Jianhong Ou
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ATACseqQC |
| Branch: RELEASE_3_7 |
| Last Commit: 29b48ac |
| Last Changed Date: 2018-09-27 12:50:36 -0400 (Thu, 27 Sep 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:30:14 -0400 (Wed, 17 Oct 2018).
| Package 80/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ATACseqQC 1.4.3 Jianhong Ou
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ATACseqQC |
| Version: 1.4.3 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ATACseqQC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ATACseqQC_1.4.3.tar.gz |
| StartedAt: 2018-10-15 22:33:34 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 22:40:18 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 403.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ATACseqQC.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ATACseqQC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ATACseqQC_1.4.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ATACseqQC.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ATACseqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ATACseqQC’ version ‘1.4.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ATACseqQC’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.2Mb
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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
enrichedFragments 64.560 0.332 65.003
footprintsScanner 24.844 0.368 25.228
distanceDyad 17.868 0.336 18.226
factorFootprints 16.692 0.880 17.654
vPlot 14.392 0.228 14.628
splitGAlignmentsByCut 7.080 0.296 7.385
* 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
‘/home/biocbuild/bbs-3.7-bioc/meat/ATACseqQC.Rcheck/00check.log’
for details.
ATACseqQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ATACseqQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘ATACseqQC’ ... ** R ** 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 * DONE (ATACseqQC)
ATACseqQC.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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
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
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 FAILED: 0
>
> proc.time()
user system elapsed
13.844 0.360 14.704
ATACseqQC.Rcheck/ATACseqQC-Ex.timings
| name | user | system | elapsed | |
| NFRscore | 1.168 | 0.036 | 1.235 | |
| PTscore | 0.672 | 0.008 | 0.682 | |
| bamQC | 2.700 | 0.036 | 2.757 | |
| distanceDyad | 17.868 | 0.336 | 18.226 | |
| enrichedFragments | 64.560 | 0.332 | 65.003 | |
| estimateLibComplexity | 3.872 | 0.000 | 3.888 | |
| factorFootprints | 16.692 | 0.880 | 17.654 | |
| footprintsScanner | 24.844 | 0.368 | 25.228 | |
| fragSizeDist | 0.688 | 0.004 | 0.722 | |
| plotCorrelation | 1.088 | 0.008 | 1.095 | |
| plotFootprints | 0.596 | 0.000 | 0.597 | |
| prepareBindingSitesList | 0.268 | 0.000 | 0.269 | |
| readBamFile | 0.932 | 0.000 | 0.935 | |
| readsDupFreq | 0.380 | 0.008 | 0.387 | |
| saturationPlot | 0.000 | 0.000 | 0.001 | |
| shiftGAlignmentsList | 4.552 | 0.168 | 4.726 | |
| splitBam | 0.004 | 0.000 | 0.001 | |
| splitGAlignmentsByCut | 7.080 | 0.296 | 7.385 | |
| vPlot | 14.392 | 0.228 | 14.628 | |
| writeListOfGAlignments | 0.260 | 0.004 | 0.266 | |