Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

CHECK report for TBSignatureProfiler on malbec1

This page was generated on 2021-05-06 12:29:24 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the TBSignatureProfiler package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1840/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TBSignatureProfiler 1.2.0  (landing page)
David Jenkins
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/TBSignatureProfiler
Branch: RELEASE_3_12
Last Commit: 16ccdd3
Last Changed Date: 2020-10-27 11:56:28 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: TBSignatureProfiler
Version: 1.2.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings TBSignatureProfiler_1.2.0.tar.gz
StartedAt: 2021-05-06 06:34:37 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:38:22 -0400 (Thu, 06 May 2021)
EllapsedTime: 225.2 seconds
RetCode: 0
Status:   OK  
CheckDir: TBSignatureProfiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings TBSignatureProfiler_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ version ‘1.2.0’
* 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 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
bootstrapAUC          8.540  0.104   8.659
compareAlgs           7.080  0.196   7.290
SignatureQuantitative 6.172  0.200   6.404
signatureROCplot_CI   6.156  0.000   6.177
signatureGeneHeatmap  5.316  0.000   5.324
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL TBSignatureProfiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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/spelling.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.152   0.020   0.171 

TBSignatureProfiler.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating PLAGE scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating PLAGE scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating PLAGE scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating PLAGE scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating PLAGE scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating PLAGE scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating ssGSEA scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

================================================================================
================================================================================
Estimating PLAGE scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating PLAGE scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating combined z-scores for 1 gene sets.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

================================================================================
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (1)

[ FAIL 0 | WARN 4 | SKIP 1 | PASS 130 ]
> 
> proc.time()
   user  system elapsed 
 67.228   0.724  68.197 

Example timings

TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings

nameusersystemelapsed
SignatureQuantitative6.1720.2006.404
TBSPapp0.0000.0000.001
TB_hiv0.0040.0000.003
TB_indian0.0040.0000.001
TBcommon0.0000.0000.001
TBsignatures0.0040.0000.001
bootstrapAUC8.5400.1048.659
common_sigAnnotData0.0040.0000.001
compareAlgs7.0800.1967.290
compareBoxplots1.6360.0121.650
deseq2_norm_rle0.4400.0000.442
distinctColors0.0000.0000.001
mkAssay2.6240.0202.648
plotQuantitative2.8400.0002.847
runTBsigProfiler0.2520.0000.249
sigAnnotData0.0000.0000.001
signatureBoxplot0.9360.0000.936
signatureGeneHeatmap5.3160.0005.324
signatureHeatmap2.1040.0042.115
signatureROCplot1.3240.0041.333
signatureROCplot_CI6.1560.0006.177
tableAUC1.0680.0161.085