Jianhong Ou
| Snapshot Date: 2022-03-13 13:55:13 -0400 (Sun, 13 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ChIPpeakAnno |
| git_branch: master |
| git_last_commit: 84091f2 |
| git_last_commit_date: 2022-02-04 15:03:54 -0400 (Fri, 04 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-14 11:06:46 -0400 (Mon, 14 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4335 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4061 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4073 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the ChIPpeakAnno package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 300/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPpeakAnno 3.29.4 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ChIPpeakAnno |
| Version: 3.29.4 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.29.4.tar.gz |
| StartedAt: 2022-03-13 18:36:00 -0400 (Sun, 13 Mar 2022) |
| EndedAt: 2022-03-13 18:44:50 -0400 (Sun, 13 Mar 2022) |
| EllapsedTime: 529.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.29.4.tar.gz
###
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##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ChIPpeakAnno.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '3.29.4'
* 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 whether package 'ChIPpeakAnno' can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.6Mb
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 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 19.64 0.47 20.11
findMotifsInPromoterSeqs 13.35 0.22 13.57
annotatePeakInBatch 8.48 0.75 9.26
summarizeOverlapsByBins 2.04 0.01 16.61
tileCount 1.07 0.01 18.16
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.
ChIPpeakAnno.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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
converting help for package 'ChIPpeakAnno'
finding HTML links ... done
ChIPpeakAnno-deprecated html
ChIPpeakAnno-package html
EnsDb2GR html
ExonPlusUtr.human.GRCh37 html
HOT.spots html
IDRfilter html
Peaks.Ste12.Replicate1 html
Peaks.Ste12.Replicate2 html
Peaks.Ste12.Replicate3 html
TSS.human.GRCh37 html
TSS.human.GRCh38 html
TSS.human.NCBI36 html
TSS.mouse.GRCm38 html
TSS.mouse.NCBIM37 html
TSS.rat.RGSC3.4 html
TSS.rat.Rnor_5.0 html
TSS.zebrafish.Zv8 html
TSS.zebrafish.Zv9 html
TxDb2GR html
addAncestors html
addGeneIDs html
addMetadata html
annoGR html
annoPeaks html
annotatePeakInBatch html
annotatedPeak html
assignChromosomeRegion html
bdp html
binOverFeature html
binOverGene html
binOverRegions html
bindist html
cntOverlaps html
condenseMatrixByColnames html
convert2EntrezID html
countPatternInSeqs html
cumulativePercentage html
downstreams html
egOrgMap html
enrichedGO html
enrichmentPlot html
estFragmentLength html
estLibSize html
featureAlignedDistribution html
featureAlignedExtendSignal html
featureAlignedHeatmap html
featureAlignedSignal html
findEnhancers html
findMotifsInPromoterSeqs html
findOverlappingPeaks html
findOverlapsOfPeaks html
genomicElementDistribution html
genomicElementUpSetR html
getAllPeakSequence html
getAnnotation html
getEnrichedGO html
getEnrichedPATH html
getGO html
getGeneSeq html
getUniqueGOidCount html
getVennCounts html
hyperGtest html
makeVennDiagram html
mergePlusMinusPeaks html
metagenePlot html
myPeakList html
oligoFrequency html
oligoSummary html
peakPermTest html
peaksNearBDP html
permPool html
pie1 html
plotBinOverRegions html
preparePool html
reCenterPeaks html
summarizeOverlapsByBins html
summarizePatternInPeaks html
tileCount html
tileGRanges html
toGRanges html
translatePattern html
wgEncodeTfbsV3 html
write2FASTA html
xget html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RLSeq' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'SNAGEE' is missing or broken
done
ChIPpeakAnno.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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 objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")
[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]
== Skipped tests ===============================================================
* empty test (6)
[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]
>
> proc.time()
user system elapsed
127.87 4.23 139.14
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0 | 0 | 0 | |
| ExonPlusUtr.human.GRCh37 | 2.89 | 0.25 | 3.14 | |
| HOT.spots | 0.10 | 0.03 | 0.12 | |
| IDRfilter | 0 | 0 | 0 | |
| Peaks.Ste12.Replicate1 | 0.03 | 0.00 | 0.04 | |
| Peaks.Ste12.Replicate2 | 0.01 | 0.00 | 0.01 | |
| Peaks.Ste12.Replicate3 | 0.00 | 0.01 | 0.02 | |
| TSS.human.GRCh37 | 0.20 | 0.02 | 0.22 | |
| TSS.human.GRCh38 | 0.14 | 0.05 | 0.19 | |
| TSS.human.NCBI36 | 0.10 | 0.03 | 0.12 | |
| TSS.mouse.GRCm38 | 0.09 | 0.03 | 0.13 | |
| TSS.mouse.NCBIM37 | 0.08 | 0.01 | 0.09 | |
| TSS.rat.RGSC3.4 | 0.05 | 0.04 | 0.08 | |
| TSS.rat.Rnor_5.0 | 0.06 | 0.00 | 0.06 | |
| TSS.zebrafish.Zv8 | 0.06 | 0.01 | 0.08 | |
| TSS.zebrafish.Zv9 | 0.06 | 0.03 | 0.10 | |
| addAncestors | 0.96 | 0.13 | 1.07 | |
| addGeneIDs | 1.98 | 1.12 | 3.11 | |
| addMetadata | 1.09 | 0.11 | 1.20 | |
| annoGR | 0.02 | 0.00 | 0.02 | |
| annoPeaks | 2.02 | 0.33 | 4.47 | |
| annotatePeakInBatch | 8.48 | 0.75 | 9.26 | |
| annotatedPeak | 0.06 | 0.00 | 0.06 | |
| assignChromosomeRegion | 0 | 0 | 0 | |
| bdp | 0 | 0 | 0 | |
| binOverFeature | 0.57 | 0.09 | 0.66 | |
| binOverGene | 0 | 0 | 0 | |
| binOverRegions | 0.00 | 0.02 | 0.02 | |
| condenseMatrixByColnames | 0 | 0 | 0 | |
| convert2EntrezID | 0.29 | 0.01 | 0.31 | |
| countPatternInSeqs | 0.19 | 0.00 | 0.19 | |
| cumulativePercentage | 0 | 0 | 0 | |
| downstreams | 0.02 | 0.00 | 0.01 | |
| egOrgMap | 0 | 0 | 0 | |
| enrichedGO | 0.00 | 0.02 | 0.02 | |
| enrichmentPlot | 0.32 | 0.01 | 0.34 | |
| estFragmentLength | 0 | 0 | 0 | |
| estLibSize | 0 | 0 | 0 | |
| featureAlignedDistribution | 0.16 | 0.03 | 0.19 | |
| featureAlignedExtendSignal | 0 | 0 | 0 | |
| featureAlignedHeatmap | 0.29 | 0.00 | 0.30 | |
| featureAlignedSignal | 0.13 | 0.01 | 0.14 | |
| findEnhancers | 19.64 | 0.47 | 20.11 | |
| findMotifsInPromoterSeqs | 13.35 | 0.22 | 13.57 | |
| findOverlappingPeaks | 0 | 0 | 0 | |
| findOverlapsOfPeaks | 1.99 | 0.00 | 1.99 | |
| genomicElementDistribution | 0 | 0 | 0 | |
| genomicElementUpSetR | 0 | 0 | 0 | |
| getAllPeakSequence | 0.61 | 0.00 | 0.61 | |
| getAnnotation | 0 | 0 | 0 | |
| getEnrichedGO | 0.01 | 0.00 | 0.01 | |
| getEnrichedPATH | 0 | 0 | 0 | |
| getGO | 0 | 0 | 0 | |
| getGeneSeq | 0 | 0 | 0 | |
| getUniqueGOidCount | 0.02 | 0.00 | 0.02 | |
| getVennCounts | 0 | 0 | 0 | |
| hyperGtest | 0 | 0 | 0 | |
| makeVennDiagram | 0 | 0 | 0 | |
| mergePlusMinusPeaks | 0 | 0 | 0 | |
| metagenePlot | 1.75 | 0.16 | 1.90 | |
| myPeakList | 0.03 | 0.00 | 0.03 | |
| oligoFrequency | 0.13 | 0.00 | 0.13 | |
| oligoSummary | 0 | 0 | 0 | |
| peakPermTest | 0 | 0 | 0 | |
| peaksNearBDP | 0 | 0 | 0 | |
| pie1 | 0.01 | 0.00 | 0.01 | |
| plotBinOverRegions | 0 | 0 | 0 | |
| preparePool | 0 | 0 | 0 | |
| reCenterPeaks | 0.02 | 0.00 | 0.02 | |
| summarizeOverlapsByBins | 2.04 | 0.01 | 16.61 | |
| summarizePatternInPeaks | 0.39 | 0.04 | 0.42 | |
| tileCount | 1.07 | 0.01 | 18.16 | |
| tileGRanges | 0.03 | 0.00 | 0.03 | |
| toGRanges | 0.11 | 0.00 | 0.11 | |
| translatePattern | 0 | 0 | 0 | |
| wgEncodeTfbsV3 | 0.17 | 0.02 | 0.19 | |
| write2FASTA | 0.01 | 0.00 | 0.01 | |
| xget | 0.1 | 0.0 | 0.1 | |