| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:23 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 307/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPpeakAnno 3.33.1 (landing page) Jianhong Ou
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: ChIPpeakAnno |
| Version: 3.33.1 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.33.1.tar.gz |
| StartedAt: 2022-12-28 22:25:53 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 22:34:12 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 498.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.33.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ChIPpeakAnno.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '3.33.1'
* 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 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 ... NOTE
oligoFrequency : <anonymous>: no visible global function definition for
'oligonucleotideFrequency'
Undefined global functions or variables:
oligonucleotideFrequency
* 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 16.40 0.69 17.10
annotatePeakInBatch 10.34 0.59 10.97
findMotifsInPromoterSeqs 9.93 0.23 10.26
summarizeOverlapsByBins 2.84 0.03 17.63
tileCount 0.94 0.01 14.93
* 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: 4 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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, 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 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("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")
[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (6)
[ FAIL 0 | WARN 4 | SKIP 6 | PASS 316 ]
>
> proc.time()
user system elapsed
137.17 5.93 144.95
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0 | 0 | 0 | |
| ExonPlusUtr.human.GRCh37 | 2.48 | 0.04 | 2.53 | |
| HOT.spots | 0.13 | 0.00 | 0.12 | |
| IDRfilter | 0 | 0 | 0 | |
| Peaks.Ste12.Replicate1 | 0.04 | 0.00 | 0.05 | |
| Peaks.Ste12.Replicate2 | 0 | 0 | 0 | |
| Peaks.Ste12.Replicate3 | 0 | 0 | 0 | |
| TSS.human.GRCh37 | 0.13 | 0.02 | 0.14 | |
| TSS.human.GRCh38 | 0.10 | 0.03 | 0.15 | |
| TSS.human.NCBI36 | 0.10 | 0.00 | 0.09 | |
| TSS.mouse.GRCm38 | 0.09 | 0.00 | 0.10 | |
| TSS.mouse.NCBIM37 | 0.10 | 0.00 | 0.09 | |
| TSS.rat.RGSC3.4 | 0.06 | 0.01 | 0.08 | |
| TSS.rat.Rnor_5.0 | 0.06 | 0.00 | 0.06 | |
| TSS.zebrafish.Zv8 | 0.06 | 0.02 | 0.08 | |
| TSS.zebrafish.Zv9 | 0.07 | 0.01 | 0.08 | |
| addAncestors | 0.75 | 0.08 | 0.83 | |
| addGeneIDs | 2.06 | 0.95 | 3.01 | |
| addMetadata | 1.23 | 0.10 | 1.33 | |
| annoGR | 0 | 0 | 0 | |
| annoPeaks | 2.53 | 0.33 | 3.20 | |
| annotatePeakInBatch | 10.34 | 0.59 | 10.97 | |
| annotatedPeak | 0.07 | 0.00 | 0.06 | |
| assignChromosomeRegion | 0 | 0 | 0 | |
| bdp | 0 | 0 | 0 | |
| binOverFeature | 0.59 | 0.02 | 0.61 | |
| binOverGene | 0 | 0 | 0 | |
| binOverRegions | 0 | 0 | 0 | |
| condenseMatrixByColnames | 0 | 0 | 0 | |
| convert2EntrezID | 0.28 | 0.00 | 0.28 | |
| countPatternInSeqs | 0.09 | 0.01 | 0.11 | |
| cumulativePercentage | 0 | 0 | 0 | |
| downstreams | 0.02 | 0.00 | 0.02 | |
| egOrgMap | 0 | 0 | 0 | |
| enrichedGO | 0.00 | 0.02 | 0.01 | |
| enrichmentPlot | 0.42 | 0.01 | 0.44 | |
| estFragmentLength | 0 | 0 | 0 | |
| estLibSize | 0 | 0 | 0 | |
| featureAlignedDistribution | 0.17 | 0.00 | 0.17 | |
| featureAlignedExtendSignal | 0 | 0 | 0 | |
| featureAlignedHeatmap | 0.25 | 0.00 | 0.25 | |
| featureAlignedSignal | 0.24 | 0.02 | 0.25 | |
| findEnhancers | 16.40 | 0.69 | 17.10 | |
| findMotifsInPromoterSeqs | 9.93 | 0.23 | 10.26 | |
| findOverlappingPeaks | 0 | 0 | 0 | |
| findOverlapsOfPeaks | 1.34 | 0.03 | 1.72 | |
| genomicElementDistribution | 0.02 | 0.00 | 0.02 | |
| genomicElementUpSetR | 0 | 0 | 0 | |
| getAllPeakSequence | 0.48 | 0.03 | 1.62 | |
| getAnnotation | 0.02 | 0.00 | 0.02 | |
| getEnrichedGO | 0 | 0 | 0 | |
| getEnrichedPATH | 0 | 0 | 0 | |
| getGO | 0 | 0 | 0 | |
| getGeneSeq | 0 | 0 | 0 | |
| getUniqueGOidCount | 0 | 0 | 0 | |
| getVennCounts | 0 | 0 | 0 | |
| hyperGtest | 0 | 0 | 0 | |
| makeVennDiagram | 0.01 | 0.00 | 0.02 | |
| mergePlusMinusPeaks | 0 | 0 | 0 | |
| metagenePlot | 1.86 | 0.11 | 1.97 | |
| myPeakList | 0.02 | 0.00 | 0.02 | |
| oligoFrequency | 0.11 | 0.02 | 0.12 | |
| oligoSummary | 0 | 0 | 0 | |
| peakPermTest | 0 | 0 | 0 | |
| peaksNearBDP | 0 | 0 | 0 | |
| pie1 | 0.01 | 0.00 | 0.02 | |
| plotBinOverRegions | 0 | 0 | 0 | |
| preparePool | 0 | 0 | 0 | |
| reCenterPeaks | 0.02 | 0.00 | 0.01 | |
| summarizeOverlapsByBins | 2.84 | 0.03 | 17.63 | |
| summarizePatternInPeaks | 0.36 | 0.02 | 0.37 | |
| tileCount | 0.94 | 0.01 | 14.93 | |
| tileGRanges | 0.03 | 0.00 | 0.03 | |
| toGRanges | 0.08 | 0.00 | 0.07 | |
| translatePattern | 0 | 0 | 0 | |
| wgEncodeTfbsV3 | 0.18 | 0.02 | 0.21 | |
| write2FASTA | 0.02 | 0.00 | 0.01 | |
| xget | 0.08 | 0.00 | 0.08 | |