Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:13 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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? 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 306/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPpeakAnno 3.31.1  (landing page)
Jianhong Ou
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/ChIPpeakAnno
git_branch: master
git_last_commit: 841797a
git_last_commit_date: 2022-06-06 13:05:24 -0400 (Mon, 06 Jun 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPpeakAnno
Version: 3.31.1
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.31.1.tar.gz
StartedAt: 2022-06-24 00:08:25 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 00:18:35 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 610.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPpeakAnno.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.31.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 '3.31.1'
* 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 ... 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            21.77   0.78   22.55
findMotifsInPromoterSeqs 14.45   0.31   14.95
annotatePeakInBatch      12.47   0.98   13.47
summarizeOverlapsByBins   2.80   0.02   19.47
tileCount                 1.36   0.00   20.61
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.



Installation output

ChIPpeakAnno.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/ChIPpeakAnno_3.31.1.tar.gz && rm -rf ChIPpeakAnno.buildbin-libdir && mkdir ChIPpeakAnno.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.31.1.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno_3.31.1.zip && rm ChIPpeakAnno_3.31.1.tar.gz ChIPpeakAnno_3.31.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 78 15.5M   78 12.2M    0     0  7887k      0  0:00:02  0:00:01  0:00:01 7892k
100 15.5M  100 15.5M    0     0  8852k      0  0:00:01  0:00:01 --:--:-- 8859k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'ChIPpeakAnno' as ChIPpeakAnno_3.31.1.zip
* DONE (ChIPpeakAnno)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'ChIPpeakAnno' successfully unpacked and MD5 sums checked

Tests output

ChIPpeakAnno.Rcheck/tests/runTests.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
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, 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 315 ]

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

[ FAIL 0 | WARN 3 | SKIP 6 | PASS 315 ]
> 
> proc.time()
   user  system elapsed 
 155.42    6.73  164.12 

Example timings

ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings

nameusersystemelapsed
ChIPpeakAnno-package000
ExonPlusUtr.human.GRCh373.200.063.26
HOT.spots0.130.010.14
IDRfilter000
Peaks.Ste12.Replicate10.060.020.08
Peaks.Ste12.Replicate20.020.000.01
Peaks.Ste12.Replicate30.020.000.02
TSS.human.GRCh370.150.030.18
TSS.human.GRCh380.130.020.15
TSS.human.NCBI360.090.010.10
TSS.mouse.GRCm380.090.020.11
TSS.mouse.NCBIM370.10.00.1
TSS.rat.RGSC3.40.060.010.08
TSS.rat.Rnor_5.00.060.000.06
TSS.zebrafish.Zv80.050.020.07
TSS.zebrafish.Zv90.060.020.08
addAncestors1.030.021.05
addGeneIDs2.581.203.78
addMetadata1.060.201.27
annoGR000
annoPeaks3.200.444.37
annotatePeakInBatch12.47 0.9813.47
annotatedPeak0.070.020.08
assignChromosomeRegion0.010.000.01
bdp000
binOverFeature0.750.020.77
binOverGene000
binOverRegions000
condenseMatrixByColnames0.020.000.01
convert2EntrezID0.400.010.43
countPatternInSeqs0.160.000.15
cumulativePercentage000
downstreams0.010.000.02
egOrgMap0.000.020.01
enrichedGO000
enrichmentPlot0.380.010.39
estFragmentLength000
estLibSize000
featureAlignedDistribution0.280.000.28
featureAlignedExtendSignal0.020.000.02
featureAlignedHeatmap0.280.000.28
featureAlignedSignal0.160.030.19
findEnhancers21.77 0.7822.55
findMotifsInPromoterSeqs14.45 0.3114.95
findOverlappingPeaks000
findOverlapsOfPeaks1.910.021.95
genomicElementDistribution000
genomicElementUpSetR0.000.010.02
getAllPeakSequence0.470.000.54
getAnnotation000
getEnrichedGO0.000.000.02
getEnrichedPATH000
getGO000
getGeneSeq000
getUniqueGOidCount000
getVennCounts000
hyperGtest000
makeVennDiagram000
mergePlusMinusPeaks000
metagenePlot1.970.102.08
myPeakList0.010.000.01
oligoFrequency0.160.020.17
oligoSummary000
peakPermTest000
peaksNearBDP000
pie10.010.000.02
plotBinOverRegions000
preparePool000
reCenterPeaks0.030.000.03
summarizeOverlapsByBins 2.80 0.0219.47
summarizePatternInPeaks0.560.000.56
tileCount 1.36 0.0020.61
tileGRanges0.030.000.03
toGRanges0.090.000.10
translatePattern000
wgEncodeTfbsV30.190.000.19
write2FASTA0.010.000.01
xget0.110.000.11