##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.21.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ggbio.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* this is package ‘ggbio’ version ‘1.21.5’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ggbio’ can be installed ... WARNING
Found the following significant warnings:
Warning: subclass "ExonrankFilter" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "SymbolFilter" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "OnlyCodingTx" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See ‘/home/biocbuild/bbs-3.4-bioc/meat/ggbio.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion'
'ggplot2:::rename_aes' 'ggplot2:::rescale01'
'ggplot2:::set_last_plot'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
autoplot,matrix: warning in scale_x_continuous(breaks = x, label =
x.lab, expand = c(0, 0)): partial argument match of 'label' to
'labels'
autoplot,matrix: warning in scale_x_continuous(breaks = NULL, label =
NULL, expand = c(0, 0)): partial argument match of 'label' to
'labels'
print,Ideogram: warning in scale_y_continuous(breaks = 5, label =
subchr): partial argument match of 'label' to 'labels'
.combineNames: no visible binding for global variable
'.layout_circle.stats'
Ideogram: no visible global function definition for 'data'
Ideogram: no visible binding for global variable 'ideoCyto'
Ideogram: no visible binding for global variable 'cytobands'
ScalePlot: no visible binding for global variable 'y'
ScalePlot2: no visible binding for global variable 'breaks'
ScalePlot2: no visible binding for global variable 'yend'
ScalePlot2: no visible binding for global variable 'y.text'
getNR: no visible global function definition for 'se'
getNR: no visible global function definition for 'indexProbesProcessed'
getNR: no visible global function definition for 'coefs'
plotInter: no visible binding for global variable 'fe'
plotInter: no visible binding for global variable 'value'
plotInter2: no visible binding for global variable 'fe'
plotInter2: no visible binding for global variable 'value'
plotKaryogram: no visible binding for global variable 'cytobands'
plotStackedOverview: no visible binding for global variable 'cytobands'
scale_x_sequnit: no visible binding for global variable '.x'
autoplot,ExpressionSet: no visible binding for global variable
'variable'
autoplot,RangedSummarizedExperiment: no visible binding for global
variable 'variable'
autoplot,VCF: no visible binding for global variable 'stepping'
autoplot,VCF: no visible binding for global variable 'value'
autoplot,VRanges: no visible binding for global variable 'midpoint'
autoplot,Views: no visible binding for global variable 'x'
autoplot,Views: no visible binding for global variable 'value'
geom_alignment,BamFile: no visible binding for global variable 'fl'
geom_alignment,BamFile: no visible binding for global variable
'stepping'
height,GGbio: no visible binding for global variable 'mt'
height,Tracked: no visible binding for global variable 'mt'
height,gg: no visible binding for global variable 'mt'
layout_karyogram,GRanges: no visible binding for global variable
'gieStain'
layout_karyogram,GRanges: no visible binding for global variable 'x'
layout_karyogram,GRanges: no visible binding for global variable 'y'
layout_karyogram,GRanges: no visible binding for global variable 'xend'
layout_karyogram,GRanges: no visible binding for global variable 'yend'
layout_karyogram,GRanges: no visible binding for global variable 'y2'
layout_karyogram,GRanges: no visible binding for global variable
'yend2'
layout_karyogram,GRanges : <anonymous>: no visible binding for global
variable 'name'
layout_karyogram,GRanges : <anonymous>: no visible binding for global
variable 'gieStain'
plotFragLength,character-GRanges: no visible binding for global
variable '.fragLength'
stat_mismatch,GRanges: no visible binding for global variable 'sts'
stat_mismatch,GRanges: no visible binding for global variable 'eds'
stat_mismatch,GRanges: no visible binding for global variable 'read'
Undefined global functions or variables:
.fragLength .layout_circle.stats .x breaks coefs cytobands data eds
fe fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se
stepping sts value variable x xend y y.text y2 yend yend2
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'PlotList,numeric,missing,ANY'
generic '[' and siglist 'Tracks,numeric,missing,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ggbio-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot
> ### Title: Generic autoplot function
> ### Aliases: autoplot autoplot,GRanges-method autoplot,GRangesList-method
> ### autoplot,IRanges-method autoplot,Seqinfo-method
> ### autoplot,BSgenome-method autoplot,GAlignments-method
> ### autoplot,BamFile-method autoplot,BamFileList-method
> ### autoplot,TxDbOREnsDb-method autoplot,character-method
> ### autoplot,Rle-method autoplot,RleList-method autoplot,matrix-method
> ### autoplot,Views-method autoplot,ExpressionSet-method
> ### autoplot,RangedSummarizedExperiment-method autoplot,VCF-method
> ### autoplot,OrganismDb-method autoplot,VRanges-method
> ### autoplot,TabixFile-method +,Bioplot,Any-method
>
> ### ** Examples
>
> library(ggbio)
>
> set.seed(1)
> N <- 1000
> library(GenomicRanges)
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
> gr <- GRanges(seqnames =
+ sample(c("chr1", "chr2", "chr3"),
+ size = N, replace = TRUE),
+ IRanges(
+ start = sample(1:300, size = N, replace = TRUE),
+ width = sample(70:75, size = N,replace = TRUE)),
+ strand = sample(c("+", "-", "*"), size = N,
+ replace = TRUE),
+ value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
+ sample = sample(c("Normal", "Tumor"),
+ size = N, replace = TRUE),
+ pair = sample(letters, size = N,
+ replace = TRUE))
>
> idx <- sample(1:length(gr), size = 50)
>
>
> ###################################################
> ### code chunk number 3: default
> ###################################################
> autoplot(gr[idx])
>
>
> ###################################################
> ### code chunk number 4: bar-default-pre
> ###################################################
> set.seed(123)
> gr.b <- GRanges(seqnames = "chr1", IRanges(start = seq(1, 100, by = 10),
+ width = sample(4:9, size = 10, replace = TRUE)),
+ score = rnorm(10, 10, 3), value = runif(10, 1, 100))
> gr.b2 <- GRanges(seqnames = "chr2", IRanges(start = seq(1, 100, by = 10),
+ width = sample(4:9, size = 10, replace = TRUE)),
+ score = rnorm(10, 10, 3), value = runif(10, 1, 100))
> gr.b <- c(gr.b, gr.b2)
Warning in .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
> head(gr.b)
GRanges object with 6 ranges and 2 metadata columns:
seqnames ranges strand | score value
<Rle> <IRanges> <Rle> | <numeric> <numeric>
[1] chr1 [ 1, 9] * | 8.31857306034336 89.0643922903109
[2] chr1 [11, 19] * | 9.30946753155016 69.5875372095034
[3] chr1 [21, 28] * | 14.6761249424474 64.4101745630614
[4] chr1 [31, 38] * | 10.2115251742737 99.4327078857459
[5] chr1 [41, 44] * | 10.3878632054828 65.9148741124664
[6] chr1 [51, 56] * | 15.1451949606498 71.144516348606
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
>
>
> ###################################################
> ### code chunk number 5: bar-default
> ###################################################
> p1 <- autoplot(gr.b, geom = "bar")
use score as y by default
> ## use value to fill the bar
> p2 <- autoplot(gr.b, geom = "bar", aes(fill = value))
use score as y by default
> tracks(default = p1, fill = p2)
>
>
> ###################################################
> ### code chunk number 6: autoplot.Rnw:236-237
> ###################################################
> autoplot(gr[idx], geom = "arch", aes(color = value), facets = sample ˜ seqnames)
>
>
> ###################################################
> ### code chunk number 7: gr-group
> ###################################################
> gra <- GRanges("chr1", IRanges(c(1,7,20), end = c(4,9,30)), group = c("a", "a", "b"))
> ## if you desn't specify group, then group based on stepping levels, and gaps are computed without
> ## considering extra group method
> p1 <- autoplot(gra, aes(fill = group), geom = "alignment")
> ## when use group method, gaps only computed for grouped intervals.
> ## default is group.selfish = TRUE, each group keep one row.
> ## in this way, group labels could be shown as y axis.
> p2 <- autoplot(gra, aes(fill = group, group = group), geom = "alignment")
> ## group.selfish = FALSE, save space
> p3 <- autoplot(gra, aes(fill = group, group = group), geom = "alignment", group.selfish = FALSE)
> tracks('non-group' = p1,'group.selfish = TRUE' = p2 , 'group.selfish = FALSE' = p3)
>
>
> ###################################################
> ### code chunk number 8: gr-facet-strand
> ###################################################
> autoplot(gr, stat = "coverage", geom = "area",
+ facets = strand ˜ seqnames, aes(fill = strand))
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
>
>
> ###################################################
> ### code chunk number 9: gr-autoplot-circle
> ###################################################
> autoplot(gr[idx], layout = 'circle')
>
>
> ###################################################
> ### code chunk number 10: gr-circle
> ###################################################
> seqlengths(gr) <- c(400, 500, 700)
> values(gr)$to.gr <- gr[sample(1:length(gr), size = length(gr))]
> idx <- sample(1:length(gr), size = 50)
> gr <- gr[idx]
> ggplot() + layout_circle(gr, geom = "ideo", fill = "gray70", radius = 7, trackWidth = 3) +
+ layout_circle(gr, geom = "bar", radius = 10, trackWidth = 4,
+ aes(fill = score, y = score)) +
+ layout_circle(gr, geom = "point", color = "red", radius = 14,
+ trackWidth = 3, grid = TRUE, aes(y = score)) +
+ layout_circle(gr, geom = "link", linked.to = "to.gr", radius = 6, trackWidth = 1)
>
>
> ###################################################
> ### code chunk number 11: seqinfo-src
> ###################################################
> data(hg19Ideogram, package = "biovizBase")
> sq <- seqinfo(hg19Ideogram)
> sq
Seqinfo object with 93 sequences from hg19 genome:
seqnames seqlengths isCircular genome
chr1 249250621 <NA> hg19
chr1_gl000191_random 106433 <NA> hg19
chr1_gl000192_random 547496 <NA> hg19
chr2 243199373 <NA> hg19
chr3 198022430 <NA> hg19
... ... ... ...
chrUn_gl000246 38154 <NA> hg19
chrUn_gl000247 36422 <NA> hg19
chrUn_gl000248 39786 <NA> hg19
chrUn_gl000249 38502 <NA> hg19
chrM 16571 <NA> hg19
>
>
> ###################################################
> ### code chunk number 12: seqinfo
> ###################################################
> autoplot(sq[paste0("chr", c(1:22, "X"))])
>
>
> ###################################################
> ### code chunk number 13: ir-load
> ###################################################
> set.seed(1)
> N <- 100
> ir <- IRanges(start = sample(1:300, size = N, replace = TRUE),
+ width = sample(70:75, size = N,replace = TRUE))
> ## add meta data
> df <- DataFrame(value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
+ sample = sample(c("Normal", "Tumor"),
+ size = N, replace = TRUE),
+ pair = sample(letters, size = N,
+ replace = TRUE))
> values(ir) <- df
> ir
IRanges object with 100 ranges and 4 metadata columns:
start end width | value score sample
<integer> <integer> <integer> | <numeric> <numeric> <character>
[1] 80 152 73 | 8.138900 112.28206 Tumor
[2] 112 183 72 | 10.126348 150.66620 Tumor
[3] 172 242 71 | 7.267235 147.59765 Normal
[4] 273 347 75 | 10.474086 90.07277 Tumor
[5] 61 133 73 | 8.036246 31.44293 Tumor
... ... ... ... . ... ... ...
[96] 240 312 73 | 6.856047 104.03343 Tumor
[97] 137 206 70 | 14.323473 122.96797 Tumor
[98] 124 198 75 | 6.952458 128.65410 Normal
[99] 244 314 71 | 11.235924 98.48303 Tumor
[100] 182 255 74 | 8.856772 90.82554 Normal
pair
<character>
[1] y
[2] x
[3] t
[4] r
[5] q
... ...
[96] q
[97] g
[98] n
[99] u
[100] j
>
>
> ###################################################
> ### code chunk number 14: ir-exp
> ###################################################
> p1 <- autoplot(ir)
> p2 <- autoplot(ir, aes(fill = pair)) + theme(legend.position = "none")
> p3 <- autoplot(ir, stat = "coverage", geom = "line", facets = sample ˜. )
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
> p4 <- autoplot(ir, stat = "reduce")
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
> tracks(p1, p2, p3, p4)
>
>
> ###################################################
> ### code chunk number 15: grl-simul
> ###################################################
> set.seed(1)
> N <- 100
> ## ======================================================================
> ## simmulated GRanges
> ## ======================================================================
> gr <- GRanges(seqnames =
+ sample(c("chr1", "chr2", "chr3"),
+ size = N, replace = TRUE),
+ IRanges(
+ start = sample(1:300, size = N, replace = TRUE),
+ width = sample(30:40, size = N,replace = TRUE)),
+ strand = sample(c("+", "-", "*"), size = N,
+ replace = TRUE),
+ value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
+ sample = sample(c("Normal", "Tumor"),
+ size = N, replace = TRUE),
+ pair = sample(letters, size = N,
+ replace = TRUE))
>
>
> grl <- split(gr, values(gr)$pair)
>
>
> ###################################################
> ### code chunk number 16: grl-exp
> ###################################################
> ## default gap.geom is 'chevron'
> p1 <- autoplot(grl, group.selfish = TRUE)
> p2 <- autoplot(grl, group.selfish = TRUE, main.geom = "arrowrect", gap.geom = "segment")
> tracks(p1, p2)
>
>
> ###################################################
> ### code chunk number 17: grl-name
> ###################################################
> autoplot(grl, aes(fill = ..grl_name..))
> ## equal to
> ## autoplot(grl, aes(fill = grl_name))
>
>
> ###################################################
> ### code chunk number 18: rle-simul
> ###################################################
> library(IRanges)
> set.seed(1)
> lambda <- c(rep(0.001, 4500), seq(0.001, 10, length = 500),
+ seq(10, 0.001, length = 500))
>
> ## @knitr create
> xVector <- rpois(1e4, lambda)
> xRle <- Rle(xVector)
> xRle
integer-Rle of length 10000 with 823 runs
Lengths: 779 1 208 1 1599 1 883 ... 1 5 2 9 1 4507
Values : 0 1 0 1 0 1 0 ... 1 0 1 0 1 0
>
>
> ###################################################
> ### code chunk number 19: rle-bin
> ###################################################
> p1 <- autoplot(xRle)
Default use binwidth: range/30
> p2 <- autoplot(xRle, nbin = 80)
Default use binwidth: range/80
> p3 <- autoplot(xRle, geom = "heatmap", nbin = 200)
Default use binwidth: range/200
> tracks('nbin = 30' = p1, "nbin = 80" = p2, "nbin = 200(heatmap)" = p3)
>
>
> ###################################################
> ### code chunk number 20: rle-id
> ###################################################
> p1 <- autoplot(xRle, stat = "identity")
> p2 <- autoplot(xRle, stat = "identity", geom = "point", color = "red")
> tracks('line' = p1, "point" = p2)
>
>
> ###################################################
> ### code chunk number 21: rle-slice
> ###################################################
> p1 <- autoplot(xRle, type = "viewMaxs", stat = "slice", lower = 5)
> p2 <- autoplot(xRle, type = "viewMaxs", stat = "slice", lower = 5, geom = "heatmap")
> tracks('bar' = p1, "heatmap" = p2)
>
>
> ###################################################
> ### code chunk number 22: rlel-simul
> ###################################################
> xRleList <- RleList(xRle, 2L * xRle)
> xRleList
RleList of length 2
[[1]]
integer-Rle of length 10000 with 823 runs
Lengths: 779 1 208 1 1599 1 883 ... 1 5 2 9 1 4507
Values : 0 1 0 1 0 1 0 ... 1 0 1 0 1 0
[[2]]
integer-Rle of length 10000 with 823 runs
Lengths: 779 1 208 1 1599 1 883 ... 1 5 2 9 1 4507
Values : 0 2 0 2 0 2 0 ... 2 0 2 0 2 0
>
>
> ###################################################
> ### code chunk number 23: rlel-bin
> ###################################################
> p1 <- autoplot(xRleList)
Default use binwidth: range/30
> p2 <- autoplot(xRleList, nbin = 80)
Default use binwidth: range/80
> p3 <- autoplot(xRleList, geom = "heatmap", nbin = 200)
Default use binwidth: range/200
> tracks('nbin = 30' = p1, "nbin = 80" = p2, "nbin = 200(heatmap)" = p3)
>
>
> ###################################################
> ### code chunk number 24: rlel-id
> ###################################################
> p1 <- autoplot(xRleList, stat = "identity")
> p2 <- autoplot(xRleList, stat = "identity", geom = "point", color = "red")
> tracks('line' = p1, "point" = p2)
>
>
> ###################################################
> ### code chunk number 25: rlel-slice
> ###################################################
> p1 <- autoplot(xRleList, type = "viewMaxs", stat = "slice", lower = 5)
> p2 <- autoplot(xRleList, type = "viewMaxs", stat = "slice", lower = 5, geom = "heatmap")
> tracks('bar' = p1, "heatmap" = p2)
>
>
> ###################################################
> ### code chunk number 26: txdb
> ###################################################
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
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")'.
> data(genesymbol, package = "biovizBase")
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>
>
> ###################################################
> ### code chunk number 27: txdb-visual
> ###################################################
> p1 <- autoplot(txdb, which = genesymbol["ALDOA"], names.expr = "tx_name:::gene_id")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
"gap" not in any of the valid gene feature terms "cds", "exon", "utr"
Constructing graphics...
> p2 <- autoplot(txdb, which = genesymbol["ALDOA"], stat = "reduce", color = "brown",
+ fill = "brown")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
"gap" not in any of the valid gene feature terms "cds", "exon", "utr"
Constructing graphics...
reduce alignemnts...
> tracks(full = p1, reduce = p2, heights = c(5, 1)) + ylab("")
>
>
> ###################################################
> ### EnsDb
> ###################################################
> ## Fetching gene models from an EnsDb object.
> library(EnsDb.Hsapiens.v75)
Loading required package: ensembldb
Error : .onLoad failed in loadNamespace() for 'EnsDb.Hsapiens.v75', details:
call: validityMethod(object)
error: could not find function "dbHasRequiredTables"
Error: package or namespace load failed for 'EnsDb.Hsapiens.v75'
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/ggbio.Rcheck/00check.log’
for details.