| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:07 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the Gviz package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Gviz.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 869/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Gviz 1.43.0 (landing page) Robert Ivanek
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: Gviz |
| Version: 1.43.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Gviz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Gviz_1.43.0.tar.gz |
| StartedAt: 2023-02-07 04:02:12 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 04:21:45 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 1173.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: Gviz.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Gviz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Gviz_1.43.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Gviz.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.43.0’
* 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 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 ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
R 1.7Mb
extdata 2.5Mb
* 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 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 ... WARNING
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* checking Rd metadata ... OK
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* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Gviz-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AnnotationTrack-class
> ### Title: AnnotationTrack class and methods
> ### Aliases: AnnotationTrack-class initialize,AnnotationTrack-method
> ### ReferenceAnnotationTrack-class
> ### initialize,ReferenceAnnotationTrack-method AnnotationTrack
> ### DetailsAnnotationTrack-class DetailsAnnotationTrack
> ### initialize,DetailsAnnotationTrack-method group,AnnotationTrack-method
> ### group<-,AnnotationTrack,character-method
> ### identifier,AnnotationTrack-method
> ### identifier<-,AnnotationTrack,character-method
> ### setStacks,AnnotationTrack-method
> ### consolidateTrack,AnnotationTrack-method
> ### collapseTrack,AnnotationTrack-method subset,AnnotationTrack-method
> ### subset,ReferenceAnnotationTrack-method drawGD,AnnotationTrack-method
> ### drawGD,DetailsAnnotationTrack-method show,AnnotationTrack-method
> ### show,ReferenceAnnotationTrack-method
> ### Keywords: internal
>
> ### ** Examples
>
> ## An empty object
> AnnotationTrack()
AnnotationTrack 'AnnotationTrack'
| genome: NA
| active chromosome: chrNA
| annotation features: 0
>
> ## Construct from individual arguments
> st <- c(2000000, 2070000, 2100000, 2160000)
> ed <- c(2050000, 2130000, 2150000, 2170000)
> str <- c("-", "+", "-", "-")
> gr <- c("Group1", "Group2", "Group1", "Group3")
>
> annTrack <- AnnotationTrack(
+ start = st, end = ed, strand = str, chromosome = 7,
+ genome = "hg19", feature = "test", group = gr,
+ id = paste("annTrack item", 1:4),
+ name = "generic annotation", stacking = "squish"
+ )
>
> ## Or from a data.frame
> df <- data.frame(
+ start = st, end = ed, strand = str, id = paste("annTrack item", 1:4),
+ feature = "test", group = gr
+ )
> annTrack <- AnnotationTrack(
+ range = df, genome = "hg19", chromosome = 7,
+ name = "generic annotation", stacking = "squish"
+ )
>
> ## Or from a GRanges object
> gr <- GRanges(
+ seqnames = "chr7", range = IRanges(start = df$start, end = df$end),
+ strand = str
+ )
> genome(gr) <- "hg19"
> mcols(gr) <- df[, -(1:3)]
> annTrack <- AnnotationTrack(
+ range = gr, name = "generic annotation",
+ stacking = "squish"
+ )
>
> ## Finally from a GRangesList
> grl <- split(gr, values(gr)$group)
> AnnotationTrack(grl)
AnnotationTrack 'AnnotationTrack'
| genome: hg19
| active chromosome: chr7
| annotation features: 4
> ## Don't show:
> ## For some annoying reason the postscript device does not know about
> ## the sans font
> if (!interactive()) {
+ font <- ps.options()$family
+ displayPars(annTrack) <- list(fontfamily = font, fontfamily.title = font)
+ }
> ## End(Don't show)
>
> ## Plotting
> plotTracks(annTrack)
>
> ## Track names
> names(annTrack)
[1] "generic annotation"
> names(annTrack) <- "foo"
> plotTracks(annTrack)
>
> ## Subsetting and splitting
> subTrack <- subset(annTrack, to = 2155000)
> length(subTrack)
[1] 3
> subTrack[1:2]
AnnotationTrack 'foo'
| genome: hg19
| active chromosome: chr7
| annotation features: 2
> split(annTrack, c(1, 2, 1, 2))
$`1`
AnnotationTrack 'foo'
| genome: hg19
| active chromosome: chr7
| annotation features: 2
$`2`
AnnotationTrack 'foo'
| genome: hg19
| active chromosome: chr7
| annotation features: 2
>
> ## Accessors
> start(annTrack)
[1] 2000000 2070000 2100000 2160000
> end(annTrack)
[1] 2050000 2130000 2150000 2170000
> width(annTrack)
[1] 50001 60001 50001 10001
> position(annTrack)
[1] 2025000 2100000 2125000 2165000
> width(subTrack) <- width(subTrack) + 1000
>
> strand(annTrack)
[1] "-" "+" "-" "-"
> strand(subTrack) <- "-"
>
> chromosome(annTrack)
[1] "chr7"
> chromosome(subTrack) <- "chrX"
>
> genome(annTrack)
chr7
"hg19"
> genome(subTrack) <- "mm9"
>
> range(annTrack)
IRanges object with 4 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 2000000 2050000 50001
[2] 2070000 2130000 60001
[3] 2100000 2150000 50001
[4] 2160000 2170000 10001
> ranges(annTrack)
GRanges object with 4 ranges and 4 metadata columns:
seqnames ranges strand | feature group id
<Rle> <IRanges> <Rle> | <character> <character> <character>
[1] chr7 2000000-2050000 - | test Group1 annTrack item 1
[2] chr7 2070000-2130000 + | test Group2 annTrack item 2
[3] chr7 2100000-2150000 - | test Group1 annTrack item 3
[4] chr7 2160000-2170000 - | test Group3 annTrack item 4
density
<numeric>
[1] 1
[2] 1
[3] 1
[4] 1
-------
seqinfo: 1 sequence from hg19 genome; no seqlengths
>
> ## Annotation
> identifier(annTrack)
[1] "Group1" "Group2" "Group1" "Group3"
> identifier(annTrack, "lowest")
[1] "annTrack item 1" "annTrack item 2" "annTrack item 3" "annTrack item 4"
> identifier(subTrack) <- "bar"
>
> feature(annTrack)
[1] "test" "test" "test" "test"
> feature(subTrack) <- "foo"
>
> values(annTrack)
feature group id density
1 test Group1 annTrack item 1 1
2 test Group2 annTrack item 2 1
3 test Group1 annTrack item 3 1
4 test Group3 annTrack item 4 1
>
> ## Grouping
> group(annTrack)
[1] "Group1" "Group2" "Group1" "Group3"
> group(subTrack) <- "Group 1"
> chromosome(subTrack) <- "chr7"
> plotTracks(subTrack)
>
> ## Stacking
> stacking(annTrack)
[1] "squish"
> stacking(annTrack) <- "dense"
> plotTracks(annTrack)
>
> ## coercion
> as(annTrack, "data.frame")
X.seqnames X.start X.end X.width X.strand X.feature X.group X.id
1 chr7 2000000 2050000 50001 - test Group1 annTrack item 1
2 chr7 2070000 2130000 60001 + test Group2 annTrack item 2
3 chr7 2100000 2150000 50001 - test Group1 annTrack item 3
4 chr7 2160000 2170000 10001 - test Group3 annTrack item 4
X.density feature group id density
1 1 test Group1 annTrack item 1 1
2 1 test Group2 annTrack item 2 1
3 1 test Group1 annTrack item 3 1
4 1 test Group3 annTrack item 4 1
> as(annTrack, "UCSCData")
UCSC track 'foo'
UCSCData object with 4 ranges and 3 metadata columns:
seqnames ranges strand | id name
<Rle> <IRanges> <Rle> | <character> <character>
[1] chr7 2000000-2050000 - | annTrack_item_1 annTrack_item_1
[2] chr7 2070000-2130000 + | annTrack_item_2 annTrack_item_2
[3] chr7 2100000-2150000 - | annTrack_item_3 annTrack_item_3
[4] chr7 2160000-2170000 - | annTrack_item_4 annTrack_item_4
itemRgb
<character>
[1] lightblue
[2] lightblue
[3] lightblue
[4] lightblue
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> ## HTML image map
> coords(annTrack)
NULL
> tags(annTrack)
NULL
> annTrack <- plotTracks(annTrack)$foo
> coords(annTrack)
x1 y1 x2 y2
annTrack item 1 37.95742 67.5 166.9058 436.5
annTrack item 3 295.85410 67.5 424.8024 436.5
annTrack item 2 218.48510 67.5 373.2231 436.5
annTrack item 4 450.59211 67.5 476.3818 436.5
> tags(annTrack)
$fill
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"lightblue" "lightblue" "lightblue" "lightblue"
$strand
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"-" "-" "+" "-"
$text
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"annTrack item 1" "annTrack item 3" "annTrack item 2" "annTrack item 4"
$start
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"2000000" "2100000" "2070000" "2160000"
$end
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"2050000" "2150000" "2130000" "2170000"
$feature
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"test" "test" "test" "test"
$group
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"Group1" "Group1" "Group2" "Group3"
$id
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"annTrack item 1" "annTrack item 3" "annTrack item 2" "annTrack item 4"
$density
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"1" "1" "1" "1"
$exonId
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"annTrack item 1" "annTrack item 3" "annTrack item 2" "annTrack item 4"
$origExonId
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"annTrack item 1" "annTrack item 3" "annTrack item 2" "annTrack item 4"
$col
annTrack item 1 annTrack item 3 annTrack item 2 annTrack item 4
"darkgray" "darkgray" "darkgray" "darkgray"
$title
[1] "Group1" "Group1" "Group2" "Group3"
>
> ## DetailsAnnotationTrack
> library(lattice) # need to use grid grapics
>
> ## generate two random distributions per row (probe/feature)
> ## the difference between the distributions increases from probe 1 to 4
> m <- matrix(c(rgamma(400, 1)), ncol = 100)
> m[, 51:100] <- m[, 51:100] + 0:3
> ## rownames must be accessible by AnnotationTrack element identifier
> rownames(m) <- identifier(annTrack, "lowest")
>
> ## create a lattice density plot for the values (signals) of the two groups
> ## as the chart must be placed into a pre-set grid view port we have to use
> ## print without calling plot.new! Note, use a common prefix for all lattice.
> ## Avoid wasting space by removing y-axis decorations.
>
> ## Note, in this example 'm' will be found in the environment the 'details'
> ## function is defined in. To avoid overwriting 'm' you should use a closure
> ## or environment to access 'm'.
> details <- function(identifier, ...) {
+ d <- data.frame(signal = m[identifier, ], group = rep(c("grp1", "grp2"), each = 50))
+ print(densityplot(~signal,
+ group = group, data = d, main = identifier,
+ scales = list(draw = FALSE, x = list(draw = TRUE)), ylab = "", xlab = "",
+ ), newpage = FALSE, prefix = "plot")
+ }
>
> deTrack <- AnnotationTrack(
+ range = gr, genome = "hg19", chromosome = 7,
+ name = "generic annotation with details per entry", stacking = "squish",
+ fun = details, details.ratio = 1
+ )
>
> plotTracks(deTrack)
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘Gviz.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Gviz.Rmd’ using rmarkdown
Quitting from lines 1808-1820 (Gviz.Rmd)
Error: processing vignette 'Gviz.Rmd' failed with diagnostics:
no slot of name "httr_config" for this object of class "Mart"
--- failed re-building ‘Gviz.Rmd’
SUMMARY: processing the following file failed:
‘Gviz.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 3 ERRORs, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/Gviz.Rcheck/00check.log’
for details.
Gviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Gviz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘Gviz’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Gviz)
Gviz.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Gviz)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
>
> test_check("Gviz")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Killed
Gviz.Rcheck/Gviz-Ex.timings
| name | user | system | elapsed | |
| AlignmentsTrack-class | 14.502 | 1.798 | 24.552 | |