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[companion gist to bioc-devel email titled:] regionReport error leads to ggbio & biovizBase issues, confusingly not on all OS though. See https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016532.html
$ R CMD build --keep-empty-dirs --no-resave-data regionReport
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
* checking for file ‘regionReport/DESCRIPTION’ ... OK
* preparing ‘regionReport’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bumphunterExample.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
Please specify either 'title' or 'pagetitle' in the metadata.
Falling back to 'bumphunterExampleOutput.utf8'
--- finished re-building ‘bumphunterExample.Rmd’
--- re-building ‘regionReport.Rmd’ using rmarkdown
Warning in citation("TxDb.Hsapiens.UCSC.hg19.knownGene") :
no date field in DESCRIPTION file of package 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Writing 34 Bibtex entries ... OK
Results written to file 'regionReportRef.bib'
Warning in getIdeoGR(data) :
geom(ideogram) need valid seqlengths information for accurate mapping,
now use reduced information as ideogram...
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Quitting from lines 224-229 (basicExploration.Rmd)
Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
invalid class "ideogramPlot" object: invalid object for slot "height" in class "ideogramPlot": got class "simpleUnit", should be or extend class "numericORunit"
--- failed re-building ‘regionReport.Rmd’
"/usr/local/lib/R/bin/Rscript" -e "library(rmarkdown); render('regionReport.Rmd')"
Attaching package: ‘BiocStyle’
The following objects are masked from ‘package:rmarkdown’:
html_document, md_document, pdf_document
processing file: regionReport.Rmd
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label: installDer (with options)
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$ eval: logi FALSE
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label: citation
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ordinary text without R code
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label: vignetteSetup (with options)
List of 3
$ echo : logi FALSE
$ message: logi FALSE
$ warning: logi FALSE
Writing 34 Bibtex entries ... OK
Results written to file 'regionReportRef.bib'
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label: overviewNotRun (with options)
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$ eval: logi FALSE
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inline R code fragments
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label: loadDerfinder
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$ eval: logi FALSE
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label: runDerfinderReal
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ordinary text without R code
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label: loadLib (with options)
List of 1
$ message: logi FALSE
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted
Killed
> library('regionReport')
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R Under development (unstable) (2020-04-03 r78147)
os Debian GNU/Linux 10 (buster)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2020-04-09
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0)
annotate 1.65.1 2020-01-27 [1] Bioconductor
AnnotationDbi 1.49.1 2020-01-25 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0)
bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.1.0)
Biobase 2.47.3 2020-03-16 [1] Bioconductor
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor
BiocGenerics 0.33.3 2020-03-23 [1] Bioconductor
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0)
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor
BiocStyle 2.15.6 2020-02-01 [1] Bioconductor
biomaRt 2.43.5 2020-04-02 [1] Bioconductor
Biostrings 2.55.7 2020-03-24 [1] Bioconductor
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0)
BSgenome 1.55.4 2020-03-19 [1] Bioconductor
bumphunter 1.29.0 2019-10-29 [1] Bioconductor
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0)
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0)
codetools 0.2-16 2018-12-24 [2] CRAN (R 4.1.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0)
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0)
DEFormats 1.15.0 2019-10-29 [1] Bioconductor
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor
derfinder 1.21.0 2019-10-29 [1] Bioconductor
derfinderHelper 1.21.0 2019-10-29 [1] Bioconductor
DESeq2 1.27.29 2020-03-17 [1] Bioconductor
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0)
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.1.0)
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0)
edgeR 3.29.1 2020-02-26 [1] Bioconductor
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0)
foreach 1.5.0 2020-03-30 [1] CRAN (R 4.1.0)
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0)
genefilter 1.69.0 2019-10-29 [1] Bioconductor
geneplotter 1.65.0 2019-10-29 [1] Bioconductor
generics 0.0.2 2018-11-29 [1] CRAN (R 4.1.0)
GenomeInfoDb 1.23.16 2020-03-27 [1] Bioconductor
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor
GenomicFeatures 1.39.7 2020-03-19 [1] Bioconductor
GenomicFiles 1.23.2 2020-03-23 [1] Bioconductor
GenomicRanges 1.39.3 2020-03-24 [1] Bioconductor
ggplot2 3.3.0 2020-03-05 [1] CRAN (R 4.1.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0)
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0)
IRanges 2.21.8 2020-03-25 [1] Bioconductor
iterators 1.0.12 2019-07-26 [1] CRAN (R 4.1.0)
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0)
jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.1.0)
knitcitations 1.0.10 2019-09-15 [1] CRAN (R 4.1.0)
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0)
knitrBootstrap 1.0.2 2018-05-24 [1] CRAN (R 4.1.0)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0)
limma 3.43.5 2020-03-06 [1] Bioconductor
locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.1.0)
lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.1.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0)
markdown 1.1 2019-08-07 [1] CRAN (R 4.1.0)
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0)
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0)
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0)
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0)
qvalue 2.19.0 2019-10-29 [1] Bioconductor
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0)
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0)
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0)
RefManageR 1.2.12 2019-04-03 [1] CRAN (R 4.1.0)
regionReport * 1.21.0 2019-10-29 [1] Bioconductor
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0)
rmarkdown 2.1 2020-01-20 [1] CRAN (R 4.1.0)
rngtools 1.5 2020-01-23 [1] CRAN (R 4.1.0)
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0)
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0)
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor
S4Vectors 0.25.15 2020-04-04 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0)
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0)
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0)
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0)
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0)
xml2 1.3.0 2020-04-01 [1] CRAN (R 4.1.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.0)
XVector 0.27.2 2020-03-24 [1] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0)
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor
[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
## Works well again, thanks to Michael Lawrence for
## bumping the version in ggbio with
## https://github.com/tengfei/ggbio/commit/6bc94f45e6479b01287e25140821f239f1a7f92d
## which includes two commits that fixed things
## although only one of them was important for
## this issue:
## https://github.com/tengfei/ggbio/commit/930e521bfe0967f5095583c69f655fa571e3fa42
##
$ R CMD build --keep-empty-dirs --no-resave-data regionReport
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
* checking for file ‘regionReport/DESCRIPTION’ ... OK
* preparing ‘regionReport’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘regionReport_1.21.1.tar.gz’
$ R
R Under development (unstable) (2020-04-03 r78147) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
> library('regionReport')
> library('ggbio')
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval,
evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
The following objects are masked from 'package:ggplot2':
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, xlim
> library('sessioninfo')
> options(width = 120)
> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R Under development (unstable) (2020-04-03 r78147)
os Debian GNU/Linux 10 (buster)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2020-04-10
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0)
annotate 1.65.1 2020-01-27 [1] Bioconductor
AnnotationDbi 1.49.1 2020-01-25 [1] Bioconductor
AnnotationFilter 1.11.0 2019-10-29 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0)
bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.1.0)
Biobase 2.47.3 2020-03-16 [1] Bioconductor
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor
BiocGenerics * 0.33.3 2020-03-23 [1] Bioconductor
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0)
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor
BiocStyle 2.15.6 2020-02-01 [1] Bioconductor
biomaRt 2.43.5 2020-04-02 [1] Bioconductor
Biostrings 2.55.7 2020-03-24 [1] Bioconductor
biovizBase 1.35.1 2019-12-03 [1] Bioconductor
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0)
BSgenome 1.55.4 2020-03-19 [1] Bioconductor
bumphunter 1.29.0 2019-10-29 [1] Bioconductor
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0)
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0)
codetools 0.2-16 2018-12-24 [2] CRAN (R 4.1.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0)
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0)
DEFormats 1.15.0 2019-10-29 [1] Bioconductor
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor
derfinder 1.21.0 2019-10-29 [1] Bioconductor
derfinderHelper 1.21.0 2019-10-29 [1] Bioconductor
DESeq2 1.27.29 2020-03-17 [1] Bioconductor
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.1.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0)
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.1.0)
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0)
edgeR 3.29.1 2020-02-26 [1] Bioconductor
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0)
ensembldb 2.11.3 2020-01-22 [1] Bioconductor
evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0)
foreach 1.5.0 2020-03-30 [1] CRAN (R 4.1.0)
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0)
genefilter 1.69.0 2019-10-29 [1] Bioconductor
geneplotter 1.65.0 2019-10-29 [1] Bioconductor
generics 0.0.2 2018-11-29 [1] CRAN (R 4.1.0)
GenomeInfoDb 1.23.16 2020-03-27 [1] Bioconductor
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor
GenomicFeatures 1.39.7 2020-03-19 [1] Bioconductor
GenomicFiles 1.23.2 2020-03-23 [1] Bioconductor
GenomicRanges 1.39.3 2020-03-24 [1] Bioconductor
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.1.0)
ggbio * 1.35.2 2020-04-10 [1] Github (tengfei/ggbio@6bc94f4)
ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.1.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0)
graph 1.65.2 2020-03-17 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0)
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0)
IRanges 2.21.8 2020-03-25 [1] Bioconductor
iterators 1.0.12 2019-07-26 [1] CRAN (R 4.1.0)
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0)
jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.1.0)
knitcitations 1.0.10 2019-09-15 [1] CRAN (R 4.1.0)
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0)
knitrBootstrap 1.0.2 2018-05-24 [1] CRAN (R 4.1.0)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0)
limma 3.43.5 2020-03-06 [1] Bioconductor
locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.1.0)
lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.1.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0)
markdown 1.1 2019-08-07 [1] CRAN (R 4.1.0)
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0)
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0)
OrganismDbi 1.29.1 2020-02-04 [1] Bioconductor
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0)
ProtGenerics 1.19.3 2019-12-25 [1] Bioconductor
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0)
qvalue 2.19.0 2019-10-29 [1] Bioconductor
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0)
RBGL 1.63.1 2019-10-30 [1] Bioconductor
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0)
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0)
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0)
RefManageR 1.2.12 2019-04-03 [1] CRAN (R 4.1.0)
regionReport * 1.21.0 2019-10-29 [1] Bioconductor
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0)
rmarkdown 2.1 2020-01-20 [1] CRAN (R 4.1.0)
rngtools 1.5 2020-01-23 [1] CRAN (R 4.1.0)
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0)
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0)
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor
S4Vectors 0.25.15 2020-04-04 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0)
sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 4.1.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0)
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0)
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0)
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0)
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0)
xml2 1.3.0 2020-04-01 [1] CRAN (R 4.1.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.0)
XVector 0.27.2 2020-03-24 [1] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0)
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor
[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
> library('derfinderPlot')
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
> example('plotCluster')
pltCls> ## Load data
pltCls> library('derfinder')
pltCls> ## Annotate the results with bumphunter::matchGenes()
pltCls> library('bumphunter')
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,
sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
pltCls> 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")'.
pltCls> library('org.Hs.eg.db')
pltCls> genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
pltCls+ annotationPackage = 'org.Hs.eg.db')
Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
Annotating genes.
pltCls> annotation <- matchGenes(x = genomeRegions$regions, subject = genes)
pltCls> ## Make the plot
pltCls> plotCluster(idx=1, regions=genomeRegions$regions, annotation=annotation,
pltCls+ coverageInfo=genomeDataRaw$coverage, groupInfo=genomeInfo$pop,
pltCls+ txdb=TxDb.Hsapiens.UCSC.hg19.knownGene)
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
Constructing graphics...
Error in validObject(.Object) :
invalid class "ideogramPlot" object: invalid object for slot "height" in class "ideogramPlot": got class "simpleUnit", should be or extend class "numericORunit"
In addition: Warning messages:
1: In getIdeoGR(data) :
geom(ideogram) need valid seqlengths information for accurate mapping,
now use reduced information as ideogram...
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead
4: `quo_expr()` is deprecated as of rlang 0.2.0.
Please use `quo_squash()` instead.
This warning is displayed once per session.
Error during wrapup: no slot of name "elementType" for this object of class "GRanges"
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
>
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R Under development (unstable) (2020-04-03 r78147)
os Debian GNU/Linux 10 (buster)
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2020-04-09
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0)
AnnotationDbi * 1.49.1 2020-01-25 [1] Bioconductor
AnnotationFilter 1.11.0 2019-10-29 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0)
Biobase * 2.47.3 2020-03-16 [1] Bioconductor
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor
BiocGenerics * 0.33.3 2020-03-23 [1] Bioconductor
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0)
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor
biomaRt 2.43.5 2020-04-02 [1] Bioconductor
Biostrings 2.55.7 2020-03-24 [1] Bioconductor
biovizBase 1.35.1 2019-12-03 [1] Bioconductor
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0)
BSgenome 1.55.4 2020-03-19 [1] Bioconductor
bumphunter * 1.29.0 2019-10-29 [1] Bioconductor
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0)
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0)
codetools 0.2-16 2018-12-24 [2] CRAN (R 4.1.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0)
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0)
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor
derfinder * 1.21.0 2019-10-29 [1] Bioconductor
derfinderHelper 1.21.0 2019-10-29 [1] Bioconductor
derfinderPlot * 1.21.0 2019-10-29 [1] Bioconductor
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.1.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0)
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.1.0)
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0)
ensembldb 2.11.3 2020-01-22 [1] Bioconductor
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0)
foreach * 1.5.0 2020-03-30 [1] CRAN (R 4.1.0)
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0)
GenomeInfoDb * 1.23.16 2020-03-27 [1] Bioconductor
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor
GenomicFeatures * 1.39.7 2020-03-19 [1] Bioconductor
GenomicFiles 1.23.2 2020-03-23 [1] Bioconductor
GenomicRanges * 1.39.3 2020-03-24 [1] Bioconductor
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.1.0)
ggbio 1.35.1 2020-01-30 [1] Bioconductor
ggplot2 3.3.0 2020-03-05 [1] CRAN (R 4.1.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0)
graph 1.65.2 2020-03-17 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0)
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0)
IRanges * 2.21.8 2020-03-25 [1] Bioconductor
iterators * 1.0.12 2019-07-26 [1] CRAN (R 4.1.0)
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0)
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0)
limma 3.43.5 2020-03-06 [1] Bioconductor
locfit * 1.5-9.4 2020-03-25 [1] CRAN (R 4.1.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0)
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0)
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0)
org.Hs.eg.db * 3.10.0 2020-04-09 [1] Bioconductor
OrganismDbi 1.29.1 2020-02-04 [1] Bioconductor
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0)
ProtGenerics 1.19.3 2019-12-25 [1] Bioconductor
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0)
qvalue 2.19.0 2019-10-29 [1] Bioconductor
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0)
RBGL 1.63.1 2019-10-30 [1] Bioconductor
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0)
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0)
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0)
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0)
rngtools 1.5 2020-01-23 [1] CRAN (R 4.1.0)
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0)
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0)
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor
S4Vectors * 0.25.15 2020-04-04 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0)
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0)
TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2020-04-09 [1] Bioconductor
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0)
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0)
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0)
XVector 0.27.2 2020-03-24 [1] Bioconductor
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor
[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
> library('ggbio')
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply,
parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
The following objects are masked from 'package:ggplot2':
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, xlim
> data(hg19IdeogramCyto, package = 'biovizBase')
> p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21')
Warning messages:
1: In getIdeoGR(data) :
geom(ideogram) need valid seqlengths information for accurate mapping,
now use reduced information as ideogram...
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead
> tracks(p.ideo)
Warning messages:
1: `panel.margin` is deprecated. Please use `panel.spacing` property instead
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead
4: `panel.margin` is deprecated. Please use `panel.spacing` property instead
5: `panel.margin` is deprecated. Please use `panel.spacing` property instead
6: `panel.margin` is deprecated. Please use `panel.spacing` property instead
7: `panel.margin` is deprecated. Please use `panel.spacing` property instead
>
> validObject(hg19IdeogramCyto)
Error in validObject(hg19IdeogramCyto) :
invalid class "GRanges" object: slots in class definition but not in object: "elementType"
>
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R Under development (unstable) (2020-04-03 r78147)
os Debian GNU/Linux 10 (buster)
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2020-04-10
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0)
AnnotationDbi 1.49.1 2020-01-25 [1] Bioconductor
AnnotationFilter 1.11.0 2019-10-29 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0)
Biobase 2.47.3 2020-03-16 [1] Bioconductor
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor
BiocGenerics * 0.33.3 2020-03-23 [1] Bioconductor
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0)
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor
biomaRt 2.43.5 2020-04-02 [1] Bioconductor
Biostrings 2.55.7 2020-03-24 [1] Bioconductor
biovizBase 1.35.1 2019-12-03 [1] Bioconductor
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0)
BSgenome 1.55.4 2020-03-19 [1] Bioconductor
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0)
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0)
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0)
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.1.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0)
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0)
ensembldb 2.11.3 2020-01-22 [1] Bioconductor
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.1.0)
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0)
GenomeInfoDb 1.23.16 2020-03-27 [1] Bioconductor
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor
GenomicFeatures 1.39.7 2020-03-19 [1] Bioconductor
GenomicRanges 1.39.3 2020-03-24 [1] Bioconductor
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.1.0)
ggbio * 1.35.2 2020-04-10 [1] Github (tengfei/ggbio@6bc94f4)
ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.1.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0)
graph 1.65.2 2020-03-17 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0)
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0)
IRanges 2.21.8 2020-03-25 [1] Bioconductor
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0)
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0)
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0)
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0)
OrganismDbi 1.29.1 2020-02-04 [1] Bioconductor
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0)
ProtGenerics 1.19.3 2019-12-25 [1] Bioconductor
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0)
RBGL 1.63.1 2019-10-30 [1] Bioconductor
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0)
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0)
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0)
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0)
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0)
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0)
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor
S4Vectors 0.25.15 2020-04-04 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0)
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0)
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0)
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0)
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0)
XVector 0.27.2 2020-03-24 [1] Bioconductor
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor
[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
>
$ R
R Under development (unstable) (2020-04-03 r78147) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
> library('ggbio')
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
The following objects are masked from 'package:ggplot2':
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
xlim
> data(hg19IdeogramCyto, package = 'biovizBase')
> p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21')
Warning messages:
1: In getIdeoGR(data) :
geom(ideogram) need valid seqlengths information for accurate mapping,
now use reduced information as ideogram...
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead
> tracks(p.ideo)
Error in validObject(.Object) :
invalid class "ideogramPlot" object: invalid object for slot "height" in class "ideogramPlot": got class "simpleUnit", should be or extend class "numericORunit"
>
> validObject(hg19IdeogramCyto)
Error in validObject(hg19IdeogramCyto) :
invalid class "GRanges" object: slots in class definition but not in object: "elementType"
>
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R Under development (unstable) (2020-04-03 r78147)
os Debian GNU/Linux 10 (buster)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2020-04-09
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0)
AnnotationDbi 1.49.1 2020-01-25 [1] Bioconductor
AnnotationFilter 1.11.0 2019-10-29 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0)
Biobase 2.47.3 2020-03-16 [1] Bioconductor
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor
BiocGenerics * 0.33.3 2020-03-23 [1] Bioconductor
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0)
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor
biomaRt 2.43.5 2020-04-02 [1] Bioconductor
Biostrings 2.55.7 2020-03-24 [1] Bioconductor
biovizBase 1.35.1 2019-12-03 [1] Bioconductor
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0)
BSgenome 1.55.4 2020-03-19 [1] Bioconductor
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0)
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0)
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0)
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.1.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0)
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0)
ensembldb 2.11.3 2020-01-22 [1] Bioconductor
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0)
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0)
GenomeInfoDb 1.23.16 2020-03-27 [1] Bioconductor
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor
GenomicFeatures 1.39.7 2020-03-19 [1] Bioconductor
GenomicRanges 1.39.3 2020-03-24 [1] Bioconductor
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.1.0)
ggbio * 1.35.1 2020-01-30 [1] Bioconductor
ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.1.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0)
graph 1.65.2 2020-03-17 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0)
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0)
IRanges 2.21.8 2020-03-25 [1] Bioconductor
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0)
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0)
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0)
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0)
OrganismDbi 1.29.1 2020-02-04 [1] Bioconductor
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0)
ProtGenerics 1.19.3 2019-12-25 [1] Bioconductor
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0)
RBGL 1.63.1 2019-10-30 [1] Bioconductor
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0)
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0)
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0)
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0)
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0)
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0)
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor
S4Vectors 0.25.15 2020-04-04 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0)
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0)
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0)
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0)
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0)
XVector 0.27.2 2020-03-24 [1] Bioconductor
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor
[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
### ~/.Rprofile content that applies here:
### (relates to the warnings shown and the session info)
options(
warnPartialMatchArgs = TRUE,
warnPartialMatchDollar = TRUE,
warnPartialMatchAttr = TRUE
)
if (interactive()) {
suppressMessages(require(devtools))
suppressMessages(require(usethis))
suppressMessages(require(testthat))
suppressMessages(require(colorout))
}
$ R CMD build --keep-empty-dirs --no-resave-data regionReport
Loading required package: colorout
* checking for file ‘regionReport/DESCRIPTION’ ... OK
* preparing ‘regionReport’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘regionReport_1.21.1.tar.gz’
$ R
R version 4.0.0 alpha (2020-04-07 r78176)
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
Natural language support but running in an English locale
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.
Loading required package: colorout
> library('regionReport')
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.0 alpha (2020-04-07 r78176)
os macOS Catalina 10.15.4
system x86_64, darwin17.0
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-04-08
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.0.0)
annotate 1.65.1 2020-04-07 [1] Bioconductor
AnnotationDbi 1.49.1 2020-04-07 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 4.0.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0)
bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.0.0)
Biobase 2.47.3 2020-04-07 [1] Bioconductor
BiocFileCache 1.11.4 2020-04-07 [1] Bioconductor
BiocGenerics 0.33.3 2020-04-07 [1] Bioconductor
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
BiocParallel 1.21.2 2020-04-07 [1] Bioconductor
BiocStyle 2.15.6 2020-04-07 [1] Bioconductor
biomaRt 2.43.5 2020-04-07 [1] Bioconductor
Biostrings 2.55.7 2020-04-07 [1] Bioconductor
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.0.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
BSgenome 1.55.4 2020-04-07 [1] Bioconductor
bumphunter 1.29.0 2020-04-07 [1] Bioconductor
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.0)
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.0)
colorout * 1.2-2 2020-03-16 [1] Github (jalvesaq/colorout@726d681)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.0)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.0.0)
DEFormats 1.15.0 2020-04-07 [1] Bioconductor
DelayedArray 0.13.10 2020-04-07 [1] Bioconductor
derfinder 1.21.0 2020-04-07 [1] Bioconductor
derfinderHelper 1.21.0 2020-04-07 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
DESeq2 1.27.29 2020-04-07 [1] Bioconductor
devtools * 2.2.2 2020-02-17 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.0.0)
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.0.0)
edgeR 3.29.1 2020-04-07 [1] Bioconductor
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
foreach 1.5.0 2020-03-30 [1] CRAN (R 4.0.0)
foreign 0.8-77 2020-03-25 [1] CRAN (R 4.0.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.0.0)
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
genefilter 1.69.0 2020-04-07 [1] Bioconductor
geneplotter 1.65.0 2020-04-07 [1] Bioconductor
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
GenomeInfoDb 1.23.16 2020-04-07 [1] Bioconductor
GenomeInfoDbData 1.2.2 2020-04-08 [1] Bioconductor
GenomicAlignments 1.23.2 2020-04-07 [1] Bioconductor
GenomicFeatures 1.39.7 2020-04-07 [1] Bioconductor
GenomicFiles 1.23.2 2020-04-07 [1] Bioconductor
GenomicRanges 1.39.3 2020-04-07 [1] Bioconductor
ggplot2 3.3.0 2020-03-05 [1] CRAN (R 4.0.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.0.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.0.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0)
IRanges 2.21.8 2020-04-07 [1] Bioconductor
iterators 1.0.12 2019-07-26 [1] CRAN (R 4.0.0)
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.0.0)
jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.0.0)
knitcitations 1.0.10 2019-09-15 [1] CRAN (R 4.0.0)
knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0)
knitrBootstrap 1.0.2 2018-05-24 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.0.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
limma 3.43.5 2020-04-07 [1] Bioconductor
locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.0.0)
lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.0.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
markdown 1.1 2019-08-07 [1] CRAN (R 4.0.0)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
nnet 7.3-13 2020-02-25 [1] CRAN (R 4.0.0)
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.0.0)
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.0.0)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 4.0.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.0)
ps 1.3.2 2020-02-13 [1] CRAN (R 4.0.0)
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.0.0)
qvalue 2.19.0 2020-04-07 [1] Bioconductor
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
Rcpp 1.0.4.6 2020-04-08 [1] Github (RcppCore/Rcpp@a831639)
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.0.0)
RefManageR 1.2.12 2019-04-03 [1] CRAN (R 4.0.0)
regionReport * 1.21.1 2020-04-07 [1] Bioconductor
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.0.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.0.0)
rmarkdown 2.1 2020-01-20 [1] CRAN (R 4.0.0)
rngtools 1.5 2020-01-23 [1] CRAN (R 4.0.0)
rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
Rsamtools 2.3.7 2020-04-07 [1] Bioconductor
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
rtracklayer 1.47.0 2020-04-07 [1] Bioconductor
S4Vectors 0.25.15 2020-04-07 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
SummarizedExperiment 1.17.5 2020-04-07 [1] Bioconductor
survival 3.1-11 2020-03-07 [1] CRAN (R 4.0.0)
testthat * 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.0.0)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.0.0)
usethis * 1.5.1 2019-07-04 [1] CRAN (R 4.0.0)
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.0.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 4.0.0)
xfun 0.12 2020-01-13 [1] CRAN (R 4.0.0)
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.0.0)
xml2 1.3.0 2020-04-01 [1] CRAN (R 4.0.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0)
XVector 0.27.2 2020-04-07 [1] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
zlibbioc 1.33.1 2020-04-07 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
### ~/.Rprofile content that applies here:
### (relates to the warnings shown and the session info)
options(
warnPartialMatchArgs = TRUE,
warnPartialMatchDollar = TRUE,
warnPartialMatchAttr = TRUE
)
if (interactive()) {
suppressMessages(require(devtools))
suppressMessages(require(usethis))
suppressMessages(require(testthat))
suppressMessages(require(colorout))
}
$ R
R version 4.0.0 alpha (2020-04-07 r78176)
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
Natural language support but running in an English locale
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.
Loading required package: colorout
> library('derfinderPlot')
apropos('example')
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
> apropos('example')
[1] "example" "run_examples" "test_example"
[4] "test_examples" "testthat_example" "testthat_examples"
>
> example(
ask= echo= lib.loc= package= run.dontrun= setRNG= verbose=
character.only= give.lines= local= prompt.prefix= run.donttest= topic=
> example('plotCluster')
pltCls> ## Load data
pltCls> library('derfinder')
pltCls> ## Annotate the results with bumphunter::matchGenes()
pltCls> library('bumphunter')
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
pltCls> 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")'.
pltCls> library('org.Hs.eg.db')
pltCls> genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
pltCls+ annotationPackage = 'org.Hs.eg.db')
Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
Annotating genes.
pltCls> annotation <- matchGenes(x = genomeRegions$regions, subject = genes)
pltCls> ## Make the plot
pltCls> plotCluster(idx=1, regions=genomeRegions$regions, annotation=annotation,
pltCls+ coverageInfo=genomeDataRaw$coverage, groupInfo=genomeInfo$pop,
pltCls+ txdb=TxDb.Hsapiens.UCSC.hg19.knownGene)
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
Constructing graphics...
Hit <Return> to see next plot:
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
pltCls> ## Resize the plot window and the labels will look good.
pltCls>
pltCls> ## Not run:
pltCls> ##D ## For a custom plot, check the ggbio and ggplot2 packages.
pltCls> ##D ## Also feel free to look at the code for this function:
pltCls> ##D plotCluster
pltCls> ##D
pltCls> ## End(Not run)
pltCls>
pltCls>
pltCls>
There were 33 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In getIdeoGR(data) :
geom(ideogram) need valid seqlengths information for accurate mapping,
now use reduced information as ideogram...
2: In .local(x, drop.empty.ranges, ...) :
partial argument match of 'ignore' to 'ignore.strand'
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead
4: `panel.margin` is deprecated. Please use `panel.spacing` property instead
5: `quo_expr()` is deprecated as of rlang 0.2.0.
Please use `quo_squash()` instead.
This warning is displayed once per session.
6: `panel.margin` is deprecated. Please use `panel.spacing` property instead
7: `panel.margin` is deprecated. Please use `panel.spacing` property instead
8: `panel.margin` is deprecated. Please use `panel.spacing` property instead
9: `panel.margin` is deprecated. Please use `panel.spacing` property instead
10: `panel.margin` is deprecated. Please use `panel.spacing` property instead
11: `panel.margin` is deprecated. Please use `panel.spacing` property instead
12: `panel.margin` is deprecated. Please use `panel.spacing` property instead
13: `panel.margin` is deprecated. Please use `panel.spacing` property instead
14: `panel.margin` is deprecated. Please use `panel.spacing` property instead
15: Transformation introduced infinite values in continuous y-axis
16: Transformation introduced infinite values in continuous y-axis
17: partial match of 'width' to 'widths'
18: partial match of 'width' to 'widths'
19: partial match of 'width' to 'widths'
20: partial match of 'width' to 'widths'
21: partial match of 'width' to 'widths'
22: partial match of 'width' to 'widths'
23: partial match of 'width' to 'widths'
24: partial match of 'width' to 'widths'
25: partial match of 'width' to 'widths'
26: partial match of 'width' to 'widths'
27: partial match of 'width' to 'widths'
28: partial match of 'width' to 'widths'
29: In rep(label.text.angle, len = length(grobs)) :
partial argument match of 'len' to 'length.out'
30: In rep(label.text.color, len = length(grobs)) :
partial argument match of 'len' to 'length.out'
31: In rep(label.text.cex, len = length(grobs)) :
partial argument match of 'len' to 'length.out'
32: In rep(label.bg.color, len = length(grobs)) :
partial argument match of 'len' to 'length.out'
33: In rep(label.bg.fill, len = length(grobs)) :
partial argument match of 'len' to 'length.out'
>
>
> q()
Save workspace image? [y/n/c]: n
09:31 Code $ R
R version 4.0.0 alpha (2020-04-07 r78176)
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
Natural language support but running in an English locale
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.
Loading required package: colorout
> library('derfinderPlot')
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
> example('plotCluster')
pltCls> ## Load data
pltCls> library('derfinder')
pltCls> ## Annotate the results with bumphunter::matchGenes()
pltCls> library('bumphunter')
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
pltCls> 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")'.
pltCls> library('org.Hs.eg.db')
pltCls> genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
pltCls+ annotationPackage = 'org.Hs.eg.db')
Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
Annotating genes.
pltCls> annotation <- matchGenes(x = genomeRegions$regions, subject = genes)
pltCls> ## Make the plot
pltCls> plotCluster(idx=1, regions=genomeRegions$regions, annotation=annotation,
pltCls+ coverageInfo=genomeDataRaw$coverage, groupInfo=genomeInfo$pop,
pltCls+ txdb=TxDb.Hsapiens.UCSC.hg19.knownGene)
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
Constructing graphics...
Hit <Return> to see next plot:
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
pltCls> ## Resize the plot window and the labels will look good.
pltCls>
pltCls> ## Not run:
pltCls> ##D ## For a custom plot, check the ggbio and ggplot2 packages.
pltCls> ##D ## Also feel free to look at the code for this function:
pltCls> ##D plotCluster
pltCls> ##D
pltCls> ## End(Not run)
pltCls>
pltCls>
pltCls>
There were 33 warnings (use warnings() to see them)
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.0 alpha (2020-04-07 r78176)
os macOS Catalina 10.15.4
system x86_64, darwin17.0
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-04-09
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.0.0)
AnnotationDbi * 1.49.1 2020-04-07 [1] Bioconductor
AnnotationFilter 1.11.0 2020-04-07 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 4.0.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0)
Biobase * 2.47.3 2020-04-07 [1] Bioconductor
BiocFileCache 1.11.4 2020-04-07 [1] Bioconductor
BiocGenerics * 0.33.3 2020-04-07 [1] Bioconductor
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
BiocParallel 1.21.2 2020-04-07 [1] Bioconductor
biomaRt 2.43.5 2020-04-07 [1] Bioconductor
Biostrings 2.55.7 2020-04-07 [1] Bioconductor
biovizBase 1.35.1 2020-04-07 [1] Bioconductor
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.0.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
BSgenome 1.55.4 2020-04-07 [1] Bioconductor
bumphunter * 1.29.0 2020-04-07 [1] Bioconductor
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.0)
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.0)
colorout * 1.2-2 2020-03-16 [1] Github (jalvesaq/colorout@726d681)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.0)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.0.0)
DelayedArray 0.13.10 2020-04-07 [1] Bioconductor
derfinder * 1.21.0 2020-04-07 [1] Bioconductor
derfinderHelper 1.21.0 2020-04-07 [1] Bioconductor
derfinderPlot * 1.21.0 2020-04-07 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools * 2.2.2 2020-02-17 [1] CRAN (R 4.0.0)
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.0.0)
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.0.0)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0)
ensembldb 2.11.3 2020-04-07 [1] Bioconductor
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
foreach * 1.5.0 2020-03-30 [1] CRAN (R 4.0.0)
foreign 0.8-77 2020-03-25 [1] CRAN (R 4.0.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.0.0)
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
GenomeInfoDb * 1.23.16 2020-04-07 [1] Bioconductor
GenomeInfoDbData 1.2.2 2020-04-08 [1] Bioconductor
GenomicAlignments 1.23.2 2020-04-07 [1] Bioconductor
GenomicFeatures * 1.39.7 2020-04-07 [1] Bioconductor
GenomicFiles 1.23.2 2020-04-07 [1] Bioconductor
GenomicRanges * 1.39.3 2020-04-07 [1] Bioconductor
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.0.0)
ggbio 1.35.1 2020-04-07 [1] Bioconductor
ggplot2 3.3.0 2020-03-05 [1] CRAN (R 4.0.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0)
graph 1.65.2 2020-04-07 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.0.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.0.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0)
IRanges * 2.21.8 2020-04-07 [1] Bioconductor
iterators * 1.0.12 2019-07-26 [1] CRAN (R 4.0.0)
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.0.0)
knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0)
labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.0.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
limma 3.43.5 2020-04-07 [1] Bioconductor
locfit * 1.5-9.4 2020-03-25 [1] CRAN (R 4.0.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
nnet 7.3-13 2020-02-25 [1] CRAN (R 4.0.0)
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.0.0)
org.Hs.eg.db * 3.10.0 2020-04-08 [1] Bioconductor
OrganismDbi 1.29.1 2020-04-07 [1] Bioconductor
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.0.0)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 4.0.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.0)
ProtGenerics 1.19.3 2020-04-07 [1] Bioconductor
ps 1.3.2 2020-02-13 [1] CRAN (R 4.0.0)
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.0.0)
qvalue 2.19.0 2020-04-07 [1] Bioconductor
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.0)
RBGL 1.63.1 2020-04-07 [1] Bioconductor
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
Rcpp 1.0.4.6 2020-04-08 [1] Github (RcppCore/Rcpp@a831639)
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.0.0)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.0.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.0.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.0.0)
rngtools 1.5 2020-01-23 [1] CRAN (R 4.0.0)
rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
Rsamtools 2.3.7 2020-04-07 [1] Bioconductor
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
rtracklayer 1.47.0 2020-04-07 [1] Bioconductor
S4Vectors * 0.25.15 2020-04-07 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
SummarizedExperiment 1.17.5 2020-04-07 [1] Bioconductor
survival 3.1-11 2020-03-07 [1] CRAN (R 4.0.0)
testthat * 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.0.0)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.0.0)
TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2020-04-08 [1] Bioconductor
usethis * 1.5.1 2019-07-04 [1] CRAN (R 4.0.0)
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.0.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 4.0.0)
xfun 0.12 2020-01-13 [1] CRAN (R 4.0.0)
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.0.0)
XVector 0.27.2 2020-04-07 [1] Bioconductor
zlibbioc 1.33.1 2020-04-07 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
### ~/.Rprofile content that applies here:
### (relates to the warnings shown and the session info)
options(
warnPartialMatchArgs = TRUE,
warnPartialMatchDollar = TRUE,
warnPartialMatchAttr = TRUE
)
if (interactive()) {
suppressMessages(require(devtools))
suppressMessages(require(usethis))
suppressMessages(require(testthat))
suppressMessages(require(colorout))
}
$ R
R version 4.0.0 alpha (2020-04-07 r78176)
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
Natural language support but running in an English locale
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.
Loading required package: colorout
> library('ggbio')
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
The following objects are masked from 'package:ggplot2':
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
xlim
> data(hg19IdeogramCyto, package = 'biovizBase')
> p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21')
Warning messages:
1: In getIdeoGR(data) :
geom(ideogram) need valid seqlengths information for accurate mapping,
now use reduced information as ideogram...
2: In .local(x, drop.empty.ranges, ...) :
partial argument match of 'ignore' to 'ignore.strand'
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead
4: `panel.margin` is deprecated. Please use `panel.spacing` property instead
> tracks(p.ideo)
There were 11 warnings (use warnings() to see them)
>
> validObject(hg19IdeogramCyto)
Error in validObject(hg19IdeogramCyto) :
invalid class "GRanges" object: slots in class definition but not in object: "elementType"
>
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.0 alpha (2020-04-07 r78176)
os macOS Catalina 10.15.4
system x86_64, darwin17.0
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-04-09
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.0.0)
AnnotationDbi 1.49.1 2020-04-07 [1] Bioconductor
AnnotationFilter 1.11.0 2020-04-07 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 4.0.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0)
Biobase 2.47.3 2020-04-07 [1] Bioconductor
BiocFileCache 1.11.4 2020-04-07 [1] Bioconductor
BiocGenerics * 0.33.3 2020-04-07 [1] Bioconductor
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
BiocParallel 1.21.2 2020-04-07 [1] Bioconductor
biomaRt 2.43.5 2020-04-07 [1] Bioconductor
Biostrings 2.55.7 2020-04-07 [1] Bioconductor
biovizBase 1.35.1 2020-04-07 [1] Bioconductor
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.0.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
BSgenome 1.55.4 2020-04-07 [1] Bioconductor
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.0)
colorout * 1.2-2 2020-03-16 [1] Github (jalvesaq/colorout@726d681)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.0)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.0.0)
DelayedArray 0.13.10 2020-04-07 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools * 2.2.2 2020-02-17 [1] CRAN (R 4.0.0)
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.0.0)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0)
ensembldb 2.11.3 2020-04-07 [1] Bioconductor
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
foreign 0.8-77 2020-03-25 [1] CRAN (R 4.0.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.0.0)
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
GenomeInfoDb 1.23.16 2020-04-07 [1] Bioconductor
GenomeInfoDbData 1.2.2 2020-04-08 [1] Bioconductor
GenomicAlignments 1.23.2 2020-04-07 [1] Bioconductor
GenomicFeatures 1.39.7 2020-04-07 [1] Bioconductor
GenomicRanges 1.39.3 2020-04-07 [1] Bioconductor
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.0.0)
ggbio * 1.35.1 2020-04-07 [1] Bioconductor
ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.0.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0)
graph 1.65.2 2020-04-07 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.0.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.0.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0)
IRanges 2.21.8 2020-04-07 [1] Bioconductor
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.0.0)
knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.0.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
nnet 7.3-13 2020-02-25 [1] CRAN (R 4.0.0)
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.0.0)
OrganismDbi 1.29.1 2020-04-07 [1] Bioconductor
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.0.0)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 4.0.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.0)
ProtGenerics 1.19.3 2020-04-07 [1] Bioconductor
ps 1.3.2 2020-02-13 [1] CRAN (R 4.0.0)
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.0)
RBGL 1.63.1 2020-04-07 [1] Bioconductor
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
Rcpp 1.0.4.6 2020-04-08 [1] Github (RcppCore/Rcpp@a831639)
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.0.0)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.0.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.0.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.0.0)
rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
Rsamtools 2.3.7 2020-04-07 [1] Bioconductor
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
rtracklayer 1.47.0 2020-04-07 [1] Bioconductor
S4Vectors 0.25.15 2020-04-07 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
SummarizedExperiment 1.17.5 2020-04-07 [1] Bioconductor
survival 3.1-11 2020-03-07 [1] CRAN (R 4.0.0)
testthat * 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.0.0)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.0.0)
usethis * 1.5.1 2019-07-04 [1] CRAN (R 4.0.0)
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.0.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 4.0.0)
xfun 0.12 2020-01-13 [1] CRAN (R 4.0.0)
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.0.0)
XVector 0.27.2 2020-04-07 [1] Bioconductor
zlibbioc 1.33.1 2020-04-07 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
library('derfinderPlot')
example('plotCluster')
options(width = 120)
sessioninfo::session_info()
library('ggbio')
data(hg19IdeogramCyto, package = 'biovizBase')
p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21')
tracks(p.ideo)
validObject(hg19IdeogramCyto)
options(width = 120)
sessioninfo::session_info()
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