Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:22:50 -0400 (Wed, 16 Oct 2019).
Package 260/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ChIPpeakAnno 3.18.2 Lihua Julie Zhu
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: ChIPpeakAnno |
Version: 3.18.2 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.18.2.tar.gz |
StartedAt: 2019-10-16 02:36:33 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 02:48:53 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 740.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPpeakAnno.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.18.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPpeakAnno.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '3.18.2' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'grid', 'IRanges', 'Biostrings', 'GenomicRanges', 'S4Vectors', 'VennDiagram' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 19.4Mb sub-directories of 1Mb or more: data 12.7Mb 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 data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed findEnhancers 14.05 0.13 14.20 summarizeOverlapsByBins 2.55 0.02 18.02 annoPeaks 2.20 0.27 5.46 tileCount 1.16 0.00 19.49 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed findEnhancers 14.83 0.18 15.01 summarizeOverlapsByBins 2.59 0.00 18.05 tileCount 0.96 0.03 17.37 * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPpeakAnno.Rcheck/00check.log' for details.
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ChIPpeakAnno_3.18.2.tar.gz && rm -rf ChIPpeakAnno.buildbin-libdir && mkdir ChIPpeakAnno.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.18.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ChIPpeakAnno_3.18.2.zip && rm ChIPpeakAnno_3.18.2.tar.gz ChIPpeakAnno_3.18.2.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 15.6M 100 15.6M 0 0 39.0M 0 --:--:-- --:--:-- --:--:-- 39.7M install for i386 * installing *source* package 'ChIPpeakAnno' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ChIPpeakAnno' finding HTML links ... done BED2RangedData html ChIPpeakAnno-deprecated html ChIPpeakAnno-package html ExonPlusUtr.human.GRCh37 html GFF2RangedData 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 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 condenseMatrixByColnames html convert2EntrezID html countPatternInSeqs html cumulativePercentage html egOrgMap html enrichedGO html estFragmentLength html estLibSize html featureAlignedDistribution html featureAlignedExtentSignal html featureAlignedHeatmap html featureAlignedSignal html findEnhancers html findOverlappingPeaks html findOverlapsOfPeaks html findVennCounts html getAllPeakSequence html getAnnotation html getEnrichedGO html getEnrichedPATH html getGeneSeq html getUniqueGOidCount html getVennCounts html hyperGtest html makeVennDiagram html mergePlusMinusPeaks 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_3.18.2.zip * DONE (ChIPpeakAnno) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'ChIPpeakAnno' successfully unpacked and MD5 sums checked
ChIPpeakAnno.Rcheck/tests_i386/runTests.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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: grid 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, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: VennDiagram Loading required package: futile.logger [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: 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") == testthat results =========================================================== [ OK: 187 | SKIPPED: 5 | WARNINGS: 6 | FAILED: 0 ] > > proc.time() user system elapsed 52.14 3.64 73.51 |
ChIPpeakAnno.Rcheck/tests_x64/runTests.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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: grid 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, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: VennDiagram Loading required package: futile.logger [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: 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") == testthat results =========================================================== [ OK: 187 | SKIPPED: 5 | WARNINGS: 6 | FAILED: 0 ] > > proc.time() user system elapsed 76.89 2.40 79.89 |
ChIPpeakAnno.Rcheck/examples_i386/ChIPpeakAnno-Ex.timings
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ChIPpeakAnno.Rcheck/examples_x64/ChIPpeakAnno-Ex.timings
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