Kevin Rue-Albrecht
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TVTB |
| Branch: RELEASE_3_10 |
| Last Commit: 09eb141 |
| Last Changed Date: 2019-10-29 13:10:13 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:44:29 -0400 (Wed, 15 Apr 2020).
| Package 1767/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TVTB 1.12.0 Kevin Rue-Albrecht
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... | ||||||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| Package: TVTB |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TVTB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TVTB_1.12.0.tar.gz |
| StartedAt: 2020-04-15 06:19:30 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:26:37 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 427.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TVTB.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TVTB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TVTB_1.12.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/TVTB.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TVTB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TVTB’ version ‘1.12.0’
* 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 ‘TVTB’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotInfo-methods 8.288 0.298 8.644
* 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
TVTB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TVTB ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘TVTB’ ... ** 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 (TVTB)
TVTB.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-apple-darwin15.6.0 (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(TVTB)
>
> test_check("TVTB")
Class: Genotypes
@ref (hom. ref.): "REF" {0/0}
@het (heter.) : "HET" {0/1, 1/0}
@alt (hom. alt.): "ALT" {1/1}class: TVTBparam
@genos: class: Genotypes
@ref (hom. ref.): "REF" {0|0}
@het (heter.): "HET" {0|1, 1|0}
@alt (hom. alt.): "ALT" {1|1}
@ranges: 0 GRanges on 0 sequence(s)
@aaf (alt. allele freq.): "AAF"
@maf (minor allele freq.): "MAF"
@vep (Ensembl VEP key): "CSQ"
@svp: <ScanVcfParam object>
@bp: <SerialParam object>
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366
TRUE FALSE FALSE FALSE FALSE FALSE
rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672
TRUE TRUE FALSE FALSE TRUE FALSE
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382
TRUE FALSE TRUE TRUE FALSE FALSE
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600
FALSE FALSE FALSE FALSE FALSE FALSE
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548
FALSE FALSE FALSE FALSE TRUE
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366
FALSE FALSE FALSE FALSE FALSE FALSE
rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672
FALSE FALSE FALSE FALSE FALSE FALSE
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382
FALSE FALSE FALSE FALSE FALSE FALSE
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600
FALSE FALSE FALSE FALSE FALSE FALSE
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548
FALSE FALSE FALSE FALSE FALSE
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366
TRUE FALSE FALSE FALSE FALSE FALSE
rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672
TRUE TRUE FALSE FALSE TRUE FALSE
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382
TRUE FALSE TRUE TRUE FALSE FALSE
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600
FALSE FALSE FALSE FALSE FALSE FALSE
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548
FALSE FALSE FALSE FALSE TRUE
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 227 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
49.962 2.541 52.849
TVTB.Rcheck/TVTB-Ex.timings
| name | user | system | elapsed | |
| Genotypes-class | 0.002 | 0.000 | 0.003 | |
| TVTBParam-class | 0.196 | 0.005 | 0.201 | |
| VcfBasicRules-class | 2.696 | 0.176 | 2.887 | |
| VcfFilterRules-class | 1.901 | 0.245 | 2.157 | |
| addCountGenos-methods | 0.958 | 0.109 | 1.073 | |
| addFrequencies-methods | 0.940 | 0.106 | 1.054 | |
| addOverallFrequencies-methods | 1.063 | 0.136 | 1.205 | |
| addPhenoLevelFrequencies-methods | 0.893 | 0.106 | 1.007 | |
| autodetectGenotypes | 0.834 | 0.154 | 0.997 | |
| countGenos-methods | 0.681 | 0.098 | 0.788 | |
| dropInfo-methods | 0.864 | 0.105 | 0.984 | |
| pairsInfo-methods | 2.011 | 0.123 | 2.151 | |
| plotInfo-methods | 8.288 | 0.298 | 8.644 | |
| readVcf-methods | 0.484 | 0.003 | 0.491 | |
| tSVE | 0.001 | 0.000 | 0.000 | |
| variantsInSamples-methods | 0.691 | 0.099 | 0.795 | |
| vepInPhenoLevel-methods | 0.921 | 0.133 | 1.061 | |