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This page was generated on 2021-10-19 12:05:42 -0400 (Tue, 19 Oct 2021).

CHECK results for TBSignatureProfiler on merida1

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 1913/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TBSignatureProfiler 1.5.14  (landing page)
Aubrey Odom
Snapshot Date: 2021-10-18 14:50:10 -0400 (Mon, 18 Oct 2021)
git_url: https://git.bioconductor.org/packages/TBSignatureProfiler
git_branch: master
git_last_commit: 8fb176f
git_last_commit_date: 2021-09-29 17:23:12 -0400 (Wed, 29 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: TBSignatureProfiler
Version: 1.5.14
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_1.5.14.tar.gz
StartedAt: 2021-10-19 09:53:51 -0400 (Tue, 19 Oct 2021)
EndedAt: 2021-10-19 09:58:48 -0400 (Tue, 19 Oct 2021)
EllapsedTime: 296.9 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_1.5.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.5.14’
* 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 14.603  0.696  15.340
bootstrapAUC          13.023  0.484  13.546
compareAlgs            8.155  0.547   8.729
SignatureQuantitative  7.852  0.262   8.142
signatureROCplot_CI    7.291  0.602   7.912
signatureGeneHeatmap   6.268  0.076   6.521
* 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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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 
  0.443   0.138   0.521 

TBSignatureProfiler.Rcheck/tests/spelling.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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 
  0.470   0.147   0.563 

TBSignatureProfiler.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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")
Estimating ssGSEA scores for 1 gene sets.
Estimating ssGSEA scores for 1 gene sets.

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Estimating ssGSEA scores for 1 gene sets.
Estimating ssGSEA scores for 1 gene sets.
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating ssGSEA scores for 1 gene sets.
================================================================================
Estimating PLAGE scores for 1 gene sets.
Estimating combined z-scores for 1 gene sets.
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating ssGSEA scores for 1 gene sets.
================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating ssGSEA scores for 1 gene sets.
================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating ssGSEA scores for 1 gene sets.
================================================================================
Estimating PLAGE scores for 1 gene sets.
Estimating combined z-scores for 1 gene sets.
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating ssGSEA scores for 1 gene sets.
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating ssGSEA scores for 1 gene sets.
Estimating ssGSEA scores for 1 gene sets.
================================================================================
Estimating ssGSEA scores for 1 gene sets.
================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating combined z-scores for 1 gene sets.
Estimating ssGSEA scores for 1 gene sets.
Estimating combined z-scores for 1 gene sets.
================================================================================
Estimating combined z-scores for 1 gene sets.
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating PLAGE scores for 1 gene sets.
Estimating ssGSEA scores for 1 gene sets.
Estimating PLAGE scores for 1 gene sets.
================================================================================
Estimating PLAGE scores for 1 gene sets.
Estimating combined z-scores for 1 gene sets.
Estimating PLAGE scores for 1 gene sets.
================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating ssGSEA scores for 1 gene sets.
Estimating ssGSEA scores for 1 gene sets.
================================================================================
================================================================================
Estimating PLAGE scores for 1 gene sets.
Estimating PLAGE scores for 1 gene sets.
Estimating combined z-scores for 1 gene sets.
Estimating combined z-scores for 1 gene sets.
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 153 ]
> 
> proc.time()
   user  system elapsed 
102.025   3.686 105.928 

Example timings

TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings

nameusersystemelapsed
COVIDsignatures0.0160.0030.020
OriginalTrainingData0.0010.0010.002
SignatureQuantitative7.8520.2628.142
TBSPapp000
TB_hiv0.0020.0010.002
TB_indian0.0010.0010.003
TBcommon0.0010.0020.003
TBsignatures0.0010.0010.003
TBsignaturesSplit0.0020.0010.003
addTBsignature0.0080.0040.012
bootstrapAUC13.023 0.48413.546
common_sigAnnotData0.0010.0010.002
compareAlgs8.1550.5478.729
compareBoxplots1.0670.0171.087
deseq2_norm_rle0.4560.0180.474
distinctColors0.0010.0010.002
evaluateOriginalModel14.603 0.69615.340
mkAssay2.0040.1422.150
plotQuantitative3.3910.1923.592
runTBsigProfiler0.3410.0060.349
sigAnnotData0.0020.0010.003
signatureBoxplot1.0220.0181.043
signatureGeneHeatmap6.2680.0766.521
signatureHeatmap0.9820.0140.999
signatureROCplot0.7750.0120.793
signatureROCplot_CI7.2910.6027.912
tableAUC0.8990.0370.941