Jennifer Tom
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/genotypeeval |
| Branch: RELEASE_3_9 |
| Last Commit: 24aab4f |
| Last Changed Date: 2019-05-02 11:53:56 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:07:07 -0400 (Wed, 16 Oct 2019).
| Package 664/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genotypeeval 1.16.0 Jennifer Tom
| 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: genotypeeval |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:genotypeeval.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings genotypeeval_1.16.0.tar.gz |
| StartedAt: 2019-10-16 01:58:02 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:04:21 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 379.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: genotypeeval.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:genotypeeval.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings genotypeeval_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/genotypeeval.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 ‘genotypeeval/DESCRIPTION’ ... OK * this is package ‘genotypeeval’ version ‘1.16.0’ * 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 ‘genotypeeval’ can be installed ... OK * checking installed package size ... OK * checking package 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 ... NOTE Missing or unexported object: ‘GenomicRanges::subset’ * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.9-bioc/meat/genotypeeval.Rcheck/00check.log’ for details.
genotypeeval.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL genotypeeval ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘genotypeeval’ ... ** 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 (genotypeeval)
genotypeeval.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(genotypeeval)
Loading required package: VariantAnnotation
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: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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: Rsamtools
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
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
>
> test_check("genotypeeval")
Reading VCF ...
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
82.286 1.936 84.997
genotypeeval.Rcheck/genotypeeval-Ex.timings
| name | user | system | elapsed | |
| GoldDataFromGRanges | 0.058 | 0.012 | 0.071 | |
| GoldDataParam | 0.001 | 0.000 | 0.001 | |
| ReadGoldData | 1.048 | 0.056 | 1.126 | |
| ReadVCFData | 2.986 | 0.059 | 3.085 | |
| ReadVCFDataChunk | 4.018 | 0.020 | 4.073 | |
| VCFEvaluate | 4.553 | 0.000 | 4.584 | |
| VCFQAParam | 0.001 | 0.000 | 0.001 | |
| didSamplePass | 2.908 | 0.044 | 2.964 | |
| didSamplePassOverall | 2.882 | 0.007 | 2.890 | |
| getName | 3.272 | 0.000 | 3.273 | |
| getPlots | 4.417 | 0.012 | 4.453 | |
| getResults | 2.914 | 0.004 | 2.973 | |
| getVR | 1.682 | 0.004 | 1.688 | |