObject, ".__hasAnno", FALSE) && !is.null(bartext) && : 'length(x) = 3 > 1' in coercion to 'logical(1)' #23

HenrikBengtsson opened this issue Feb 16, 2020 · 2 comments
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@HenrikBengtsson
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HenrikBengtsson commented Feb 16, 2020 •
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R CMD check with (e.g. in ~/.R/check.Renviron):

## Check for bugs like if (c(TRUE, FALSE)). Supported since R (>= 3.4.0)
_R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,verbose

## Check for bugs like c(TRUE, FALSE) && TRUE. Supported since R (>= 3.6.0)
_R_CHECK_LENGTH_1_LOGIC2_=package:_R_CHECK_PACKAGE_NAME_,verbose

produces:

* using log directory ‘/wynton/home/cbi/hb/repositories/matrixStats/revdep/checks/Gviz/new/Gviz.Rcheck’
* using R version 3.6.2 (2019-12-12)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.30.1’
* package encoding: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Gviz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Gviz-Ex.R’ failed
The error most likely occurred in:

> ### Name: GeneRegionTrack-class
> ### Title: GeneRegionTrack class and methods
> ### Aliases: GeneRegionTrack-class GeneRegionTrack
> ###   coerce,GeneRegionTrack,UCSCData-method
> ###   collapseTrack,GeneRegionTrack-method exon exon,GeneRegionTrack-method
> ###   exon<- exon<-,GeneRegionTrack,character-method
> ###   gene,GeneRegionTrack-method gene
> ###   gene<-,GeneRegionTrack,character-method gene<-
> ###   group,GeneRegionTrack-method group<-,GeneRegionTrack,character-method
> ###   identifier,GeneRegionTrack-method
> ###   identifier<-,GeneRegionTrack,character-method
> ###   initialize,GeneRegionTrack-method
> ###   initialize,ReferenceGeneRegionTrack-method
> ###   show,GeneRegionTrack-method show,ReferenceGeneRegionTrack-method
> ###   symbol,GeneRegionTrack-method
> ###   symbol<-,GeneRegionTrack,character-method symbol symbol<-
> ###   transcript,GeneRegionTrack-method
> ###   transcript<-,GeneRegionTrack,character-method transcript transcript<-
> ###   coerce,GRanges,GeneRegionTrack-method
> ###   coerce,GRangesList,GeneRegionTrack-method
> ###   coerce,TxDb,GeneRegionTrack-method
> ###   subset,ReferenceGeneRegionTrack-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> 
> ## The empty object
> GeneRegionTrack()
GeneRegionTrack 'GeneRegionTrack'
| genome: NA
| active chromosome: chrNA
| annotation features: 0
> 
> ## Load some sample data
> data(cyp2b10)
> 
> ## Construct the object
> grTrack <- GeneRegionTrack(start=26682683, end=26711643,
+ rstart=cyp2b10$start, rends=cyp2b10$end, chromosome=7, genome="mm9",
+ transcript=cyp2b10$transcript, gene=cyp2b10$gene, symbol=cyp2b10$symbol,
+ feature=cyp2b10$feature, exon=cyp2b10$exon,
+ name="Cyp2b10", strand=cyp2b10$strand)
> 
> ## Directly from the data.frame
> grTrack <- GeneRegionTrack(cyp2b10)
> 
> ## From a TxDb object
> if(require(GenomicFeatures)){
+ samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite", package="GenomicFeatures")
+ txdb <- loadDb(samplefile)
+ GeneRegionTrack(txdb)
+ GeneRegionTrack(txdb, chromosome="chr6", start=35000000, end=40000000)
+ }
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

GeneRegionTrack 'GeneRegionTrack'
| genome: hg19
| active chromosome: chr6
| annotation features: 71
> 
> 
> 
> ## Don't show: 
> ## For some annoying reason the postscript device does not know about
> ## the sans font
> if(!interactive())
+ {
+ font <- ps.options()$family
+ displayPars(grTrack) <- list(fontfamily=font, fontfamily.title=font)
+ }
> ## End(Don't show)
> 
> ## Plotting
> plotTracks(grTrack)
> 
> ## Track names
> names(grTrack)
[1] "GeneRegionTrack"
> names(grTrack) <- "foo"
> plotTracks(grTrack)
> 
> ## Subsetting and splitting
> subTrack <- subset(grTrack, from=26700000, to=26705000)
> length(subTrack)
[1] 0
> subTrack <- grTrack[transcript(grTrack)=="ENSMUST00000144140"]
> split(grTrack, transcript(grTrack))
$ENSMUST00000005477
GeneRegionTrack 'foo'
| genome: NA
| active chromosome: chr7
| annotation features: 12

$ENSMUST00000072438
GeneRegionTrack 'foo'
| genome: NA
| active chromosome: chr7
| annotation features: 11

$ENSMUST00000144140
GeneRegionTrack 'foo'
| genome: NA
| active chromosome: chr7
| annotation features: 2

> 
> ## Accessors
> start(grTrack)
 [1] 25897620 25897676 25897685 25897685 25911238 25911238 25911554 25911554
 [9] 25913865 25913865 25914748 25914748 25915392 25915392 25916766 25916934
[17] 25916934 25917288 25917288 25917288 25925373 25926068 25926068 25926250
[25] 25926250
> end(grTrack)
 [1] 25897684 25897684 25897855 25897855 25911400 25911400 25911703 25911703
 [9] 25914025 25914025 25914924 25914924 25915533 25915533 25917121 25917121
[17] 25917121 25917429 25917429 25917430 25925399 25926249 25926249 25926559
[25] 25926624
> width(grTrack)
 [1]  65   9 171 171 163 163 150 150 161 161 177 177 142 142 356 188 188 142 142
[20] 143  27 182 182 310 375
> position(grTrack)
 [1] 25897652 25897680 25897770 25897770 25911319 25911319 25911628 25911628
 [9] 25913945 25913945 25914836 25914836 25915462 25915462 25916944 25917028
[17] 25917028 25917358 25917358 25917359 25925386 25926158 25926158 25926404
[25] 25926437
> width(subTrack) <- width(subTrack)+100
> 
> strand(grTrack)
 [1] "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+"
[20] "+" "+" "+" "+" "+" "+"
> strand(subTrack) <- "-"
> 
> chromosome(grTrack)
[1] "chr7"
> chromosome(subTrack) <- "chrX"
> 
> genome(grTrack)
[1] NA
> genome(subTrack) <- "hg19"
> 
> range(grTrack)
IRanges object with 25 ranges and 0 metadata columns:
           start       end     width
       <integer> <integer> <integer>
   [1]  25897620  25897684        65
   [2]  25897676  25897684         9
   [3]  25897685  25897855       171
   [4]  25897685  25897855       171
   [5]  25911238  25911400       163
   ...       ...       ...       ...
  [21]  25925373  25925399        27
  [22]  25926068  25926249       182
  [23]  25926068  25926249       182
  [24]  25926250  25926559       310
  [25]  25926250  25926624       375
> ranges(grTrack)
GRanges object with 25 ranges and 7 metadata columns:
       seqnames            ranges strand |        feature          id
          <Rle>         <IRanges>  <Rle> |       <factor> <character>
   [1]     chr7 25897620-25897684      + |           utr5     unknown
   [2]     chr7 25897676-25897684      + |           utr5     unknown
   [3]     chr7 25897685-25897855      + | protein_coding     unknown
   [4]     chr7 25897685-25897855      + | protein_coding     unknown
   [5]     chr7 25911238-25911400      + | protein_coding     unknown
   ...      ...               ...    ... .            ...         ...
  [21]     chr7 25925373-25925399      + | protein_coding     unknown
  [22]     chr7 25926068-25926249      + | protein_coding     unknown
  [23]     chr7 25926068-25926249      + | protein_coding     unknown
  [24]     chr7 25926250-25926559      + |           utr3     unknown
  [25]     chr7 25926250-25926624      + |           utr3     unknown
                     exon         transcript               gene   symbol
                 <factor>           <factor>           <factor> <factor>
   [1] ENSMUSE00000742021 ENSMUST00000072438 ENSMUSG00000030483  Cyp2b10
   [2] ENSMUSE00000489385 ENSMUST00000005477 ENSMUSG00000030483  Cyp2b10
   [3] ENSMUSE00000742021 ENSMUST00000072438 ENSMUSG00000030483  Cyp2b10
   [4] ENSMUSE00000489385 ENSMUST00000005477 ENSMUSG00000030483  Cyp2b10
   [5] ENSMUSE00000973560 ENSMUST00000072438 ENSMUSG00000030483  Cyp2b10
   ...                ...                ...                ...      ...
  [21] ENSMUSE00000496705 ENSMUST00000005477 ENSMUSG00000030483  Cyp2b10
  [22] ENSMUSE00000498616 ENSMUST00000072438 ENSMUSG00000030483  Cyp2b10
  [23] ENSMUSE00000750625 ENSMUST00000005477 ENSMUSG00000030483  Cyp2b10
  [24] ENSMUSE00000750625 ENSMUST00000005477 ENSMUSG00000030483  Cyp2b10
  [25] ENSMUSE00000498616 ENSMUST00000072438 ENSMUSG00000030483  Cyp2b10
         density
       <numeric>
   [1]         1
   [2]         1
   [3]         1
   [4]         1
   [5]         1
   ...       ...
  [21]         1
  [22]         1
  [23]         1
  [24]         1
  [25]         1
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## Annotation
> identifier(grTrack)
 [1] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
 [8] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
[15] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
[22] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
> identifier(grTrack, "lowest")
 [1] "ENSMUSE00000742021" "ENSMUSE00000489385" "ENSMUSE00000742021"
 [4] "ENSMUSE00000489385" "ENSMUSE00000973560" "ENSMUSE00000973560"
 [7] "ENSMUSE00001043622" "ENSMUSE00001043622" "ENSMUSE00001013991"
[10] "ENSMUSE00001013991" "ENSMUSE00000996531" "ENSMUSE00000996531"
[13] "ENSMUSE00000999790" "ENSMUSE00000999790" "ENSMUSE00000736922"
[16] "ENSMUSE00000963884" "ENSMUSE00000963884" "ENSMUSE00001063063"
[19] "ENSMUSE00001063063" "ENSMUSE00000748299" "ENSMUSE00000496705"
[22] "ENSMUSE00000498616" "ENSMUSE00000750625" "ENSMUSE00000750625"
[25] "ENSMUSE00000498616"
> identifier(subTrack) <- "bar"
> 
> feature(grTrack)
 [1] "utr5"           "utr5"           "protein_coding" "protein_coding"
 [5] "protein_coding" "protein_coding" "protein_coding" "protein_coding"
 [9] "protein_coding" "protein_coding" "protein_coding" "protein_coding"
[13] "protein_coding" "protein_coding" "protein_coding" "protein_coding"
[17] "protein_coding" "protein_coding" "protein_coding" "protein_coding"
[21] "protein_coding" "protein_coding" "protein_coding" "utr3"          
[25] "utr3"          
> feature(subTrack) <- "foo"
> 
> exon(grTrack)
 [1] "ENSMUSE00000742021" "ENSMUSE00000489385" "ENSMUSE00000742021"
 [4] "ENSMUSE00000489385" "ENSMUSE00000973560" "ENSMUSE00000973560"
 [7] "ENSMUSE00001043622" "ENSMUSE00001043622" "ENSMUSE00001013991"
[10] "ENSMUSE00001013991" "ENSMUSE00000996531" "ENSMUSE00000996531"
[13] "ENSMUSE00000999790" "ENSMUSE00000999790" "ENSMUSE00000736922"
[16] "ENSMUSE00000963884" "ENSMUSE00000963884" "ENSMUSE00001063063"
[19] "ENSMUSE00001063063" "ENSMUSE00000748299" "ENSMUSE00000496705"
[22] "ENSMUSE00000498616" "ENSMUSE00000750625" "ENSMUSE00000750625"
[25] "ENSMUSE00000498616"
> exon(subTrack) <- letters[1:2]
> 
> gene(grTrack)
 [1] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
 [4] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
 [7] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[10] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[13] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[16] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[19] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[22] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[25] "ENSMUSG00000030483"
> gene(subTrack) <- "bar"
> 
> symbol(grTrack)
 [1] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
 [8] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
[15] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
[22] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
> symbol(subTrack) <- "foo"
> 
> transcript(grTrack)
 [1] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000072438"
 [4] "ENSMUST00000005477" "ENSMUST00000072438" "ENSMUST00000005477"
 [7] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000072438"
[10] "ENSMUST00000005477" "ENSMUST00000072438" "ENSMUST00000005477"
[13] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000144140"
[16] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000072438"
[19] "ENSMUST00000005477" "ENSMUST00000144140" "ENSMUST00000005477"
[22] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000005477"
[25] "ENSMUST00000072438"
> transcript(subTrack) <- c("foo", "bar")
> chromosome(subTrack) <- "chr7"
> plotTracks(subTrack)
> 
> values(grTrack)
          feature      id               exon         transcript
1            utr5 unknown ENSMUSE00000742021 ENSMUST00000072438
2            utr5 unknown ENSMUSE00000489385 ENSMUST00000005477
3  protein_coding unknown ENSMUSE00000742021 ENSMUST00000072438
4  protein_coding unknown ENSMUSE00000489385 ENSMUST00000005477
5  protein_coding unknown ENSMUSE00000973560 ENSMUST00000072438
6  protein_coding unknown ENSMUSE00000973560 ENSMUST00000005477
7  protein_coding unknown ENSMUSE00001043622 ENSMUST00000072438
8  protein_coding unknown ENSMUSE00001043622 ENSMUST00000005477
9  protein_coding unknown ENSMUSE00001013991 ENSMUST00000072438
10 protein_coding unknown ENSMUSE00001013991 ENSMUST00000005477
11 protein_coding unknown ENSMUSE00000996531 ENSMUST00000072438
12 protein_coding unknown ENSMUSE00000996531 ENSMUST00000005477
13 protein_coding unknown ENSMUSE00000999790 ENSMUST00000072438
14 protein_coding unknown ENSMUSE00000999790 ENSMUST00000005477
15 protein_coding unknown ENSMUSE00000736922 ENSMUST00000144140
16 protein_coding unknown ENSMUSE00000963884 ENSMUST00000072438
17 protein_coding unknown ENSMUSE00000963884 ENSMUST00000005477
18 protein_coding unknown ENSMUSE00001063063 ENSMUST00000072438
19 protein_coding unknown ENSMUSE00001063063 ENSMUST00000005477
20 protein_coding unknown ENSMUSE00000748299 ENSMUST00000144140
21 protein_coding unknown ENSMUSE00000496705 ENSMUST00000005477
22 protein_coding unknown ENSMUSE00000498616 ENSMUST00000072438
23 protein_coding unknown ENSMUSE00000750625 ENSMUST00000005477
24           utr3 unknown ENSMUSE00000750625 ENSMUST00000005477
25           utr3 unknown ENSMUSE00000498616 ENSMUST00000072438
                 gene  symbol density
1  ENSMUSG00000030483 Cyp2b10       1
2  ENSMUSG00000030483 Cyp2b10       1
3  ENSMUSG00000030483 Cyp2b10       1
4  ENSMUSG00000030483 Cyp2b10       1
5  ENSMUSG00000030483 Cyp2b10       1
6  ENSMUSG00000030483 Cyp2b10       1
7  ENSMUSG00000030483 Cyp2b10       1
8  ENSMUSG00000030483 Cyp2b10       1
9  ENSMUSG00000030483 Cyp2b10       1
10 ENSMUSG00000030483 Cyp2b10       1
11 ENSMUSG00000030483 Cyp2b10       1
12 ENSMUSG00000030483 Cyp2b10       1
13 ENSMUSG00000030483 Cyp2b10       1
14 ENSMUSG00000030483 Cyp2b10       1
15 ENSMUSG00000030483 Cyp2b10       1
16 ENSMUSG00000030483 Cyp2b10       1
17 ENSMUSG00000030483 Cyp2b10       1
18 ENSMUSG00000030483 Cyp2b10       1
19 ENSMUSG00000030483 Cyp2b10       1
20 ENSMUSG00000030483 Cyp2b10       1
21 ENSMUSG00000030483 Cyp2b10       1
22 ENSMUSG00000030483 Cyp2b10       1
23 ENSMUSG00000030483 Cyp2b10       1
24 ENSMUSG00000030483 Cyp2b10       1
25 ENSMUSG00000030483 Cyp2b10       1
> 
> ## Grouping
> group(grTrack)
 [1] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000072438"
 [4] "ENSMUST00000005477" "ENSMUST00000072438" "ENSMUST00000005477"
 [7] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000072438"
[10] "ENSMUST00000005477" "ENSMUST00000072438" "ENSMUST00000005477"
[13] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000144140"
[16] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000072438"
[19] "ENSMUST00000005477" "ENSMUST00000144140" "ENSMUST00000005477"
[22] "ENSMUST00000072438" "ENSMUST00000005477" "ENSMUST00000005477"
[25] "ENSMUST00000072438"
> group(subTrack) <- "Group 1"
> transcript(subTrack)
[1] "Group 1" "Group 1"
> plotTracks(subTrack)
> 
> ## Collapsing transcripts
> plotTracks(grTrack, collapseTranscripts=TRUE, showId=TRUE,
+ extend.left=10000, shape="arrow")
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
Gviz
 --- call from context --- 
.local(GdObject, ...)
 --- call from argument --- 
.dpOrDefault(GdObject, ".__hasAnno", FALSE) && !is.null(bartext) && 
    !is.na(bartext)
 --- R stacktrace ---
where 1: .local(GdObject, ...)
where 2: .nextMethod(GdObject = GdObject, ... = ...)
where 3: callNextMethod()
where 4: drawGD(expandedTrackList[[i]], minBase = ranges["from"], maxBase = ranges["to"], 
    subset = FALSE)
where 5: drawGD(expandedTrackList[[i]], minBase = ranges["from"], maxBase = ranges["to"], 
    subset = FALSE)
where 6: plotTracks(grTrack, collapseTranscripts = TRUE, showId = TRUE, 
    extend.left = 10000, shape = "arrow")

 --- value of length: 3 type: logical ---
                    txt    x    y
ENSMUSG00000030483 TRUE TRUE TRUE
 --- function from context --- 
function (GdObject, minBase, maxBase, prepare = FALSE, subset = TRUE, 
    ...) 
{
    debug <- .dpOrDefault(GdObject, "debug", FALSE)
    if ((is.logical(debug) && debug) || debug == "prepare") 
        browser()
    imageMap(GdObject) <- NULL
    if (!length(GdObject)) 
        return(invisible(GdObject))
    if (prepare) {
        GdObject <- callNextMethod(GdObject, ...)
        bins <- stacks(GdObject)
        stacks <- max(bins)
        pushViewport(dataViewport(xData = c(minBase, maxBase), 
            extension = 0, yscale = c(1, stacks + 1), clip = TRUE))
        GdObject <- collapseTrack(GdObject, diff = .pxResolution(coord = "x"), 
            xrange = c(minBase, maxBase))
        popViewport(1)
        return(invisible(GdObject))
    }
    if ((is.logical(debug) && debug) || debug == "draw") 
        browser()
    bins <- stacks(GdObject)
    stacks <- max(bins)
    rev <- .dpOrDefault(GdObject, "reverseStrand", FALSE)
    xscale <- if (!rev) 
        c(minBase, maxBase)
    else c(maxBase, minBase)
    yscale <- if (!.dpOrDefault(GdObject, "reverseStacking", 
        FALSE)) 
        c(1, stacks + 1)
    else c(stacks + 1, 1)
    pushViewport(dataViewport(xscale = xscale, extension = 0, 
        yscale = yscale, clip = TRUE))
    res <- .pxResolution(coord = "x")
    curVp <- vpLocation()
    if (curVp$size["height"]/stacks < .dpOrDefault(GdObject, 
        "min.height", 3)) 
        stop("Too many stacks to draw. Either increase the device size or limit the drawing to a smaller region.")
    if (.dpOrDefault(GdObject, "showOverplotting", FALSE)) {
        dens <- as.numeric(values(GdObject)$density)
        if (length(unique(dens)) != 1) {
            minSat <- max(0.25, 1/max(dens))
            minDens <- min(dens)
            rDens <- diff(range(dens))
            saturation <- minSat + ((dens - minDens)/rDens/(1/(1 - 
                minSat)))
            bc <- unique(.getBiotypeColor(GdObject))
            baseCol <- rgb2hsv(col2rgb(bc))
            desatCols <- unlist(lapply(saturation, function(x) hsv(baseCol[1, 
                ], x, baseCol[3, ])))
            names(desatCols) <- paste(unique(feature(GdObject)), 
                rep(dens, each = length(bc)), sep = "_")
            feature(GdObject) <- paste(feature(GdObject), dens, 
                sep = "_")
            desatCols <- desatCols[unique(names(desatCols))]
            displayPars(GdObject) <- as.list(desatCols)
        }
    }
    box <- .boxes(GdObject, (stacks - bins) + 1)
    barsAndLab <- .barsAndLabels(GdObject)
    bar <- barsAndLab$bars
    bartext <- barsAndLab$labels
    shape <- .dpOrDefault(GdObject, "shape", "arrow")
    col.line <- .dpOrDefault(GdObject, "col.line")[1]
    border <- .dpOrDefault(GdObject, "col")[1]
    if (is.null(border)) 
        border <- ifelse(is(GdObject, "GeneRegionTrack"), NA, 
            "transparent")
    lwd <- .dpOrDefault(GdObject, "lwd", 2)
    lty <- .dpOrDefault(GdObject, "lty", 1)
    alpha <- .dpOrDefault(GdObject, "alpha", 1)
    rotation <- .dpOrDefaultFont(GdObject, "rotation", "item", 
        0)
    rotation.group <- .dpOrDefaultFont(GdObject, "rotation", 
        "group", 0)
    just <- .dpOrDefault(GdObject, "just.group", "left")
    if (nrow(box) > 0) {
        drawLabel <- .dpOrDefault(GdObject, ".__hasAnno", FALSE) && 
            !is.null(bartext) && !is.na(bartext) && nrow(bartext) > 
            0 && stacking(GdObject) != "dense"
        bs <- as.vector((stacks - bins) + 1)
        if (drawLabel && just %in% c("above", "below")) {
            labelHeights <- max(.getStringDims(GdObject, bartext$txt, 
                subtype = "group")$height)
            labelSpace <- as.numeric(convertHeight(unit(2, "points"), 
                "native"))
            avSpace <- (1 - max(box$cy2 - box$cy1))/2
            vadjust <- max(0, (labelHeights + (2 * labelSpace)) - 
                avSpace)
            bh <- 1 - (avSpace * 2)
            bhNew <- bh - vadjust
            sfac <- bhNew/bh
            if (just == "above") {
                bar$y <- bar$y - (vadjust/2)
                box$textY <- box$textY - (vadjust/2)
                bartext$y <- bartext$y - labelSpace
                box$cy1 <- bs + ((box$cy1%%1 - avSpace) * sfac) + 
                  avSpace
                box$cy2 <- bs + ((box$cy2%%1 - avSpace) * sfac) + 
                  avSpace
            }
            else {
                bar$y <- bar$y + (vadjust/2)
                box$textY <- box$textY + (vadjust/2)
                bartext$y <- bartext$y + labelSpace
                box$cy1 <- bs + ((box$cy1%%1 - avSpace) * sfac) + 
                  avSpace + vadjust
                box$cy2 <- bs + ((box$cy2%%1 - avSpace) * sfac) + 
                  avSpace + vadjust
            }
        }
        if (nrow(bar) > 0) 
            .arrowBar(bar$sx1, bar$sx2, y = bar$y, bar$strand, 
                box[, 1:4, drop = FALSE], W = .dpOrDefault(GdObject, 
                  "arrowFeatherWidth", 3), D = .dpOrDefault(GdObject, 
                  "arrowFeatherDistance", 20), col = if (is.null(col.line)) 
                  bar$col
                else rep(col.line, length(bar$col)), lwd = lwd, 
                lty = lty, alpha = alpha, barOnly = (!"smallArrow" %in% 
                  .dpOrDefault(GdObject, "shape", "box") || stacking(GdObject) == 
                  "dense"), diff = res, min.height = .dpOrDefault(GdObject, 
                  "min.height", 3))
        box$col <- if (is.na(border)) 
            box$fill
        else border
        if ("box" %in% shape || ("smallArrow" %in% shape && !("arrow" %in% 
            shape || "ellipse" %in% shape))) {
            .filledBoxes(box, lwd = lwd, lty = lty, alpha = alpha)
        }
        if ("ellipse" %in% shape) {
            ellCoords <- .box2Ellipse(box)
            grid.polygon(x = ellCoords$x1, y = ellCoords$y1, 
                id = ellCoords$id, gp = gpar(col = if (is.na(border)) 
                  box$fill
                else border, fill = box$fill, lwd = lwd, lty = lty, 
                  alpha = alpha), default.units = "native")
        }
        if ("arrow" %in% shape && !"box" %in% shape) {
            .filledArrow(box, lwd = lwd, lty = lty, alpha = alpha, 
                min.width = 4 * res, max.width = .dpOrDefault(GdObject, 
                  "arrowHeadMaxWidth", 40) * res)
        }
        if ("fixedArrow" %in% shape && !"box" %in% shape) {
            .filledArrow(box, lwd = lwd, lty = lty, alpha = alpha, 
                min.width = 4 * res, absoluteWidth = TRUE, W = .dpOrDefault(GdObject, 
                  "arrowHeadWidth", 30) * res)
        }
        if (.dpOrDefault(GdObject, "showFeatureId", FALSE)) 
            grid.text(box$text, box$textX, box$textY, rot = rotation, 
                gp = .fontGp(GdObject, subtype = "item"), default.units = "native", 
                just = c("center", "center"))
        if (drawLabel) {
            grid.text(bartext$txt, bartext$x, bartext$y, rot = rotation.group, 
                gp = .fontGp(GdObject, subtype = "group"), default.units = "native", 
                just = barsAndLab$align)
        }
    }
    popViewport(1)
    im <- if (!is.null(box)) {
        coords <- as.matrix(box[, c("x1", "y1", "x2", "y2"), 
            drop = FALSE])
        restCols <- setdiff(colnames(box), c("x1", "x2", "y1", 
            "y2", "cx1", "cx2", "cy1", "cy2", "textX", "textY"))
        tags <- sapply(restCols, function(x) {
            tmp <- as.character(box[, x])
                box$textY <- box$textY - (vadjust/2)
                bartext$y <- bartext$y - labelSpace
                box$cy1 <- bs + ((box$cy1%%1 - avSpace) * sfac) + 
                  avSpace
                box$cy2 <- bs + ((box$cy2%%1 - avSpace) * sfac) + 
                  avSpace
            }
            else {
                bar$y <- bar$y + (vadjust/2)
                box$textY <- box$textY + (vadjust/2)
                bartext$y <- bartext$y + labelSpace
                box$cy1 <- bs + ((box$cy1%%1 - avSpace) * sfac) + 
                  avSpace + vadjust
                box$cy2 <- bs + ((box$cy2%%1 - avSpace) * sfac) + 
                  avSpace + vadjust
            }
        }
        if (nrow(bar) > 0) 
            .arrowBar(bar$sx1, bar$sx2, y = bar$y, bar$strand, 
                box[, 1:4, drop = FALSE], W = .dpOrDefault(GdObject, 
                  "arrowFeatherWidth", 3), D = .dpOrDefault(GdObject, 
                  "arrowFeatherDistance", 20), col = if (is.null(col.line)) 
                  bar$col
                else rep(col.line, length(bar$col)), lwd = lwd, 
                lty = lty, alpha = alpha, barOnly = (!"smallArrow" %in% 
                  .dpOrDefault(GdObject, "shape", "box") || stacking(GdObject) == 
                  "dense"), diff = res, min.height = .dpOrDefault(GdObject, 
                  "min.height", 3))
        box$col <- if (is.na(border)) 
            box$fill
        else border
        if ("box" %in% shape || ("smallArrow" %in% shape && !("arrow" %in% 
            shape || "ellipse" %in% shape))) {
            .filledBoxes(box, lwd = lwd, lty = lty, alpha = alpha)
        }
        if ("ellipse" %in% shape) {
            ellCoords <- .box2Ellipse(box)
            grid.polygon(x = ellCoords$x1, y = ellCoords$y1, 
                id = ellCoords$id, gp = gpar(col = if (is.na(border)) 
                  box$fill
                else border, fill = box$fill, lwd = lwd, lty = lty, 
                  alpha = alpha), default.units = "native")
        }
        if ("arrow" %in% shape && !"box" %in% shape) {
            .filledArrow(box, lwd = lwd, lty = lty, alpha = alpha, 
                min.width = 4 * res, max.width = .dpOrDefault(GdObject, 
                  "arrowHeadMaxWidth", 40) * res)
        }
        if ("fixedArrow" %in% shape && !"box" %in% shape) {
            .filledArrow(box, lwd = lwd, lty = lty, alpha = alpha, 
                min.width = 4 * res, absoluteWidth = TRUE, W = .dpOrDefault(GdObject, 
                  "arrowHeadWidth", 30) * res)
        }
        if (.dpOrDefault(GdObject, "showFeatureId", FALSE)) 
            grid.text(box$text, box$textX, box$textY, rot = rotation, 
                gp = .fontGp(GdObject, subtype = "item"), default.units = "native", 
                just = c("center", "center"))
        if (drawLabel) {
            grid.text(bartext$txt, bartext$x, bartext$y, rot = rotation.group, 
                gp = .fontGp(GdObject, subtype = "group"), default.units = "native", 
                just = barsAndLab$align)
        }
    }
    popViewport(1)
    im <- if (!is.null(box)) {
        coords <- as.matrix(box[, c("x1", "y1", "x2", "y2"), 
            drop = FALSE])
        restCols <- setdiff(colnames(box), c("x1", "x2", "y1", 
            "y2", "cx1", "cx2", "cy1", "cy2", "textX", "textY"))
        tags <- sapply(restCols, function(x) {
            tmp <- as.character(box[, x])
            names(tmp) <- rownames(coords)
            tmp
        }, simplify = FALSE)
        tags$title <- identifier(GdObject)
        ImageMap(coords = coords, tags = tags)
    }
    else NULL
    imageMap(GdObject) <- im
    return(invisible(GdObject))
}
<environment: namespace:Gviz>
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Error in .dpOrDefault(GdObject, ".__hasAnno", FALSE) && !is.null(bartext) &&  : 
  'length(x) = 3 > 1' in coercion to 'logical(1)'
Calls: plotTracks ... drawGD -> drawGD -> callNextMethod -> .nextMethod -> .local
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... NONE
  ‘Gviz.Rmd’using ‘UTF-8’... OK
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 ERROR

See also

You can read about the type of bug in HenrikBengtsson/Wishlist-for-R#48
@ivanek ivanek added the bug Something isn't working label Feb 17, 2020
@ivanek
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ivanek commented Feb 17, 2020

Hi @HenrikBengtsson,
I committed a fix also to current release (bioc 3.10, Gviz version 1.30.3). I already fixed that before in devel version (bioc 3.11, Gviz version 1.31.4).
Best, Robert

@ivanek ivanek closed this as completed Feb 17, 2020
@HenrikBengtsson
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thxs

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@ivanek @HenrikBengtsson