Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:36:55 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 328/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPpeakAnno 3.34.1 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
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: 3.34.1 |
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_3.34.1.tar.gz |
StartedAt: 2023-10-15 23:43:15 -0400 (Sun, 15 Oct 2023) |
EndedAt: 2023-10-16 00:08:38 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 1522.5 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_3.34.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ChIPpeakAnno.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPpeakAnno’ version ‘3.34.1’ * 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 ... OK * 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 56.637 1.036 74.044 findMotifsInPromoterSeqs 30.906 0.513 44.068 annotatePeakInBatch 25.888 1.058 37.680 annoPeaks 6.624 0.690 10.967 summarizeOverlapsByBins 5.884 0.642 8.618 addGeneIDs 3.732 1.190 6.497 ExonPlusUtr.human.GRCh37 4.061 0.172 5.375 findOverlapsOfPeaks 4.054 0.063 6.222 metagenePlot 3.896 0.096 5.767 * 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: 3 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-x86_64/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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 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: 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") INFO [2023-10-16 00:07:55] $cat.cex INFO [2023-10-16 00:07:55] [1] 1 INFO [2023-10-16 00:07:55] INFO [2023-10-16 00:07:55] $cat.col INFO [2023-10-16 00:07:55] [1] "black" INFO [2023-10-16 00:07:55] INFO [2023-10-16 00:07:55] $cat.fontface INFO [2023-10-16 00:07:55] [1] "plain" INFO [2023-10-16 00:07:55] INFO [2023-10-16 00:07:55] $cat.fontfamily INFO [2023-10-16 00:07:55] [1] "serif" INFO [2023-10-16 00:07:55] INFO [2023-10-16 00:07:55] $x INFO [2023-10-16 00:07:55] $x$TF1 INFO [2023-10-16 00:07:55] [1] 3 4 5 INFO [2023-10-16 00:07:55] INFO [2023-10-16 00:07:55] $x$TF2 INFO [2023-10-16 00:07:55] [1] 1 2 3 4 5 INFO [2023-10-16 00:07:55] INFO [2023-10-16 00:07:55] INFO [2023-10-16 00:07:55] $filename INFO [2023-10-16 00:07:55] NULL 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TRUE INFO [2023-10-16 00:08:02] [ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ] ══ 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 4 | SKIP 6 | PASS 316 ] > > proc.time() user system elapsed 362.595 8.712 526.916
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
name | user | system | elapsed | |
ChIPpeakAnno-package | 0.001 | 0.001 | 0.002 | |
ExonPlusUtr.human.GRCh37 | 4.061 | 0.172 | 5.375 | |
HOT.spots | 0.206 | 0.021 | 0.270 | |
IDRfilter | 0.002 | 0.001 | 0.006 | |
Peaks.Ste12.Replicate1 | 0.101 | 0.005 | 0.135 | |
Peaks.Ste12.Replicate2 | 0.026 | 0.004 | 0.035 | |
Peaks.Ste12.Replicate3 | 0.025 | 0.004 | 0.039 | |
TSS.human.GRCh37 | 0.254 | 0.030 | 0.365 | |
TSS.human.GRCh38 | 0.207 | 0.018 | 0.340 | |
TSS.human.NCBI36 | 0.157 | 0.016 | 0.263 | |
TSS.mouse.GRCm38 | 0.146 | 0.015 | 0.255 | |
TSS.mouse.NCBIM37 | 0.133 | 0.015 | 0.211 | |
TSS.rat.RGSC3.4 | 0.114 | 0.013 | 0.157 | |
TSS.rat.Rnor_5.0 | 0.097 | 0.011 | 0.128 | |
TSS.zebrafish.Zv8 | 0.103 | 0.015 | 0.144 | |
TSS.zebrafish.Zv9 | 0.125 | 0.016 | 0.211 | |
addAncestors | 2.481 | 0.130 | 3.545 | |
addGeneIDs | 3.732 | 1.190 | 6.497 | |
addMetadata | 2.793 | 0.128 | 4.066 | |
annoGR | 0.000 | 0.000 | 0.001 | |
annoPeaks | 6.624 | 0.690 | 10.967 | |
annotatePeakInBatch | 25.888 | 1.058 | 37.680 | |
annotatedPeak | 0.093 | 0.006 | 0.139 | |
assignChromosomeRegion | 0.003 | 0.002 | 0.009 | |
bdp | 0.001 | 0.001 | 0.002 | |
binOverFeature | 1.520 | 0.033 | 2.207 | |
binOverGene | 0.001 | 0.001 | 0.002 | |
binOverRegions | 0.002 | 0.001 | 0.002 | |
condenseMatrixByColnames | 0.022 | 0.001 | 0.032 | |
convert2EntrezID | 0.673 | 0.008 | 0.952 | |
countPatternInSeqs | 0.286 | 0.008 | 0.400 | |
cumulativePercentage | 0.000 | 0.001 | 0.001 | |
downstreams | 0.051 | 0.001 | 0.071 | |
egOrgMap | 0.000 | 0.000 | 0.002 | |
enrichedGO | 0.004 | 0.004 | 0.015 | |
enrichmentPlot | 1.261 | 0.033 | 1.795 | |
estFragmentLength | 0.001 | 0.000 | 0.002 | |
estLibSize | 0.001 | 0.001 | 0.001 | |
featureAlignedDistribution | 0.480 | 0.003 | 0.681 | |
featureAlignedExtendSignal | 0.003 | 0.001 | 0.005 | |
featureAlignedHeatmap | 0.693 | 0.005 | 0.956 | |
featureAlignedSignal | 0.441 | 0.139 | 0.800 | |
findEnhancers | 56.637 | 1.036 | 74.044 | |
findMotifsInPromoterSeqs | 30.906 | 0.513 | 44.068 | |
findOverlappingPeaks | 0.002 | 0.002 | 0.010 | |
findOverlapsOfPeaks | 4.054 | 0.063 | 6.222 | |
genomicElementDistribution | 0.004 | 0.002 | 0.008 | |
genomicElementUpSetR | 0.001 | 0.001 | 0.002 | |
getAllPeakSequence | 0.890 | 0.028 | 1.304 | |
getAnnotation | 0.003 | 0.002 | 0.007 | |
getEnrichedGO | 0.021 | 0.013 | 0.048 | |
getEnrichedPATH | 0.001 | 0.002 | 0.007 | |
getGO | 0.000 | 0.001 | 0.002 | |
getGeneSeq | 0.002 | 0.002 | 0.008 | |
getUniqueGOidCount | 0.002 | 0.000 | 0.003 | |
getVennCounts | 0.002 | 0.001 | 0.004 | |
hyperGtest | 0.002 | 0.001 | 0.002 | |
makeVennDiagram | 0.005 | 0.002 | 0.011 | |
mergePlusMinusPeaks | 0.002 | 0.000 | 0.006 | |
metagenePlot | 3.896 | 0.096 | 5.767 | |
myPeakList | 0.022 | 0.004 | 0.041 | |
oligoFrequency | 0.301 | 0.022 | 0.467 | |
oligoSummary | 0.001 | 0.000 | 0.001 | |
peakPermTest | 0.002 | 0.001 | 0.004 | |
peaksNearBDP | 0.002 | 0.001 | 0.007 | |
pie1 | 0.009 | 0.002 | 0.014 | |
plotBinOverRegions | 0.001 | 0.001 | 0.002 | |
preparePool | 0.001 | 0.001 | 0.006 | |
reCenterPeaks | 0.051 | 0.001 | 0.068 | |
summarizeOverlapsByBins | 5.884 | 0.642 | 8.618 | |
summarizePatternInPeaks | 0.991 | 0.133 | 1.591 | |
tileCount | 0.737 | 0.522 | 0.979 | |
tileGRanges | 0.086 | 0.024 | 0.151 | |
toGRanges | 0.206 | 0.035 | 0.387 | |
translatePattern | 0.001 | 0.001 | 0.001 | |
wgEncodeTfbsV3 | 0.339 | 0.026 | 0.603 | |
write2FASTA | 0.034 | 0.006 | 0.074 | |
xget | 0.170 | 0.022 | 0.316 | |