Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-02-01 11:06:30 -0500 (Wed, 01 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TBSignatureProfiler on nebbiolo1


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? 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 2012/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TBSignatureProfiler 1.11.0  (landing page)
Aubrey R. Odom-Mabey
Snapshot Date: 2023-01-31 14:00:20 -0500 (Tue, 31 Jan 2023)
git_url: https://git.bioconductor.org/packages/TBSignatureProfiler
git_branch: master
git_last_commit: 7b6a6a5
git_last_commit_date: 2023-01-27 11:47:21 -0500 (Fri, 27 Jan 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: TBSignatureProfiler
Version: 1.11.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TBSignatureProfiler_1.11.0.tar.gz
StartedAt: 2023-02-01 00:19:13 -0500 (Wed, 01 Feb 2023)
EndedAt: 2023-02-01 00:22:28 -0500 (Wed, 01 Feb 2023)
EllapsedTime: 194.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: TBSignatureProfiler.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TBSignatureProfiler_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TBSignatureProfiler.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ version ‘1.11.0’
* 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
bootstrapAUC        10.193  0.412  10.609
signatureROCplot_CI  5.626  0.124   5.749
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘packagecoverage.R’
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. └─testthat::expect_output(...) at test-bootstrap.R:48:2
   2.   └─testthat:::quasi_capture(...)
   3.     ├─testthat (local) .capture(...)
   4.     │ └─testthat::capture_output_lines(code, print, width = width)
   5.     │   └─testthat:::eval_with_output(code, print = print, width = width)
   6.     │     ├─withr::with_output_sink(path, withVisible(code))
   7.     │     │ └─base::force(code)
   8.     │     └─base::withVisible(code)
   9.     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 141 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘tbspVignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/TBSignatureProfiler.Rcheck/00check.log’
for details.


Installation output

TBSignatureProfiler.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TBSignatureProfiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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/packagecoverage.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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.

> # 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 
  0.163   0.027   0.177 

TBSignatureProfiler.Rcheck/tests/spelling.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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 
  0.192   0.033   0.213 

TBSignatureProfiler.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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")

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Estimating ssGSEA scores for 1 gene sets.
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[1] "Calculating absolute values from ranks..."

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[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
Estimating GSVA scores for 1 gene sets.
Estimating ECDFs with Gaussian kernels

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

Estimating ssGSEA scores for 1 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
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Estimating GSVA scores for 1 gene sets.
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Estimating ssGSEA scores for 1 gene sets.
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[1] "Normalizing..."
Estimating ssGSEA scores for 1 gene sets.
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[1] "Normalizing..."
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Estimating GSVA scores for 1 gene sets.
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Estimating combined z-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.
Estimating ECDFs with Gaussian kernels

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Estimating GSVA scores for 1 gene sets.
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[ FAIL 1 | WARN 3 | SKIP 0 | PASS 141 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bootstrap.R:48'): Run tableAUC ─────────────────────────────────
Error in `tableAUC(SE_scored = scored_testdata, signatureColNames = "sig1", 
    annotationColName = "Disease", pROC = FALSE, num.boot = 5)`: unused argument (pROC = FALSE)
Backtrace:
    ▆
 1. └─testthat::expect_output(...) at test-bootstrap.R:48:2
 2.   └─testthat:::quasi_capture(...)
 3.     ├─testthat (local) .capture(...)
 4.     │ └─testthat::capture_output_lines(code, print, width = width)
 5.     │   └─testthat:::eval_with_output(code, print = print, width = width)
 6.     │     ├─withr::with_output_sink(path, withVisible(code))
 7.     │     │ └─base::force(code)
 8.     │     └─base::withVisible(code)
 9.     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))

[ FAIL 1 | WARN 3 | SKIP 0 | PASS 141 ]
Error: Test failures
Execution halted

Example timings

TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings

nameusersystemelapsed
COVIDsignatures0.0120.0080.020
OriginalTrainingData0.0000.0010.001
SignatureQuantitative3.3530.1283.481
TBSPapp000
TB_hiv0.0010.0000.001
TB_indian0.0010.0000.001
TBcommon0.0000.0000.001
TBsignatures0.0010.0000.001
TBsignaturesSplit0.0010.0000.000
addTBsignature0.0060.0040.009
bootstrapAUC10.193 0.41210.609
common_sigAnnotData0.0000.0000.001
compareAlgs1.4320.1201.552
compareBoxplots0.8010.0240.825
deseq2_norm_rle0.1850.0200.205
distinctColors0.0010.0000.001
evaluateOriginalModel0.1710.0120.184
mkAssay2.7240.0722.796
plotQuantitative1.6300.0871.717
runTBsigProfiler0.2530.0100.263
sigAnnotData0.0000.0010.001
signatureBoxplot0.7010.0280.729
signatureGeneHeatmap3.6220.0923.715
signatureHeatmap0.6760.0120.688
signatureROCplot0.7140.0160.731
signatureROCplot_CI5.6260.1245.749
tableAUC0.6020.0160.617