Lihua Julie Zhu
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/ChIPpeakAnno |
| Branch: master |
| Last Commit: 78fb465 |
| Last Changed Date: 2019-12-13 11:00:48 -0500 (Fri, 13 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:32:06 -0500 (Thu, 16 Jan 2020).
| Package 274/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChIPpeakAnno 3.21.2 Lihua Julie Zhu
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ChIPpeakAnno |
| Version: 3.21.2 |
| 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_3.21.2.tar.gz |
| StartedAt: 2020-01-16 02:45:43 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:59:33 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 829.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_3.21.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘3.21.2’
* 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 19.0Mb
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 ... 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 41.317 0.543 42.059
ExonPlusUtr.human.GRCh37 4.940 0.317 5.265
annotatePeakInBatch 4.793 0.388 5.188
* 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-3.11-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 ** 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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
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: 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")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 185 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
148.273 6.336 163.688
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0.001 | 0.000 | 0.002 | |
| ExonPlusUtr.human.GRCh37 | 4.940 | 0.317 | 5.265 | |
| HOT.spots | 0.206 | 0.078 | 0.286 | |
| IDRfilter | 0.002 | 0.000 | 0.001 | |
| Peaks.Ste12.Replicate1 | 0.093 | 0.062 | 0.320 | |
| Peaks.Ste12.Replicate2 | 0.033 | 0.063 | 0.095 | |
| Peaks.Ste12.Replicate3 | 0.032 | 0.059 | 0.090 | |
| TSS.human.GRCh37 | 0.234 | 0.065 | 0.300 | |
| TSS.human.GRCh38 | 0.885 | 0.027 | 0.913 | |
| TSS.human.NCBI36 | 0.235 | 0.068 | 0.303 | |
| TSS.mouse.GRCm38 | 0.224 | 0.071 | 0.295 | |
| TSS.mouse.NCBIM37 | 0.359 | 0.073 | 0.431 | |
| TSS.rat.RGSC3.4 | 0.15 | 0.06 | 0.21 | |
| TSS.rat.Rnor_5.0 | 0.139 | 0.057 | 0.196 | |
| TSS.zebrafish.Zv8 | 0.148 | 0.060 | 0.208 | |
| TSS.zebrafish.Zv9 | 0.185 | 0.061 | 0.246 | |
| addAncestors | 4.258 | 0.322 | 4.584 | |
| addGeneIDs | 3.100 | 0.706 | 3.844 | |
| addMetadata | 2.754 | 0.292 | 3.046 | |
| annoGR | 0.001 | 0.000 | 0.001 | |
| annoPeaks | 3.644 | 0.732 | 4.721 | |
| annotatePeakInBatch | 4.793 | 0.388 | 5.188 | |
| annotatedPeak | 0.137 | 0.013 | 0.150 | |
| assignChromosomeRegion | 0.005 | 0.001 | 0.006 | |
| bdp | 0.001 | 0.000 | 0.001 | |
| binOverFeature | 1.573 | 0.063 | 1.745 | |
| binOverGene | 0.002 | 0.001 | 0.003 | |
| binOverRegions | 0.002 | 0.001 | 0.002 | |
| condenseMatrixByColnames | 0.029 | 0.001 | 0.030 | |
| convert2EntrezID | 0.452 | 0.013 | 0.469 | |
| countPatternInSeqs | 0.196 | 0.004 | 0.201 | |
| cumulativePercentage | 0 | 0 | 0 | |
| egOrgMap | 0.001 | 0.001 | 0.002 | |
| enrichedGO | 0.004 | 0.003 | 0.008 | |
| estFragmentLength | 0.001 | 0.000 | 0.002 | |
| estLibSize | 0.001 | 0.000 | 0.001 | |
| featureAlignedDistribution | 0.482 | 0.002 | 0.486 | |
| featureAlignedExtentSignal | 0.003 | 0.001 | 0.005 | |
| featureAlignedHeatmap | 0.734 | 0.011 | 0.746 | |
| featureAlignedSignal | 0.447 | 0.077 | 0.524 | |
| findEnhancers | 41.317 | 0.543 | 42.059 | |
| findOverlappingPeaks | 0.002 | 0.000 | 0.002 | |
| findOverlapsOfPeaks | 1.030 | 0.011 | 1.048 | |
| getAllPeakSequence | 0.846 | 0.048 | 0.901 | |
| getAnnotation | 0.000 | 0.001 | 0.001 | |
| getEnrichedGO | 0.028 | 0.007 | 0.034 | |
| getEnrichedPATH | 0.001 | 0.000 | 0.001 | |
| getGO | 0.000 | 0.000 | 0.001 | |
| getGeneSeq | 0.004 | 0.000 | 0.004 | |
| getUniqueGOidCount | 0.002 | 0.000 | 0.002 | |
| getVennCounts | 0.002 | 0.000 | 0.002 | |
| hyperGtest | 0.003 | 0.001 | 0.003 | |
| makeVennDiagram | 0.005 | 0.001 | 0.006 | |
| mergePlusMinusPeaks | 0.001 | 0.000 | 0.002 | |
| myPeakList | 0.026 | 0.005 | 0.032 | |
| oligoFrequency | 0.016 | 0.006 | 0.020 | |
| oligoSummary | 0.001 | 0.001 | 0.001 | |
| peakPermTest | 0.002 | 0.001 | 0.002 | |
| peaksNearBDP | 0.003 | 0.001 | 0.003 | |
| pie1 | 0.012 | 0.001 | 0.013 | |
| plotBinOverRegions | 0.002 | 0.000 | 0.003 | |
| preparePool | 0.002 | 0.000 | 0.003 | |
| reCenterPeaks | 0.050 | 0.001 | 0.051 | |
| summarizeOverlapsByBins | 3.565 | 0.849 | 3.837 | |
| summarizePatternInPeaks | 1.089 | 0.178 | 1.267 | |
| tileCount | 0.912 | 0.646 | 0.936 | |
| tileGRanges | 0.100 | 0.018 | 0.119 | |
| toGRanges | 0.454 | 0.078 | 0.535 | |
| translatePattern | 0.002 | 0.001 | 0.002 | |
| wgEncodeTfbsV3 | 0.355 | 0.061 | 0.744 | |
| write2FASTA | 0.053 | 0.015 | 0.124 | |
| xget | 0.234 | 0.044 | 0.425 | |