Jianhong Ou
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ATACseqQC |
| Branch: RELEASE_3_6 |
| Last Commit: 920bfd2 |
| Last Changed Date: 2018-03-07 15:44:55 -0400 (Wed, 07 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:16:14 -0400 (Thu, 12 Apr 2018).
| Package 78/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ATACseqQC 1.2.10 Jianhong Ou
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: ATACseqQC |
| Version: 1.2.10 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ATACseqQC_1.2.10.tar.gz |
| StartedAt: 2018-04-11 21:34:13 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 21:42:16 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 483.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ATACseqQC.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ATACseqQC_1.2.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ATACseqQC.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.10’
* 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 9.5Mb
sub-directories of 1Mb or more:
doc 1.9Mb
extdata 7.5Mb
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
enrichedFragments 101.364 0.464 101.922
splitBam 86.084 0.912 87.383
factorFootprints 20.688 0.632 22.013
splitGAlignmentsByCut 6.000 0.640 6.658
shiftGAlignmentsList 5.456 0.208 5.670
* 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-3.6-bioc/meat/ATACseqQC.Rcheck/00check.log’
for details.
ATACseqQC.Rcheck/00install.out
* installing *source* package ‘ATACseqQC’ ... ** R ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
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
14.488 0.288 15.196
ATACseqQC.Rcheck/ATACseqQC-Ex.timings
| name | user | system | elapsed | |
| bamQC | 3.432 | 0.040 | 3.476 | |
| enrichedFragments | 101.364 | 0.464 | 101.922 | |
| factorFootprints | 20.688 | 0.632 | 22.013 | |
| fragSizeDist | 0.436 | 0.020 | 0.454 | |
| plotFootprints | 1.384 | 0.528 | 1.953 | |
| readBamFile | 0.928 | 0.036 | 0.963 | |
| shiftGAlignmentsList | 5.456 | 0.208 | 5.670 | |
| splitBam | 86.084 | 0.912 | 87.383 | |
| splitGAlignmentsByCut | 6.000 | 0.640 | 6.658 | |
| writeListOfGAlignments | 0.392 | 0.004 | 0.396 | |