Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:38:27 -0400 (Wed, 16 Oct 2019).
Package 91/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ATACseqQC 1.8.5 Jianhong Ou
| 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: ATACseqQC |
Version: 1.8.5 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ATACseqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ATACseqQC_1.8.5.tar.gz |
StartedAt: 2019-10-16 02:01:11 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 02:15:28 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 856.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ATACseqQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ATACseqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ATACseqQC_1.8.5.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ATACseqQC.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 'ATACseqQC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ATACseqQC' version '1.8.5' * 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 'ATACseqQC' can be installed ... OK * checking installed package size ... NOTE installed size is 11.4Mb sub-directories of 1Mb or more: extdata 10.9Mb * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed enrichedFragments 59.70 3.19 64.03 distanceDyad 24.66 0.61 25.26 vPlot 22.11 0.26 22.37 factorFootprints 20.49 0.33 20.81 splitGAlignmentsByCut 19.53 1.13 22.46 footprintsScanner 12.18 0.66 12.94 shiftGAlignmentsList 7.76 0.72 8.48 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed enrichedFragments 90.70 3.67 94.40 factorFootprints 27.13 0.34 27.47 distanceDyad 26.84 0.30 27.14 vPlot 23.65 0.35 24.02 splitGAlignmentsByCut 22.52 1.26 30.59 footprintsScanner 16.85 0.56 17.42 shiftGAlignmentsList 8.93 0.63 9.57 estimateLibComplexity 5.12 0.00 5.12 * 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-3.9-bioc/meat/ATACseqQC.Rcheck/00check.log' for details.
ATACseqQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ATACseqQC_1.8.5.tar.gz && rm -rf ATACseqQC.buildbin-libdir && mkdir ATACseqQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ATACseqQC.buildbin-libdir ATACseqQC_1.8.5.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ATACseqQC_1.8.5.zip && rm ATACseqQC_1.8.5.tar.gz ATACseqQC_1.8.5.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 11.0M 100 11.0M 0 0 65.6M 0 --:--:-- --:--:-- --:--:-- 67.2M install for i386 * installing *source* package 'ATACseqQC' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ATACseqQC' finding HTML links ... done ATACseqQC-package html DB html NFRscore html PTscore html TSSEscore html bamQC html distanceDyad html enrichedFragments html estimateLibComplexity html factorFootprints html footprintsScanner html fragSizeDist html peakdet html plotCorrelation html plotFootprints html prepareBindingSitesList html pwmscores html readBamFile html finding level-2 HTML links ... done readsDupFreq html saturationPlot html shiftGAlignmentsList html shiftReads html splitBam html splitGAlignmentsByCut html vPlot html writeListOfGAlignments 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 'ATACseqQC' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ATACseqQC' as ATACseqQC_1.8.5.zip * DONE (ATACseqQC) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'ATACseqQC' successfully unpacked and MD5 sums checked
ATACseqQC.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("ATACseqQC") || stop("unable to load Package:ATACseqQC") Loading required package: ATACseqQC 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 [1] TRUE > require("GenomicAlignments") || stop("unable to load Package:GenomicAlignments") Loading required package: GenomicAlignments Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: SummarizedExperiment 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")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: Rsamtools [1] TRUE > require("BSgenome") || stop("unable to load Package:BSgenome") Loading required package: BSgenome Loading required package: rtracklayer [1] TRUE > require("rtracklayer") || stop("unable to load Package:rtracklayer") [1] TRUE > require("utils") || stop("unable to load Package:utils") [1] TRUE > require("testthat") || stop("unable to load testthat") Loading required package: testthat [1] TRUE > test_check("ATACseqQC") == testthat results =========================================================== [ OK: 21 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 17.64 1.56 19.18 |
ATACseqQC.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("ATACseqQC") || stop("unable to load Package:ATACseqQC") Loading required package: ATACseqQC 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 [1] TRUE > require("GenomicAlignments") || stop("unable to load Package:GenomicAlignments") Loading required package: GenomicAlignments Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: SummarizedExperiment 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")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: Rsamtools [1] TRUE > require("BSgenome") || stop("unable to load Package:BSgenome") Loading required package: BSgenome Loading required package: rtracklayer [1] TRUE > require("rtracklayer") || stop("unable to load Package:rtracklayer") [1] TRUE > require("utils") || stop("unable to load Package:utils") [1] TRUE > require("testthat") || stop("unable to load testthat") Loading required package: testthat [1] TRUE > test_check("ATACseqQC") == testthat results =========================================================== [ OK: 21 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 17.84 0.59 18.40 |
ATACseqQC.Rcheck/examples_i386/ATACseqQC-Ex.timings
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ATACseqQC.Rcheck/examples_x64/ATACseqQC-Ex.timings
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