Qian Liu
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/SeqSQC |
| Branch: RELEASE_3_10 |
| Last Commit: fbc7a0d |
| Last Changed Date: 2020-02-14 14:37:07 -0400 (Fri, 14 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:13:27 -0400 (Wed, 15 Apr 2020).
| Package 1569/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SeqSQC 1.8.1 Qian Liu
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SeqSQC |
| Version: 1.8.1 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SeqSQC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SeqSQC_1.8.1.tar.gz |
| StartedAt: 2020-04-15 05:16:42 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:19:36 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 173.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SeqSQC.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SeqSQC.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SeqSQC_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/SeqSQC.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqSQC/DESCRIPTION’ ... OK
* this is package ‘SeqSQC’ version ‘1.8.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SeqSQC’ can be installed ... OK
* checking installed package size ... OK
* 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
LoadVfile 22.232 1.744 25.721
Inbreeding 5.316 0.112 5.440
RenderReport 4.752 0.296 5.126
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: OK
SeqSQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SeqSQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘SeqSQC’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SeqSQC)
SeqSQC.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> library(testthat)
> library(SeqSQC)
Loading required package: ExperimentHub
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: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: SNPRelate
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
>
> test_check("SeqSQC")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
7.104 0.180 7.325
SeqSQC.Rcheck/SeqSQC-Ex.timings
| name | user | system | elapsed | |
| IBDCheck | 0.700 | 0.008 | 0.791 | |
| IBDRemove | 1.06 | 0.00 | 1.06 | |
| Inbreeding | 5.316 | 0.112 | 5.440 | |
| LoadVfile | 22.232 | 1.744 | 25.721 | |
| MissingRate | 0.208 | 0.056 | 0.266 | |
| PCACheck | 0.780 | 0.020 | 0.807 | |
| RenderReport | 4.752 | 0.296 | 5.126 | |
| SeqOpen | 0.020 | 0.012 | 0.035 | |
| SeqSQC-class | 0.016 | 0.004 | 0.017 | |
| SexCheck | 0.400 | 0.008 | 0.425 | |
| plotQC | 0.352 | 0.040 | 0.393 | |
| problemList | 0.012 | 0.000 | 0.014 | |
| sampleQC | 0.000 | 0.000 | 0.001 | |