Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-01 17:18:36 -0500 (Wed, 01 Dec 2021).

CHECK results for TBSignatureProfiler on machv2

To the developers/maintainers of the TBSignatureProfiler package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TBSignatureProfiler.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 1935/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TBSignatureProfiler 1.6.0  (landing page)
Aubrey Odom
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/TBSignatureProfiler
git_branch: RELEASE_3_14
git_last_commit: fe6bf5e
git_last_commit_date: 2021-10-26 12:59:18 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TBSignatureProfiler
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TBSignatureProfiler_1.6.0.tar.gz
StartedAt: 2021-11-30 22:14:20 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 22:19:10 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 290.1 seconds
RetCode: 0
Status:   OK  
CheckDir: TBSignatureProfiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TBSignatureProfiler_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ 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 ‘TBSignatureProfiler’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
evaluateOriginalModel 14.477  0.896  15.389
bootstrapAUC          13.225  0.485  13.719
compareAlgs            8.075  0.625   8.705
signatureROCplot_CI    7.350  0.908   8.260
SignatureQuantitative  7.705  0.233   7.945
signatureGeneHeatmap   6.820  0.075   6.903
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘packagecoverage.R’
  Running ‘spelling.R’
  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


Installation output

TBSignatureProfiler.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘TBSignatureProfiler’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (TBSignatureProfiler)

Tests output

TBSignatureProfiler.Rcheck/tests/packagecoverage.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> # Coverage Script
> # Run tests and generate Code Coverage Report
> 
> # Look at a specific script ---------------------------------------------------
> #test_for_me <- function(codefile, testfile) {
> #  test_file(testfile)
> #  res <- covr::file_coverage(codefile, testfile)
> #  print(res)
> #  covr::report(res)
> #}
> 
> #test_for_me("R/evaluate.R", "tests/testthat/test-evaluate.R")
>   
> # Look at whole package -------------------------------------------------------
> 
> # Gets percent coverage for entire package, by script
>   
> #covr::package_coverage()
> #
> # Report with gui (probably the best here)
> #covr::report()
> 
> 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.319   0.078   0.372 

TBSignatureProfiler.Rcheck/tests/spelling.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> if (requireNamespace("spelling", quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.268   0.064   0.305 

TBSignatureProfiler.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(TBSignatureProfiler)
> 
> test_check("TBSignatureProfiler")

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Estimating GSVA scores for 1 gene sets.
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Estimating GSVA scores for 1 gene sets.
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Estimating GSVA scores for 1 gene sets.
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══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 153 ]
> 
> proc.time()
   user  system elapsed 
102.893   4.169 107.148 

Example timings

TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings

nameusersystemelapsed
COVIDsignatures0.0130.0040.017
OriginalTrainingData0.0010.0020.003
SignatureQuantitative7.7050.2337.945
TBSPapp0.0000.0000.001
TB_hiv0.0020.0020.003
TB_indian0.0020.0020.003
TBcommon0.0010.0010.003
TBsignatures0.0010.0010.002
TBsignaturesSplit0.0010.0010.002
addTBsignature0.0090.0030.012
bootstrapAUC13.225 0.48513.719
common_sigAnnotData0.0010.0020.002
compareAlgs8.0750.6258.705
compareBoxplots0.9350.0130.949
deseq2_norm_rle0.5000.0230.545
distinctColors0.0020.0010.002
evaluateOriginalModel14.477 0.89615.389
mkAssay1.9210.1542.075
plotQuantitative3.4400.1973.644
runTBsigProfiler0.3840.0070.391
sigAnnotData0.0020.0010.003
signatureBoxplot1.1320.0211.153
signatureGeneHeatmap6.8200.0756.903
signatureHeatmap1.0980.0291.162
signatureROCplot0.7500.0060.757
signatureROCplot_CI7.3500.9088.260
tableAUC0.8470.0490.897