Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
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 294/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPpeakAnno 3.26.4 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ChIPpeakAnno |
Version: 3.26.4 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.26.4.tar.gz |
StartedAt: 2021-10-14 20:59:30 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:16:02 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 992.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPpeakAnno.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.26.4.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPpeakAnno.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '3.26.4' * 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 19.7Mb 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findEnhancers 29.49 0.33 29.86 annotatePeakInBatch 14.56 0.76 15.33 findMotifsInPromoterSeqs 13.26 0.58 16.12 annoPeaks 4.06 0.57 9.69 summarizeOverlapsByBins 2.15 0.01 19.06 tileCount 1.19 0.01 18.31 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findEnhancers 31.82 0.42 32.24 annotatePeakInBatch 20.09 0.44 20.58 findMotifsInPromoterSeqs 16.00 0.13 16.12 annoPeaks 4.44 0.23 6.57 summarizeOverlapsByBins 3.14 0.02 20.01 tileCount 1.57 0.00 20.28 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPpeakAnno.Rcheck/00check.log' for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ChIPpeakAnno_3.26.4.tar.gz && rm -rf ChIPpeakAnno.buildbin-libdir && mkdir ChIPpeakAnno.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.26.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno_3.26.4.zip && rm ChIPpeakAnno_3.26.4.tar.gz ChIPpeakAnno_3.26.4.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 13 15.7M 13 2189k 0 0 2355k 0 0:00:06 --:--:-- 0:00:06 2356k 36 15.7M 36 5833k 0 0 3042k 0 0:00:05 0:00:01 0:00:04 3043k 64 15.7M 64 10.1M 0 0 3588k 0 0:00:04 0:00:02 0:00:02 3588k 99 15.7M 99 15.6M 0 0 4090k 0 0:00:03 0:00:03 --:--:-- 4090k 100 15.7M 100 15.7M 0 0 4092k 0 0:00:03 0:00:03 --:--:-- 4092k install for i386 * 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 install for x64 * installing *source* package 'ChIPpeakAnno' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ChIPpeakAnno' as ChIPpeakAnno_3.26.4.zip * DONE (ChIPpeakAnno) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'ChIPpeakAnno' successfully unpacked and MD5 sums checked
ChIPpeakAnno.Rcheck/tests_i386/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 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.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") == Skipped tests =============================================================== * empty test (6) [ FAIL 0 | WARN 3 | SKIP 6 | PASS 214 ] > > proc.time() user system elapsed 125.21 6.81 142.42 |
ChIPpeakAnno.Rcheck/tests_x64/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" 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 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.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") == Skipped tests =============================================================== * empty test (6) [ FAIL 0 | WARN 3 | SKIP 6 | PASS 214 ] > > proc.time() user system elapsed 122.21 3.68 130.36 |
ChIPpeakAnno.Rcheck/examples_i386/ChIPpeakAnno-Ex.timings
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ChIPpeakAnno.Rcheck/examples_x64/ChIPpeakAnno-Ex.timings
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