Qian Liu
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SeqSQC |
| Branch: RELEASE_3_9 |
| Last Commit: 48c3f1b |
| Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:12:34 -0400 (Wed, 16 Oct 2019).
| Package 1500/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SeqSQC 1.6.0 Qian Liu
| 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: SeqSQC |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SeqSQC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SeqSQC_1.6.0.tar.gz |
| StartedAt: 2019-10-16 04:57:42 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:00:39 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 176.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SeqSQC.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SeqSQC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SeqSQC_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SeqSQC.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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 23.488 1.945 29.447
Inbreeding 5.256 0.084 5.340
* 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-3.9-bioc/R/bin/R CMD INSTALL SeqSQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
6.548 0.234 6.765
SeqSQC.Rcheck/SeqSQC-Ex.timings
| name | user | system | elapsed | |
| IBDCheck | 0.514 | 0.017 | 0.575 | |
| IBDRemove | 0.424 | 0.000 | 0.424 | |
| Inbreeding | 5.256 | 0.084 | 5.340 | |
| LoadVfile | 23.488 | 1.945 | 29.447 | |
| MissingRate | 0.146 | 0.064 | 0.209 | |
| PCACheck | 0.627 | 0.012 | 0.638 | |
| RenderReport | 3.801 | 0.320 | 4.135 | |
| SeqOpen | 0.035 | 0.000 | 0.036 | |
| SeqSQC-class | 0.012 | 0.004 | 0.016 | |
| SexCheck | 0.437 | 0.019 | 0.470 | |
| plotQC | 0.550 | 0.044 | 0.594 | |
| problemList | 0.022 | 0.000 | 0.022 | |
| sampleQC | 0 | 0 | 0 | |