Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:37 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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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 308/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPpeakAnno 3.33.1 (landing page) Jianhong Ou
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: ChIPpeakAnno |
Version: 3.33.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ChIPpeakAnno_3.33.1.tar.gz |
StartedAt: 2023-02-27 23:14:50 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 23:35:59 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 1269.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPpeakAnno.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ChIPpeakAnno_3.33.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPpeakAnno’ version ‘3.33.1’ * 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 30.173 0.644 30.819 findMotifsInPromoterSeqs 18.888 0.293 19.186 annotatePeakInBatch 15.942 1.103 17.288 summarizeOverlapsByBins 5.622 0.501 5.787 annoPeaks 4.015 0.345 10.159 * 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 ... ‘ChIPpeakAnno.Rmd’ using ‘UTF-8’... OK ‘FAQs.Rmd’ using ‘UTF-8’... OK ‘pipeline.Rmd’ using ‘UTF-8’... OK ‘quickStart.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’ for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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 229.387 4.696 248.920
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
name | user | system | elapsed | |
ChIPpeakAnno-package | 0 | 0 | 0 | |
ExonPlusUtr.human.GRCh37 | 3.391 | 0.168 | 3.559 | |
HOT.spots | 0.118 | 0.008 | 0.126 | |
IDRfilter | 0.001 | 0.000 | 0.001 | |
Peaks.Ste12.Replicate1 | 0.066 | 0.000 | 0.066 | |
Peaks.Ste12.Replicate2 | 0.016 | 0.000 | 0.016 | |
Peaks.Ste12.Replicate3 | 0.013 | 0.004 | 0.017 | |
TSS.human.GRCh37 | 0.203 | 0.012 | 0.216 | |
TSS.human.GRCh38 | 0.136 | 0.004 | 0.140 | |
TSS.human.NCBI36 | 0.094 | 0.012 | 0.106 | |
TSS.mouse.GRCm38 | 0.089 | 0.012 | 0.101 | |
TSS.mouse.NCBIM37 | 0.075 | 0.016 | 0.091 | |
TSS.rat.RGSC3.4 | 0.065 | 0.012 | 0.077 | |
TSS.rat.Rnor_5.0 | 0.057 | 0.012 | 0.069 | |
TSS.zebrafish.Zv8 | 0.068 | 0.004 | 0.072 | |
TSS.zebrafish.Zv9 | 0.088 | 0.000 | 0.088 | |
addAncestors | 1.407 | 0.028 | 1.435 | |
addGeneIDs | 2.160 | 0.252 | 2.414 | |
addMetadata | 1.756 | 0.150 | 1.906 | |
annoGR | 0 | 0 | 0 | |
annoPeaks | 4.015 | 0.345 | 10.159 | |
annotatePeakInBatch | 15.942 | 1.103 | 17.288 | |
annotatedPeak | 0.058 | 0.001 | 0.058 | |
assignChromosomeRegion | 0.001 | 0.000 | 0.001 | |
bdp | 0.001 | 0.000 | 0.000 | |
binOverFeature | 0.953 | 0.059 | 1.014 | |
binOverGene | 0 | 0 | 0 | |
binOverRegions | 0 | 0 | 0 | |
condenseMatrixByColnames | 0.014 | 0.000 | 0.014 | |
convert2EntrezID | 0.461 | 0.016 | 0.477 | |
countPatternInSeqs | 0.182 | 0.012 | 0.195 | |
cumulativePercentage | 0 | 0 | 0 | |
downstreams | 0.031 | 0.000 | 0.030 | |
egOrgMap | 0.001 | 0.000 | 0.001 | |
enrichedGO | 0.002 | 0.000 | 0.003 | |
enrichmentPlot | 0.651 | 0.008 | 0.660 | |
estFragmentLength | 0 | 0 | 0 | |
estLibSize | 0 | 0 | 0 | |
featureAlignedDistribution | 0.283 | 0.016 | 0.300 | |
featureAlignedExtendSignal | 0.001 | 0.000 | 0.001 | |
featureAlignedHeatmap | 0.416 | 0.000 | 0.416 | |
featureAlignedSignal | 0.224 | 0.032 | 0.257 | |
findEnhancers | 30.173 | 0.644 | 30.819 | |
findMotifsInPromoterSeqs | 18.888 | 0.293 | 19.186 | |
findOverlappingPeaks | 0.001 | 0.000 | 0.001 | |
findOverlapsOfPeaks | 2.419 | 0.052 | 2.472 | |
genomicElementDistribution | 0.001 | 0.000 | 0.001 | |
genomicElementUpSetR | 0.000 | 0.000 | 0.001 | |
getAllPeakSequence | 0.591 | 0.051 | 0.646 | |
getAnnotation | 0.001 | 0.000 | 0.001 | |
getEnrichedGO | 0.008 | 0.004 | 0.011 | |
getEnrichedPATH | 0.001 | 0.000 | 0.000 | |
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 | 0.003 | 0.000 | 0.002 | |
mergePlusMinusPeaks | 0.000 | 0.000 | 0.001 | |
metagenePlot | 2.652 | 0.032 | 2.688 | |
myPeakList | 0.010 | 0.004 | 0.014 | |
oligoFrequency | 0.212 | 0.000 | 0.212 | |
oligoSummary | 0.000 | 0.000 | 0.001 | |
peakPermTest | 0.001 | 0.000 | 0.001 | |
peaksNearBDP | 0.001 | 0.000 | 0.001 | |
pie1 | 0.007 | 0.000 | 0.007 | |
plotBinOverRegions | 0.001 | 0.000 | 0.001 | |
preparePool | 0 | 0 | 0 | |
reCenterPeaks | 0.034 | 0.000 | 0.034 | |
summarizeOverlapsByBins | 5.622 | 0.501 | 5.787 | |
summarizePatternInPeaks | 0.639 | 0.083 | 0.723 | |
tileCount | 0.117 | 0.091 | 0.395 | |
tileGRanges | 0.312 | 0.263 | 0.062 | |
toGRanges | 0.136 | 0.016 | 0.152 | |
translatePattern | 0.001 | 0.000 | 0.001 | |
wgEncodeTfbsV3 | 0.191 | 0.016 | 0.206 | |
write2FASTA | 0.023 | 0.000 | 0.023 | |
xget | 0.110 | 0.024 | 0.134 | |