* 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
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