Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:42 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 337/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPpeakAnno 3.38.1 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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. |
Package: ChIPpeakAnno |
Version: 3.38.1 |
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_3.38.1.tar.gz |
StartedAt: 2024-08-12 14:28:21 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 14:41:21 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 779.9 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_3.38.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPpeakAnno’ version ‘3.38.1’ * 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 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) summarizePatternInPeaks.Rd:63: Lost braces; missing escapes or markup? 63 | {shuffle_sequences}} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:69: Lost braces; missing escapes or markup? 69 | \item{"patternNum"}: {number of matched pattern} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:70-71: Lost braces 70 | \item{"totalNumPatternWithSameLen"}: {total number of pattern with the | ^ checkRd: (-1) summarizePatternInPeaks.Rd:72: Lost braces; missing escapes or markup? 72 | \item{"expectedRate"}: {expected rate of pattern for 'binom.test' method} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:73: Lost braces; missing escapes or markup? 73 | \item{"patternRate"}: {real rate of pattern for 'permutation.test' method} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:74: Lost braces; missing escapes or markup? 74 | \item{"pValueBinomTest"}: {p value of bimom test for 'binom.test' method} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:75-76: Lost braces 75 | \item{"cutOffPermutationTest"}: {cut off of permutation test for | ^ checkRd: (-1) summarizePatternInPeaks.Rd:82: Lost braces; missing escapes or markup? 82 | \item{"motifChr"}: {Chromosome of motif} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:83: Lost braces; missing escapes or markup? 83 | \item{"motifStartInChr"}: {motif start position in chromosome} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:84: Lost braces; missing escapes or markup? 84 | \item{"motifEndInChr"}: {motif end position in chromosome} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:85: Lost braces; missing escapes or markup? 85 | \item{"motifName"}: {motif name} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:86: Lost braces; missing escapes or markup? 86 | \item{"motifPattern"}: {motif pattern} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:87: Lost braces; missing escapes or markup? 87 | \item{"motifStartInPeak"}: {motif start position in peak} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:88: Lost braces; missing escapes or markup? 88 | \item{"motifEndInPeak"}: {motif end position in peak} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:89: Lost braces; missing escapes or markup? 89 | \item{"motifFound"}: {specific motif Found in peak} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:90-91: Lost braces 90 | \item{"motifFoundStrand"}: {strand of specific motif Found in peak, "-" | ^ checkRd: (-1) summarizePatternInPeaks.Rd:92: Lost braces; missing escapes or markup? 92 | \item{"peakChr"}: {Chromosome of peak} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:93: Lost braces; missing escapes or markup? 93 | \item{"peakStart"}: {peak start position} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:94: Lost braces; missing escapes or markup? 94 | \item{"peakEnd"}: {peak end position} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:95: Lost braces; missing escapes or markup? 95 | \item{"peakWidth"}: {peak width} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:96: Lost braces; missing escapes or markup? 96 | \item{"peakStrand"}: {peak strand} | ^ * 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 25.829 0.646 27.012 annotatePeakInBatch 15.626 0.690 16.630 findMotifsInPromoterSeqs 15.881 0.311 16.607 summarizeOverlapsByBins 7.479 0.492 7.840 ExonPlusUtr.human.GRCh37 5.098 0.085 5.313 annoPeaks 3.573 0.316 13.721 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-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/4.4-arm64/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 ** 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 version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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, table, tapply, union, 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 [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 [2024-08-12 14:40:49] $cat.cex INFO [2024-08-12 14:40:49] [1] 1 INFO [2024-08-12 14:40:49] INFO [2024-08-12 14:40:49] $cat.col INFO [2024-08-12 14:40:49] [1] "black" INFO [2024-08-12 14:40:49] INFO [2024-08-12 14:40:49] $cat.fontface INFO [2024-08-12 14:40:49] [1] "plain" INFO [2024-08-12 14:40:49] INFO [2024-08-12 14:40:49] $cat.fontfamily INFO [2024-08-12 14:40:49] [1] "serif" INFO [2024-08-12 14:40:49] INFO [2024-08-12 14:40:49] $x INFO [2024-08-12 14:40:49] $x$TF1 INFO [2024-08-12 14:40:49] [1] 3 4 5 INFO [2024-08-12 14:40:49] INFO [2024-08-12 14:40:49] $x$TF2 INFO [2024-08-12 14:40:49] [1] 1 2 3 4 5 INFO [2024-08-12 14:40:49] INFO [2024-08-12 14:40:49] INFO [2024-08-12 14:40:49] $disable.logging INFO [2024-08-12 14:40:49] 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14:40:50] [1] 1 2 3 INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] $disable.logging INFO [2024-08-12 14:40:50] [1] TRUE INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] $filename INFO [2024-08-12 14:40:50] NULL INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] $scaled INFO [2024-08-12 14:40:50] [1] FALSE INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] $euler.d INFO [2024-08-12 14:40:50] [1] FALSE INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] $cat.cex INFO [2024-08-12 14:40:50] [1] 1 INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] $cat.col INFO [2024-08-12 14:40:50] [1] "black" INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] $cat.fontface INFO [2024-08-12 14:40:50] [1] "plain" INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] $cat.fontfamily INFO [2024-08-12 14:40:50] [1] "serif" INFO [2024-08-12 14:40:50] INFO [2024-08-12 14:40:50] $x INFO [2024-08-12 14:40:50] $x$TF1 INFO [2024-08-12 14:40:50] [1] 4 5 6 INFO 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NULL INFO [2024-08-12 14:40:52] [ 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 196.054 5.136 221.950
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
name | user | system | elapsed | |
ChIPpeakAnno-package | 0.000 | 0.000 | 0.001 | |
ExonPlusUtr.human.GRCh37 | 5.098 | 0.085 | 5.313 | |
HOT.spots | 0.109 | 0.007 | 0.120 | |
IDRfilter | 0.000 | 0.000 | 0.001 | |
Peaks.Ste12.Replicate1 | 0.047 | 0.002 | 0.052 | |
Peaks.Ste12.Replicate2 | 0.014 | 0.003 | 0.022 | |
Peaks.Ste12.Replicate3 | 0.010 | 0.003 | 0.020 | |
TSS.human.GRCh37 | 0.198 | 0.014 | 0.222 | |
TSS.human.GRCh38 | 0.166 | 0.009 | 0.208 | |
TSS.human.NCBI36 | 0.131 | 0.007 | 0.166 | |
TSS.mouse.GRCm38 | 0.170 | 0.009 | 0.184 | |
TSS.mouse.NCBIM37 | 0.147 | 0.008 | 0.159 | |
TSS.rat.RGSC3.4 | 0.129 | 0.007 | 0.140 | |
TSS.rat.Rnor_5.0 | 0.109 | 0.007 | 0.121 | |
TSS.zebrafish.Zv8 | 0.118 | 0.007 | 0.130 | |
TSS.zebrafish.Zv9 | 0.145 | 0.008 | 0.167 | |
addAncestors | 1.505 | 0.061 | 1.614 | |
addGeneIDs | 2.588 | 0.668 | 3.365 | |
addMetadata | 1.768 | 0.048 | 1.844 | |
annoGR | 0.000 | 0.000 | 0.001 | |
annoPeaks | 3.573 | 0.316 | 13.721 | |
annotatePeakInBatch | 15.626 | 0.690 | 16.630 | |
annotatedPeak | 0.090 | 0.005 | 0.099 | |
assignChromosomeRegion | 0.002 | 0.000 | 0.002 | |
bdp | 0 | 0 | 0 | |
binOverFeature | 0.943 | 0.039 | 1.000 | |
binOverGene | 0.001 | 0.000 | 0.002 | |
binOverRegions | 0.000 | 0.000 | 0.001 | |
condenseMatrixByColnames | 0.011 | 0.001 | 0.011 | |
convert2EntrezID | 0.530 | 0.008 | 0.557 | |
countPatternInSeqs | 0.197 | 0.006 | 0.208 | |
cumulativePercentage | 0.001 | 0.000 | 0.000 | |
downstreams | 0.025 | 0.001 | 0.025 | |
egOrgMap | 0 | 0 | 0 | |
enrichedGO | 0.002 | 0.002 | 0.006 | |
enrichmentPlot | 0.557 | 0.016 | 0.584 | |
estFragmentLength | 0.000 | 0.000 | 0.001 | |
estLibSize | 0.000 | 0.000 | 0.001 | |
featureAlignedDistribution | 0.250 | 0.004 | 0.259 | |
featureAlignedExtendSignal | 0.003 | 0.000 | 0.002 | |
featureAlignedHeatmap | 0.353 | 0.005 | 0.373 | |
featureAlignedSignal | 0.311 | 0.051 | 0.376 | |
findEnhancers | 25.829 | 0.646 | 27.012 | |
findMotifsInPromoterSeqs | 15.881 | 0.311 | 16.607 | |
findOverlappingPeaks | 0.001 | 0.001 | 0.002 | |
findOverlapsOfPeaks | 2.054 | 0.028 | 2.117 | |
genomicElementDistribution | 0.002 | 0.000 | 0.002 | |
genomicElementUpSetR | 0.001 | 0.000 | 0.001 | |
getAllPeakSequence | 0.665 | 0.030 | 0.725 | |
getAnnotation | 0.001 | 0.000 | 0.002 | |
getEnrichedGO | 0.012 | 0.006 | 0.018 | |
getEnrichedPATH | 0.001 | 0.001 | 0.001 | |
getGO | 0.001 | 0.000 | 0.001 | |
getGeneSeq | 0.002 | 0.001 | 0.003 | |
getUniqueGOidCount | 0.001 | 0.000 | 0.001 | |
getVennCounts | 0.002 | 0.000 | 0.001 | |
hyperGtest | 0.001 | 0.001 | 0.001 | |
makeVennDiagram | 0.003 | 0.001 | 0.004 | |
mergePlusMinusPeaks | 0.001 | 0.000 | 0.001 | |
metagenePlot | 2.522 | 0.083 | 2.667 | |
myPeakList | 0.025 | 0.002 | 0.028 | |
oligoFrequency | 0.120 | 0.007 | 0.129 | |
oligoSummary | 0.001 | 0.000 | 0.001 | |
peakPermTest | 0.002 | 0.001 | 0.003 | |
peaks1 | 0.008 | 0.003 | 0.012 | |
peaks2 | 0.010 | 0.003 | 0.013 | |
peaks3 | 0.007 | 0.003 | 0.010 | |
peaksNearBDP | 0.001 | 0.000 | 0.001 | |
pie1 | 0.006 | 0.003 | 0.009 | |
plotBinOverRegions | 0.001 | 0.000 | 0.001 | |
preparePool | 0.001 | 0.001 | 0.000 | |
reCenterPeaks | 0.027 | 0.000 | 0.028 | |
summarizeOverlapsByBins | 7.479 | 0.492 | 7.840 | |
summarizePatternInPeaks | 1.529 | 0.400 | 2.002 | |
tileCount | 0.363 | 0.368 | 0.485 | |
tileGRanges | 0.041 | 0.016 | 0.060 | |
toGRanges | 0.089 | 0.024 | 0.115 | |
translatePattern | 0.001 | 0.000 | 0.001 | |
wgEncodeTfbsV3 | 0.321 | 0.021 | 0.349 | |
write2FASTA | 0.017 | 0.004 | 0.021 | |
xget | 0.141 | 0.018 | 0.160 | |