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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 2157/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TVTB 1.26.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/TVTB
git_branch: RELEASE_3_17
git_last_commit: f28d805
git_last_commit_date: 2023-04-25 10:50:43 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for TVTB on kjohnson2


To the developers/maintainers of the TVTB package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TVTB
Version: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2023-10-19 08:44:13 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 08:57:27 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 794.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TVTB.Rcheck
Warnings: 1

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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TVTB.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TVTB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TVTB’ version ‘1.26.0’
* 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 ... WARNING
checkRd: (5) VcfBasicRules-class.Rd:133-136: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:137-140: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:141-146: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:147-151: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:161-164: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:165-168: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:179-192: \item in \describe must have non-empty label
checkRd: (5) VcfBasicRules-class.Rd:193-201: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:85-92: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:93-96: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:97-103: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:104-108: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:120-123: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:124-127: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:134-140: \item in \describe must have non-empty label
checkRd: (5) VcfFilterRules-class.Rd:141-149: \item in \describe must have non-empty label
* 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    8.150  0.389  17.195
VcfBasicRules-class 2.897  0.152   5.328
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_VcfFilterRules-class.R:438:1',
  'test_VcfFilterRules-class.R:468:1'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]
> 
> proc.time()
   user  system elapsed 
 48.009   4.681 116.072 

Example timings

TVTB.Rcheck/TVTB-Ex.timings

nameusersystemelapsed
Genotypes-class0.0030.0010.013
TVTBParam-class0.2010.0060.357
VcfBasicRules-class2.8970.1525.328
VcfFilterRules-class1.8570.0603.390
addCountGenos-methods0.9140.0371.709
addFrequencies-methods0.8710.0381.622
addOverallFrequencies-methods0.8660.0371.598
addPhenoLevelFrequencies-methods0.8380.0341.705
autodetectGenotypes0.7230.0361.347
countGenos-methods0.7260.0381.352
dropInfo-methods0.9330.0431.730
pairsInfo-methods1.8700.0633.451
plotInfo-methods 8.150 0.38917.195
readVcf-methods0.5060.0091.348
tSVE000
variantsInSamples-methods0.7230.0602.118
vepInPhenoLevel-methods0.9260.1292.730