Jianhong Ou
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/ChIPpeakAnno |
| git_branch: devel |
| git_last_commit: cfbf335 |
| git_last_commit_date: 2025-01-03 09:42:19 -0500 (Fri, 03 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:46 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 | ||||
| Package 331/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPpeakAnno 3.41.1 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the ChIPpeakAnno package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPpeakAnno.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ChIPpeakAnno |
| Version: 3.41.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChIPpeakAnno_3.41.1.tar.gz |
| StartedAt: 2025-01-04 04:47:34 -0000 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 05:01:18 -0000 (Sat, 04 Jan 2025) |
| EllapsedTime: 823.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChIPpeakAnno_3.41.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.41.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘ChIPpeakAnno’ can be installed ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/ChIPpeakAnno.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 21.1Mb
sub-directories of 1Mb or more:
R 1.0Mb
data 12.6Mb
extdata 7.2Mb
* 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 code 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findEnhancers 34.485 0.750 35.323
findMotifsInPromoterSeqs 19.962 0.248 20.257
annotatePeakInBatch 16.906 0.977 17.934
summarizeOverlapsByBins 6.450 0.514 6.649
annoPeaks 3.861 0.227 10.447
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘ChIPpeakAnno’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (ChIPpeakAnno)
ChIPpeakAnno.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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.
> require("ChIPpeakAnno") || stop("unable to load Package:ChIPpeakAnno")
Loading required package: ChIPpeakAnno
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Warning: program compiled against libxml 212 using older 211
[1] TRUE
> require("BSgenome.Drerio.UCSC.danRer7") || stop("unable to load Package:BSgenome.Drerio.UCSC.danRer7")
Loading required package: BSgenome.Drerio.UCSC.danRer7
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: BiocIO
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:BiocIO':
FileForFormat
[1] TRUE
> require("BSgenome.Hsapiens.UCSC.hg19") || stop("unable to load Package:BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome.Hsapiens.UCSC.hg19
[1] TRUE
> require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db")
Loading required package: org.Hs.eg.db
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")'.
[1] TRUE
> require("org.Ce.eg.db") || stop("unable to load Package:org.Ce.eg.db")
Loading required package: org.Ce.eg.db
[1] TRUE
> require("BSgenome.Celegans.UCSC.ce10") || stop("unable to load Package:BSgenome.Celegans.UCSC.ce10")
Loading required package: BSgenome.Celegans.UCSC.ce10
[1] TRUE
> require("EnsDb.Hsapiens.v79") || stop("unable to load Package:EnsDb.Hsapiens.v79")
Loading required package: EnsDb.Hsapiens.v79
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
The following object is masked from 'package:stats':
filter
[1] TRUE
> require("TxDb.Hsapiens.UCSC.hg38.knownGene") || stop("unable to load TxDb.Hsapiens.UCSC.hg38.knownGene")
Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene
[1] TRUE
> require("biomaRt") || stop("unable to load biomaRt")
Loading required package: biomaRt
[1] TRUE
> require("reactome.db") || stop("unable to load reactome.db")
Loading required package: reactome.db
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
Attaching package: 'testthat'
The following object is masked from 'package:AnnotationFilter':
not
[1] TRUE
> test_check("ChIPpeakAnno")
INFO [2025-01-04 05:00:55] $cat.cex
INFO [2025-01-04 05:00:55] [1] 1
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $cat.col
INFO [2025-01-04 05:00:55] [1] "black"
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $cat.fontface
INFO [2025-01-04 05:00:55] [1] "plain"
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $cat.fontfamily
INFO [2025-01-04 05:00:55] [1] "serif"
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $x
INFO [2025-01-04 05:00:55] $x$TF1
INFO [2025-01-04 05:00:55] [1] 3 4 5
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $x$TF2
INFO [2025-01-04 05:00:55] [1] 1 2 3 4 5
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $disable.logging
INFO [2025-01-04 05:00:55] [1] TRUE
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $filename
INFO [2025-01-04 05:00:55] NULL
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $cat.cex
INFO [2025-01-04 05:00:55] [1] 1
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $cat.col
INFO [2025-01-04 05:00:55] [1] "black"
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $cat.fontface
INFO [2025-01-04 05:00:55] [1] "plain"
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $cat.fontfamily
INFO [2025-01-04 05:00:55] [1] "serif"
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $x
INFO [2025-01-04 05:00:55] $x$TF1
INFO [2025-01-04 05:00:55] [1] 3 4 5
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $x$TF2
INFO [2025-01-04 05:00:55] [1] 1 2 4 5
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $x$TF3
INFO [2025-01-04 05:00:55] [1] 3 4 5
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $x$TF4
INFO [2025-01-04 05:00:55] [1] 1 2 4 5
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $disable.logging
INFO [2025-01-04 05:00:55] [1] TRUE
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:55] $filename
INFO [2025-01-04 05:00:55] NULL
INFO [2025-01-04 05:00:55]
INFO [2025-01-04 05:00:56] $scaled
INFO [2025-01-04 05:00:56] [1] FALSE
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $euler.d
INFO [2025-01-04 05:00:56] [1] FALSE
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $cat.cex
INFO [2025-01-04 05:00:56] [1] 1
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $cat.col
INFO [2025-01-04 05:00:56] [1] "black"
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $cat.fontface
INFO [2025-01-04 05:00:56] [1] "plain"
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $cat.fontfamily
INFO [2025-01-04 05:00:56] [1] "serif"
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $x
INFO [2025-01-04 05:00:56] $x$TF1
INFO [2025-01-04 05:00:56] [1] 1 2 3
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $x$TF2
INFO [2025-01-04 05:00:56] [1] 1 2 3
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $disable.logging
INFO [2025-01-04 05:00:56] [1] TRUE
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $filename
INFO [2025-01-04 05:00:56] NULL
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $scaled
INFO [2025-01-04 05:00:56] [1] FALSE
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $euler.d
INFO [2025-01-04 05:00:56] [1] FALSE
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $cat.cex
INFO [2025-01-04 05:00:56] [1] 1
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $cat.col
INFO [2025-01-04 05:00:56] [1] "black"
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $cat.fontface
INFO [2025-01-04 05:00:56] [1] "plain"
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $cat.fontfamily
INFO [2025-01-04 05:00:56] [1] "serif"
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $x
INFO [2025-01-04 05:00:56] $x$TF1
INFO [2025-01-04 05:00:56] [1] 4 5 6
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $x$TF2
INFO [2025-01-04 05:00:56] [1] 1 2 3
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $disable.logging
INFO [2025-01-04 05:00:56] [1] TRUE
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:56] $filename
INFO [2025-01-04 05:00:56] NULL
INFO [2025-01-04 05:00:56]
INFO [2025-01-04 05:00:57] $scaled
INFO [2025-01-04 05:00:57] [1] FALSE
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $euler.d
INFO [2025-01-04 05:00:57] [1] FALSE
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.cex
INFO [2025-01-04 05:00:57] [1] 1
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.col
INFO [2025-01-04 05:00:57] [1] "black"
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.fontface
INFO [2025-01-04 05:00:57] [1] "plain"
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.fontfamily
INFO [2025-01-04 05:00:57] [1] "serif"
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $x
INFO [2025-01-04 05:00:57] $x$TF1
INFO [2025-01-04 05:00:57] [1] 4 5 6
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $x$TF2
INFO [2025-01-04 05:00:57] [1] 1 2 3
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $disable.logging
INFO [2025-01-04 05:00:57] [1] TRUE
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $filename
INFO [2025-01-04 05:00:57] NULL
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $scaled
INFO [2025-01-04 05:00:57] [1] FALSE
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $euler.d
INFO [2025-01-04 05:00:57] [1] FALSE
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.cex
INFO [2025-01-04 05:00:57] [1] 1
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.col
INFO [2025-01-04 05:00:57] [1] "black"
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.fontface
INFO [2025-01-04 05:00:57] [1] "plain"
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.fontfamily
INFO [2025-01-04 05:00:57] [1] "serif"
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $x
INFO [2025-01-04 05:00:57] $x$TF1
INFO [2025-01-04 05:00:57] [1] 4 5 6
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $x$TF2
INFO [2025-01-04 05:00:57] [1] 1 2 3
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $x$TF3
INFO [2025-01-04 05:00:57] [1] 2 3 6
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $disable.logging
INFO [2025-01-04 05:00:57] [1] TRUE
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $filename
INFO [2025-01-04 05:00:57] NULL
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $scaled
INFO [2025-01-04 05:00:57] [1] FALSE
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $euler.d
INFO [2025-01-04 05:00:57] [1] FALSE
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.cex
INFO [2025-01-04 05:00:57] [1] 1
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.col
INFO [2025-01-04 05:00:57] [1] "black"
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.fontface
INFO [2025-01-04 05:00:57] [1] "plain"
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $cat.fontfamily
INFO [2025-01-04 05:00:57] [1] "serif"
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $x
INFO [2025-01-04 05:00:57] $x$TF1
INFO [2025-01-04 05:00:57] [1] 3 4 5
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $x$TF2
INFO [2025-01-04 05:00:57] [1] 1 2 5
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $x$TF3
INFO [2025-01-04 05:00:57] [1] 1 2 5
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $disable.logging
INFO [2025-01-04 05:00:57] [1] TRUE
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:57] $filename
INFO [2025-01-04 05:00:57] NULL
INFO [2025-01-04 05:00:57]
INFO [2025-01-04 05:00:58] $scaled
INFO [2025-01-04 05:00:58] [1] FALSE
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $euler.d
INFO [2025-01-04 05:00:58] [1] FALSE
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $cat.cex
INFO [2025-01-04 05:00:58] [1] 1
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $cat.col
INFO [2025-01-04 05:00:58] [1] "black"
INFO [2025-01-04 05:00:58]
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INFO [2025-01-04 05:00:58] [1] "plain"
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $cat.fontfamily
INFO [2025-01-04 05:00:58] [1] "serif"
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $x
INFO [2025-01-04 05:00:58] $x$TF1
INFO [2025-01-04 05:00:58] [1] 3 4 5
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $x$TF2
INFO [2025-01-04 05:00:58] [1] 1 2 5
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $x$TF3
INFO [2025-01-04 05:00:58] [1] 1 2 5
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $x$TF4
INFO [2025-01-04 05:00:58] [1] 1 2 5
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $disable.logging
INFO [2025-01-04 05:00:58] [1] TRUE
INFO [2025-01-04 05:00:58]
INFO [2025-01-04 05:00:58] $filename
INFO [2025-01-04 05:00:58] NULL
INFO [2025-01-04 05:00:58]
[ FAIL 0 | WARN 3 | SKIP 6 | PASS 320 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• empty test (6): 'test_binOverGene.R:1:1', 'test_binOverRegions.R:1:1',
'test_enrichmentPlot.R:1:1', 'test_getAnnotation.R:1:1',
'test_reCenterPeaks.R:1:1', 'test_write2FASTA.R:1:1'
[ FAIL 0 | WARN 3 | SKIP 6 | PASS 320 ]
>
> proc.time()
user system elapsed
234.081 2.667 253.714
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0.001 | 0.000 | 0.000 | |
| ExonPlusUtr.human.GRCh37 | 3.943 | 0.040 | 3.993 | |
| HOT.spots | 0.114 | 0.011 | 0.126 | |
| IDRfilter | 0.000 | 0.000 | 0.001 | |
| Peaks.Ste12.Replicate1 | 0.067 | 0.000 | 0.067 | |
| Peaks.Ste12.Replicate2 | 0.017 | 0.000 | 0.017 | |
| Peaks.Ste12.Replicate3 | 0.016 | 0.000 | 0.016 | |
| TSS.human.GRCh37 | 0.199 | 0.000 | 0.200 | |
| TSS.human.GRCh38 | 0.14 | 0.00 | 0.14 | |
| TSS.human.NCBI36 | 0.101 | 0.003 | 0.106 | |
| TSS.mouse.GRCm38 | 0.096 | 0.004 | 0.101 | |
| TSS.mouse.NCBIM37 | 0.082 | 0.008 | 0.090 | |
| TSS.rat.RGSC3.4 | 0.070 | 0.004 | 0.074 | |
| TSS.rat.Rnor_5.0 | 0.066 | 0.000 | 0.066 | |
| TSS.zebrafish.Zv8 | 0.066 | 0.004 | 0.070 | |
| TSS.zebrafish.Zv9 | 0.085 | 0.000 | 0.084 | |
| addAncestors | 1.239 | 0.028 | 1.272 | |
| addGeneIDs | 1.022 | 0.028 | 1.057 | |
| addMetadata | 1.385 | 0.076 | 1.480 | |
| annoGR | 0.001 | 0.000 | 0.000 | |
| annoPeaks | 3.861 | 0.227 | 10.447 | |
| annotatePeakInBatch | 16.906 | 0.977 | 17.934 | |
| annotatedPeak | 0.056 | 0.004 | 0.061 | |
| assignChromosomeRegion | 0.001 | 0.000 | 0.001 | |
| bdp | 0 | 0 | 0 | |
| binOverFeature | 0.939 | 0.026 | 0.970 | |
| binOverGene | 0.000 | 0.000 | 0.001 | |
| binOverRegions | 0.000 | 0.000 | 0.001 | |
| condenseMatrixByColnames | 0.098 | 0.004 | 0.103 | |
| convert2EntrezID | 0.425 | 0.020 | 0.446 | |
| countPatternInSeqs | 0.216 | 0.004 | 0.221 | |
| cumulativePercentage | 0 | 0 | 0 | |
| downstreams | 0.031 | 0.004 | 0.034 | |
| egOrgMap | 0.001 | 0.000 | 0.000 | |
| enrichedGO | 0.000 | 0.003 | 0.002 | |
| enrichmentPlot | 0.676 | 0.025 | 0.703 | |
| estFragmentLength | 0.000 | 0.000 | 0.001 | |
| estLibSize | 0.001 | 0.000 | 0.001 | |
| featureAlignedDistribution | 0.299 | 0.000 | 0.299 | |
| featureAlignedExtendSignal | 0.001 | 0.000 | 0.001 | |
| featureAlignedHeatmap | 0.422 | 0.012 | 0.436 | |
| featureAlignedSignal | 0.250 | 0.016 | 0.267 | |
| findEnhancers | 34.485 | 0.750 | 35.323 | |
| findMotifsInPromoterSeqs | 19.962 | 0.248 | 20.257 | |
| findOverlappingPeaks | 0.001 | 0.000 | 0.001 | |
| findOverlapsOfPeaks | 2.423 | 0.040 | 2.471 | |
| genomicElementDistribution | 0.001 | 0.000 | 0.001 | |
| genomicElementUpSetR | 0.001 | 0.000 | 0.000 | |
| getAllPeakSequence | 0.657 | 0.016 | 0.684 | |
| getAnnotation | 0.001 | 0.000 | 0.001 | |
| getEnrichedGO | 0.011 | 0.000 | 0.011 | |
| getEnrichedPATH | 0.000 | 0.000 | 0.001 | |
| getGO | 0 | 0 | 0 | |
| getGeneSeq | 0.001 | 0.000 | 0.001 | |
| getUniqueGOidCount | 0.001 | 0.000 | 0.001 | |
| getVennCounts | 0.001 | 0.000 | 0.001 | |
| hyperGtest | 0.001 | 0.000 | 0.001 | |
| makeVennDiagram | 0.002 | 0.000 | 0.002 | |
| mergePlusMinusPeaks | 0.000 | 0.000 | 0.001 | |
| metagenePlot | 2.775 | 0.036 | 2.824 | |
| myPeakList | 0.016 | 0.000 | 0.016 | |
| oligoFrequency | 0.126 | 0.000 | 0.126 | |
| oligoSummary | 0 | 0 | 0 | |
| peakPermTest | 0.002 | 0.000 | 0.002 | |
| peaks1 | 0.010 | 0.000 | 0.011 | |
| peaks2 | 0.010 | 0.000 | 0.011 | |
| peaks3 | 0.010 | 0.000 | 0.011 | |
| peaksNearBDP | 0.001 | 0.000 | 0.001 | |
| pie1 | 0.007 | 0.000 | 0.006 | |
| plotBinOverRegions | 0.001 | 0.000 | 0.000 | |
| preparePool | 0.001 | 0.000 | 0.000 | |
| reCenterPeaks | 0.036 | 0.000 | 0.036 | |
| summarizeOverlapsByBins | 6.450 | 0.514 | 6.649 | |
| summarizePatternInPeaks | 1.898 | 0.355 | 2.262 | |
| tileCount | 0.265 | 0.218 | 0.452 | |
| tileGRanges | 0.162 | 0.191 | 0.055 | |
| toGRanges | 0.139 | 0.024 | 0.164 | |
| translatePattern | 0.001 | 0.000 | 0.001 | |
| wgEncodeTfbsV3 | 0.196 | 0.039 | 0.237 | |
| write2FASTA | 0.018 | 0.019 | 0.038 | |
| xget | 0.174 | 0.040 | 0.214 | |