Jianhong Ou
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ChIPpeakAnno |
| Branch: RELEASE_3_12 |
| Last Commit: 09d9fec |
| Last Changed Date: 2021-03-30 09:36:14 -0400 (Tue, 30 Mar 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:31 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the ChIPpeakAnno package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 286/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPpeakAnno 3.24.2 (landing page) Jianhong Ou
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ChIPpeakAnno |
| Version: 3.24.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPpeakAnno_3.24.2.tar.gz |
| StartedAt: 2021-05-06 00:10:32 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:21:19 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 646.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPpeakAnno_3.24.2.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.24.2’
* 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 27.6Mb
sub-directories of 1Mb or more:
data 21.1Mb
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 ... 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 ... OK
* 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 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 33.515 0.417 33.983
findMotifsInPromoterSeqs 17.364 0.138 17.525
annotatePeakInBatch 13.888 0.360 14.321
annoPeaks 3.336 0.257 12.203
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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:base':
expand.grid
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("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")
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
[ FAIL 0 | WARN 1 | SKIP 5 | PASS 214 ]
>
> proc.time()
user system elapsed
129.547 3.062 146.019
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0.001 | 0.001 | 0.002 | |
| ExonPlusUtr.human.GRCh37 | 3.203 | 0.100 | 3.306 | |
| HOT.spots | 0.049 | 0.009 | 0.058 | |
| IDRfilter | 0.002 | 0.000 | 0.002 | |
| Peaks.Ste12.Replicate1 | 0.064 | 0.003 | 0.067 | |
| Peaks.Ste12.Replicate2 | 0.019 | 0.003 | 0.020 | |
| Peaks.Ste12.Replicate3 | 0.015 | 0.003 | 0.018 | |
| TSS.human.GRCh37 | 0.159 | 0.019 | 0.178 | |
| TSS.human.GRCh38 | 0.084 | 0.010 | 0.093 | |
| TSS.human.NCBI36 | 0.060 | 0.006 | 0.066 | |
| TSS.mouse.GRCm38 | 0.051 | 0.004 | 0.055 | |
| TSS.mouse.NCBIM37 | 0.052 | 0.005 | 0.057 | |
| TSS.rat.RGSC3.4 | 0.047 | 0.007 | 0.054 | |
| TSS.rat.Rnor_5.0 | 0.037 | 0.004 | 0.042 | |
| TSS.zebrafish.Zv8 | 0.043 | 0.007 | 0.050 | |
| TSS.zebrafish.Zv9 | 0.160 | 0.016 | 0.177 | |
| addAncestors | 1.752 | 0.068 | 1.823 | |
| addGeneIDs | 2.416 | 0.523 | 2.950 | |
| addMetadata | 2.008 | 0.075 | 2.085 | |
| annoGR | 0.000 | 0.001 | 0.000 | |
| annoPeaks | 3.336 | 0.257 | 12.203 | |
| annotatePeakInBatch | 13.888 | 0.360 | 14.321 | |
| annotatedPeak | 0.047 | 0.004 | 0.051 | |
| assignChromosomeRegion | 0.003 | 0.001 | 0.004 | |
| bdp | 0.000 | 0.001 | 0.001 | |
| binOverFeature | 1.003 | 0.013 | 1.018 | |
| binOverGene | 0.001 | 0.001 | 0.002 | |
| binOverRegions | 0.001 | 0.000 | 0.001 | |
| condenseMatrixByColnames | 0.015 | 0.000 | 0.016 | |
| convert2EntrezID | 0.387 | 0.003 | 0.390 | |
| countPatternInSeqs | 0.212 | 0.004 | 0.217 | |
| cumulativePercentage | 0 | 0 | 0 | |
| downstreams | 0.025 | 0.001 | 0.025 | |
| egOrgMap | 0 | 0 | 0 | |
| enrichedGO | 0.002 | 0.001 | 0.003 | |
| enrichmentPlot | 0.656 | 0.010 | 0.668 | |
| estFragmentLength | 0.001 | 0.001 | 0.002 | |
| estLibSize | 0.001 | 0.001 | 0.002 | |
| featureAlignedDistribution | 0.459 | 0.004 | 0.465 | |
| featureAlignedExtendSignal | 0.004 | 0.001 | 0.005 | |
| featureAlignedHeatmap | 0.457 | 0.005 | 0.464 | |
| featureAlignedSignal | 0.246 | 0.055 | 0.300 | |
| findEnhancers | 33.515 | 0.417 | 33.983 | |
| findMotifsInPromoterSeqs | 17.364 | 0.138 | 17.525 | |
| findOverlappingPeaks | 0.002 | 0.000 | 0.003 | |
| findOverlapsOfPeaks | 0.771 | 0.012 | 0.785 | |
| genomicElementDistribution | 0.005 | 0.001 | 0.007 | |
| genomicElementUpSetR | 0.002 | 0.000 | 0.002 | |
| getAllPeakSequence | 0.685 | 0.018 | 0.708 | |
| getAnnotation | 0.001 | 0.001 | 0.001 | |
| getEnrichedGO | 0.018 | 0.008 | 0.026 | |
| getEnrichedPATH | 0.003 | 0.001 | 0.003 | |
| getGO | 0.001 | 0.000 | 0.001 | |
| getGeneSeq | 0.003 | 0.001 | 0.004 | |
| getUniqueGOidCount | 0.001 | 0.000 | 0.002 | |
| getVennCounts | 0.003 | 0.001 | 0.004 | |
| hyperGtest | 0.002 | 0.001 | 0.003 | |
| makeVennDiagram | 0.005 | 0.001 | 0.006 | |
| mergePlusMinusPeaks | 0.002 | 0.000 | 0.003 | |
| metagenePlot | 3.072 | 0.055 | 3.133 | |
| myPeakList | 0.008 | 0.002 | 0.010 | |
| oligoFrequency | 0.209 | 0.011 | 0.220 | |
| oligoSummary | 0.001 | 0.000 | 0.001 | |
| peakPermTest | 0.003 | 0.000 | 0.003 | |
| peaksNearBDP | 0.001 | 0.000 | 0.002 | |
| pie1 | 0.005 | 0.000 | 0.006 | |
| plotBinOverRegions | 0.001 | 0.000 | 0.002 | |
| preparePool | 0.001 | 0.000 | 0.001 | |
| reCenterPeaks | 0.043 | 0.000 | 0.044 | |
| summarizeOverlapsByBins | 2.866 | 0.523 | 2.924 | |
| summarizePatternInPeaks | 0.720 | 0.062 | 0.782 | |
| tileCount | 0.671 | 0.542 | 0.683 | |
| tileGRanges | 0.065 | 0.014 | 0.079 | |
| toGRanges | 0.166 | 0.020 | 0.186 | |
| translatePattern | 0.000 | 0.001 | 0.002 | |
| wgEncodeTfbsV3 | 0.071 | 0.013 | 0.084 | |
| write2FASTA | 0.023 | 0.003 | 0.026 | |
| xget | 0.126 | 0.010 | 0.136 | |