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This page was generated on 2022-01-20 11:10:42 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
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

CHECK results for ChIPpeakAnno on merida1


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.

raw results

Package 299/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.29.3  (landing page)
Jianhong Ou
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: master
git_last_commit: a414709
git_last_commit_date: 2022-01-06 13:23:08 -0500 (Thu, 06 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'IRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPpeakAnno
Version: 3.29.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.29.3.tar.gz
StartedAt: 2022-01-19 23:09:58 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 23:26:36 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 997.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.29.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘3.29.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 19.2Mb
  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            42.467  0.447  42.963
findMotifsInPromoterSeqs 26.245  0.200  26.688
annotatePeakInBatch      22.124  0.624  22.807
annoPeaks                 5.308  0.334  13.001
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPpeakAnno
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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)

Tests output

ChIPpeakAnno.Rcheck/tests/runTests.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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

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

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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (6)

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 313 ]
> 
> proc.time()
   user  system elapsed 
299.703   4.716 326.179 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package0.0000.0000.001
ExonPlusUtr.human.GRCh373.9420.1424.087
HOT.spots0.2090.0140.224
IDRfilter0.0020.0000.002
Peaks.Ste12.Replicate10.0880.0050.092
Peaks.Ste12.Replicate20.0230.0030.026
Peaks.Ste12.Replicate30.0230.0020.025
TSS.human.GRCh370.2630.0230.286
TSS.human.GRCh380.1950.0170.214
TSS.human.NCBI360.1480.0110.159
TSS.mouse.GRCm380.1390.0150.153
TSS.mouse.NCBIM370.1280.0090.136
TSS.rat.RGSC3.40.1040.0080.114
TSS.rat.Rnor_5.00.0950.0080.103
TSS.zebrafish.Zv80.1010.0090.111
TSS.zebrafish.Zv90.1290.0090.137
addAncestors2.2890.0992.391
addGeneIDs3.1990.6443.849
addMetadata2.0740.2202.297
annoGR0.0000.0010.001
annoPeaks 5.308 0.33413.001
annotatePeakInBatch22.124 0.62422.807
annotatedPeak0.0900.0050.096
assignChromosomeRegion0.0030.0000.003
bdp0.0010.0010.001
binOverFeature1.4170.0321.454
binOverGene0.0020.0000.002
binOverRegions0.0010.0000.002
condenseMatrixByColnames0.0210.0000.022
convert2EntrezID0.5820.0050.588
countPatternInSeqs0.2610.0040.267
cumulativePercentage000
downstreams0.0420.0010.043
egOrgMap0.0010.0000.001
enrichedGO0.0030.0020.006
enrichmentPlot0.8550.0090.867
estFragmentLength0.0010.0000.001
estLibSize0.0010.0000.001
featureAlignedDistribution0.3990.0020.402
featureAlignedExtendSignal0.0040.0000.004
featureAlignedHeatmap0.6420.0090.655
featureAlignedSignal0.3250.0350.360
findEnhancers42.467 0.44742.963
findMotifsInPromoterSeqs26.245 0.20026.688
findOverlappingPeaks0.0020.0000.002
findOverlapsOfPeaks3.6060.0263.818
genomicElementDistribution0.0030.0000.004
genomicElementUpSetR0.0020.0000.001
getAllPeakSequence0.9250.0210.992
getAnnotation0.0020.0000.003
getEnrichedGO0.0200.0040.027
getEnrichedPATH0.0020.0000.002
getGO0.0000.0010.001
getGeneSeq0.0030.0000.003
getUniqueGOidCount0.0010.0000.002
getVennCounts0.0020.0010.002
hyperGtest0.0010.0000.002
makeVennDiagram0.0050.0000.007
mergePlusMinusPeaks0.0010.0000.002
metagenePlot3.9070.0584.122
myPeakList0.0200.0030.023
oligoFrequency0.2850.0120.299
oligoSummary0.0010.0000.001
peakPermTest0.0020.0010.002
peaksNearBDP0.0010.0000.001
pie10.0090.0000.009
plotBinOverRegions0.0010.0000.002
preparePool0.0010.0000.001
reCenterPeaks0.0480.0000.049
summarizeOverlapsByBins3.8280.7403.961
summarizePatternInPeaks0.9350.0821.018
tileCount0.8460.6240.858
tileGRanges0.0730.0110.086
toGRanges0.2040.0200.225
translatePattern0.0010.0000.001
wgEncodeTfbsV30.3350.0150.355
write2FASTA0.0300.0040.036
xget0.1630.0110.183