Lihua Julie Zhu
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ChIPpeakAnno |
| Branch: RELEASE_3_9 |
| Last Commit: 6d1c24d |
| Last Changed Date: 2019-07-26 13:39:35 -0400 (Fri, 26 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:57:33 -0400 (Wed, 16 Oct 2019).
| Package 260/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChIPpeakAnno 3.18.2 Lihua Julie Zhu
| malbec2 | Linux (Ubuntu 18.04.2 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: 3.18.2 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.18.2.tar.gz |
| StartedAt: 2019-10-16 00:27:14 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:34:40 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 445.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIPpeakAnno_3.18.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘3.18.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'grid', 'IRanges', 'Biostrings', 'GenomicRanges', 'S4Vectors',
'VennDiagram'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 12.7Mb
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 or elapsed time > 5s
user system elapsed
findEnhancers 17.457 0.056 17.622
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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: grid
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
Loading required package: VennDiagram
Loading required package: futile.logger
[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: 187 | SKIPPED: 5 | WARNINGS: 6 | FAILED: 0 ]
>
> proc.time()
user system elapsed
67.544 1.168 69.310
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| BED2RangedData | 0.05 | 0.00 | 0.05 | |
| ChIPpeakAnno-package | 0.001 | 0.000 | 0.000 | |
| ExonPlusUtr.human.GRCh37 | 4.395 | 0.060 | 4.465 | |
| GFF2RangedData | 0.012 | 0.004 | 0.016 | |
| HOT.spots | 0.182 | 0.008 | 0.190 | |
| IDRfilter | 0.000 | 0.001 | 0.001 | |
| Peaks.Ste12.Replicate1 | 0.197 | 0.010 | 0.207 | |
| Peaks.Ste12.Replicate2 | 0.139 | 0.000 | 0.139 | |
| Peaks.Ste12.Replicate3 | 0.126 | 0.000 | 0.126 | |
| TSS.human.GRCh37 | 0.189 | 0.000 | 0.190 | |
| TSS.human.GRCh38 | 0.551 | 0.012 | 0.563 | |
| TSS.human.NCBI36 | 0.170 | 0.000 | 0.169 | |
| TSS.mouse.GRCm38 | 0.238 | 0.004 | 0.242 | |
| TSS.mouse.NCBIM37 | 0.177 | 0.000 | 0.177 | |
| TSS.rat.RGSC3.4 | 0.143 | 0.000 | 0.143 | |
| TSS.rat.Rnor_5.0 | 0.132 | 0.000 | 0.131 | |
| TSS.zebrafish.Zv8 | 0.128 | 0.004 | 0.133 | |
| TSS.zebrafish.Zv9 | 0.165 | 0.000 | 0.165 | |
| addAncestors | 2.616 | 0.056 | 2.686 | |
| addGeneIDs | 1.833 | 0.071 | 2.008 | |
| addMetadata | 1.188 | 0.076 | 1.263 | |
| annoGR | 0.000 | 0.000 | 0.001 | |
| annoPeaks | 2.269 | 0.116 | 3.437 | |
| annotatePeakInBatch | 2.268 | 0.056 | 2.328 | |
| annotatedPeak | 0.117 | 0.004 | 0.122 | |
| assignChromosomeRegion | 0.003 | 0.000 | 0.002 | |
| bdp | 0.000 | 0.000 | 0.001 | |
| binOverFeature | 0.778 | 0.000 | 0.917 | |
| binOverGene | 0.002 | 0.000 | 0.001 | |
| binOverRegions | 0.001 | 0.000 | 0.002 | |
| condenseMatrixByColnames | 0.019 | 0.000 | 0.019 | |
| convert2EntrezID | 0.368 | 0.000 | 0.373 | |
| countPatternInSeqs | 0.128 | 0.004 | 0.215 | |
| cumulativePercentage | 0 | 0 | 0 | |
| egOrgMap | 0.001 | 0.000 | 0.000 | |
| enrichedGO | 0.003 | 0.000 | 0.003 | |
| estFragmentLength | 0.000 | 0.000 | 0.001 | |
| estLibSize | 0.001 | 0.000 | 0.000 | |
| featureAlignedDistribution | 0.334 | 0.012 | 0.348 | |
| featureAlignedExtentSignal | 0.003 | 0.000 | 0.003 | |
| featureAlignedHeatmap | 0.438 | 0.000 | 0.439 | |
| featureAlignedSignal | 0.195 | 0.032 | 0.227 | |
| findEnhancers | 17.457 | 0.056 | 17.622 | |
| findOverlappingPeaks | 0.000 | 0.002 | 0.001 | |
| findOverlapsOfPeaks | 0.495 | 0.001 | 0.497 | |
| getAllPeakSequence | 0.447 | 0.004 | 0.463 | |
| getAnnotation | 0 | 0 | 0 | |
| getEnrichedGO | 0.011 | 0.000 | 0.011 | |
| getEnrichedPATH | 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 | 0.002 | 0.000 | 0.002 | |
| mergePlusMinusPeaks | 0.000 | 0.000 | 0.001 | |
| myPeakList | 0.019 | 0.000 | 0.019 | |
| oligoFrequency | 0.003 | 0.004 | 0.007 | |
| oligoSummary | 0.000 | 0.000 | 0.001 | |
| peakPermTest | 0.001 | 0.000 | 0.001 | |
| peaksNearBDP | 0 | 0 | 0 | |
| pie1 | 0.008 | 0.000 | 0.008 | |
| plotBinOverRegions | 0.001 | 0.000 | 0.000 | |
| preparePool | 0 | 0 | 0 | |
| reCenterPeaks | 0.011 | 0.000 | 0.012 | |
| summarizeOverlapsByBins | 3.245 | 0.664 | 3.915 | |
| summarizePatternInPeaks | 0.572 | 0.036 | 0.608 | |
| tileCount | 1.166 | 0.248 | 1.563 | |
| tileGRanges | 0.296 | 0.185 | 0.035 | |
| toGRanges | 0.214 | 0.004 | 0.292 | |
| translatePattern | 0.000 | 0.000 | 0.001 | |
| wgEncodeTfbsV3 | 0.282 | 0.012 | 0.293 | |
| write2FASTA | 0.009 | 0.004 | 0.012 | |
| xget | 0.13 | 0.00 | 0.13 | |