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This page was generated on 2022-01-21 11:12:35 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TVTB on merida1


To the developers/maintainers of the TVTB package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TVTB.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2009/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TVTB 1.21.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/TVTB
git_branch: master
git_last_commit: 9cb742d
git_last_commit_date: 2021-10-26 12:31:08 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64... NOT SUPPORTED ...
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TVTB
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TVTB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TVTB_1.21.0.tar.gz
StartedAt: 2022-01-21 06:55:58 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 07:06:08 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 609.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TVTB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TVTB.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TVTB_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/TVTB.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
plotInfo-methods    10.613  0.237  11.019
VcfBasicRules-class  5.493  0.296   5.803
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/TVTB.Rcheck/00check.log’
for details.



Installation output

TVTB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TVTB
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘TVTB’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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)

Tests output

TVTB.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]
> 
> proc.time()
   user  system elapsed 
 69.839   2.145  72.651 

Example timings

TVTB.Rcheck/TVTB-Ex.timings

nameusersystemelapsed
Genotypes-class0.0030.0010.005
TVTBParam-class0.3100.0040.315
VcfBasicRules-class5.4930.2965.803
VcfFilterRules-class2.9190.1153.040
addCountGenos-methods1.4560.0231.498
addFrequencies-methods1.4280.0401.501
addOverallFrequencies-methods1.3380.0181.366
addPhenoLevelFrequencies-methods1.3980.0221.453
autodetectGenotypes1.2220.0241.262
countGenos-methods1.2390.0491.347
dropInfo-methods1.4270.0241.516
pairsInfo-methods2.6430.0322.691
plotInfo-methods10.613 0.23711.019
readVcf-methods0.8160.0040.833
tSVE000
variantsInSamples-methods1.1720.0221.199
vepInPhenoLevel-methods1.3530.0531.410