Jianhong Ou
| Snapshot Date: 2023-03-23 14:00:15 -0400 (Thu, 23 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/ChIPpeakAnno |
| git_branch: devel |
| git_last_commit: 88d5ada |
| git_last_commit_date: 2023-03-14 15:02:32 -0400 (Tue, 14 Mar 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-24 11:06:39 -0400 (Fri, 24 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4546 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4307 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4299 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the ChIPpeakAnno package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 323/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPpeakAnno 3.33.2 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ChIPpeakAnno |
| Version: 3.33.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.33.2.tar.gz |
| StartedAt: 2023-03-23 23:31:41 -0400 (Thu, 23 Mar 2023) |
| EndedAt: 2023-03-23 23:57:18 -0400 (Thu, 23 Mar 2023) |
| EllapsedTime: 1537.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.33.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.33.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.1Mb
sub-directories of 1Mb or more:
data 12.6Mb
extdata 5.2Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ensembldb’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
oligoFrequency : <anonymous>: no visible global function definition for
‘oligonucleotideFrequency’
Undefined global functions or variables:
oligonucleotideFrequency
* checking Rd files ... NOTE
checkRd: (-1) assignChromosomeRegion.Rd:133: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking 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 49.313 0.542 68.164
findMotifsInPromoterSeqs 30.254 0.269 45.332
annotatePeakInBatch 25.322 0.746 35.360
annoPeaks 6.163 0.449 9.533
summarizeOverlapsByBins 5.921 0.629 8.723
addGeneIDs 3.654 0.725 5.932
ExonPlusUtr.human.GRCh37 4.189 0.163 5.747
metagenePlot 3.836 0.052 5.811
findOverlapsOfPeaks 3.856 0.025 5.816
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’ * installing *source* package ‘ChIPpeakAnno’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for ‘annoGR’ with signature ‘"EnsDb"’: no definition for class “EnsDb” in method for ‘toGRanges’ with signature ‘"EnsDb"’: no definition for class “EnsDb” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ChIPpeakAnno)
ChIPpeakAnno.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 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.
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
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
[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: rtracklayer
[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")
[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (6)
[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]
>
> proc.time()
user system elapsed
356.409 5.578 524.828
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0.001 | 0.001 | 0.001 | |
| ExonPlusUtr.human.GRCh37 | 4.189 | 0.163 | 5.747 | |
| HOT.spots | 0.218 | 0.018 | 0.301 | |
| IDRfilter | 0.001 | 0.001 | 0.009 | |
| Peaks.Ste12.Replicate1 | 0.100 | 0.004 | 0.143 | |
| Peaks.Ste12.Replicate2 | 0.022 | 0.002 | 0.035 | |
| Peaks.Ste12.Replicate3 | 0.025 | 0.002 | 0.038 | |
| TSS.human.GRCh37 | 0.257 | 0.023 | 0.377 | |
| TSS.human.GRCh38 | 0.214 | 0.019 | 0.332 | |
| TSS.human.NCBI36 | 0.154 | 0.011 | 0.229 | |
| TSS.mouse.GRCm38 | 0.148 | 0.016 | 0.229 | |
| TSS.mouse.NCBIM37 | 0.135 | 0.012 | 0.193 | |
| TSS.rat.RGSC3.4 | 0.112 | 0.011 | 0.167 | |
| TSS.rat.Rnor_5.0 | 0.100 | 0.010 | 0.158 | |
| TSS.zebrafish.Zv8 | 0.105 | 0.009 | 0.150 | |
| TSS.zebrafish.Zv9 | 0.125 | 0.011 | 0.184 | |
| addAncestors | 2.384 | 0.099 | 3.366 | |
| addGeneIDs | 3.654 | 0.725 | 5.932 | |
| addMetadata | 2.719 | 0.096 | 3.817 | |
| annoGR | 0.000 | 0.000 | 0.006 | |
| annoPeaks | 6.163 | 0.449 | 9.533 | |
| annotatePeakInBatch | 25.322 | 0.746 | 35.360 | |
| annotatedPeak | 0.095 | 0.003 | 0.131 | |
| assignChromosomeRegion | 0.003 | 0.000 | 0.007 | |
| bdp | 0.000 | 0.001 | 0.001 | |
| binOverFeature | 1.588 | 0.026 | 2.168 | |
| binOverGene | 0.001 | 0.000 | 0.005 | |
| binOverRegions | 0.001 | 0.000 | 0.001 | |
| condenseMatrixByColnames | 0.023 | 0.001 | 0.030 | |
| convert2EntrezID | 0.792 | 0.012 | 1.108 | |
| countPatternInSeqs | 0.290 | 0.005 | 0.406 | |
| cumulativePercentage | 0 | 0 | 0 | |
| downstreams | 0.046 | 0.001 | 0.065 | |
| egOrgMap | 0.001 | 0.000 | 0.001 | |
| enrichedGO | 0.003 | 0.003 | 0.010 | |
| enrichmentPlot | 1.091 | 0.013 | 1.475 | |
| estFragmentLength | 0.001 | 0.001 | 0.001 | |
| estLibSize | 0.001 | 0.000 | 0.001 | |
| featureAlignedDistribution | 0.473 | 0.002 | 0.638 | |
| featureAlignedExtendSignal | 0.003 | 0.000 | 0.004 | |
| featureAlignedHeatmap | 0.680 | 0.004 | 0.884 | |
| featureAlignedSignal | 0.397 | 0.044 | 0.602 | |
| findEnhancers | 49.313 | 0.542 | 68.164 | |
| findMotifsInPromoterSeqs | 30.254 | 0.269 | 45.332 | |
| findOverlappingPeaks | 0.002 | 0.000 | 0.002 | |
| findOverlapsOfPeaks | 3.856 | 0.025 | 5.816 | |
| genomicElementDistribution | 0.003 | 0.000 | 0.003 | |
| genomicElementUpSetR | 0.002 | 0.000 | 0.006 | |
| getAllPeakSequence | 1.055 | 0.030 | 1.580 | |
| getAnnotation | 0.002 | 0.000 | 0.008 | |
| getEnrichedGO | 0.021 | 0.004 | 0.038 | |
| getEnrichedPATH | 0.002 | 0.000 | 0.007 | |
| getGO | 0.000 | 0.000 | 0.001 | |
| getGeneSeq | 0.003 | 0.000 | 0.003 | |
| getUniqueGOidCount | 0.001 | 0.000 | 0.002 | |
| getVennCounts | 0.003 | 0.001 | 0.003 | |
| hyperGtest | 0.002 | 0.000 | 0.003 | |
| makeVennDiagram | 0.004 | 0.000 | 0.005 | |
| mergePlusMinusPeaks | 0.001 | 0.000 | 0.001 | |
| metagenePlot | 3.836 | 0.052 | 5.811 | |
| myPeakList | 0.022 | 0.003 | 0.040 | |
| oligoFrequency | 0.441 | 0.025 | 0.687 | |
| oligoSummary | 0.001 | 0.000 | 0.001 | |
| peakPermTest | 0.002 | 0.000 | 0.003 | |
| peaksNearBDP | 0.001 | 0.000 | 0.009 | |
| pie1 | 0.009 | 0.000 | 0.012 | |
| plotBinOverRegions | 0.001 | 0.000 | 0.002 | |
| preparePool | 0.001 | 0.001 | 0.002 | |
| reCenterPeaks | 0.052 | 0.001 | 0.086 | |
| summarizeOverlapsByBins | 5.921 | 0.629 | 8.723 | |
| summarizePatternInPeaks | 0.980 | 0.093 | 1.391 | |
| tileCount | 0.702 | 0.461 | 0.838 | |
| tileGRanges | 0.080 | 0.014 | 0.114 | |
| toGRanges | 0.241 | 0.026 | 0.405 | |
| translatePattern | 0.000 | 0.001 | 0.001 | |
| wgEncodeTfbsV3 | 0.339 | 0.015 | 0.527 | |
| write2FASTA | 0.034 | 0.005 | 0.059 | |
| xget | 0.168 | 0.012 | 0.284 | |