Multiple platform build/check report for BioC 3.23 - CHECK results for TBSignatureProfiler on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4872
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4580
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:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: TBSignatureProfiler

Version: 1.23.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings TBSignatureProfiler_1.23.0.tar.gz

StartedAt: 2025-12-11 06:19:35 -0500 (Thu, 11 Dec 2025)

EndedAt: 2025-12-11 06:22:11 -0500 (Thu, 11 Dec 2025)

EllapsedTime: 155.2 seconds

RetCode: 1

Status: ERROR

CheckDir: TBSignatureProfiler.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings TBSignatureProfiler_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/TBSignatureProfiler.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ version ‘1.23.0’
* 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 code 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 loading without being on the library search path ... 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 10.6  0.606   11.21
* 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:
  Error in `if (nrow(path) <= 1) {     next }`: argument is of length zero
  Backtrace:
      ▆
   1. ├─testthat::expect_is(...) at test-profile.R:186:3
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─TBSignatureProfiler::runTBsigProfiler(...)
   5.   └─TBSignatureProfiler:::score_algorithm(...)
   6.     └─ASSIGN::assign.wrapper(...)
   7.       └─ASSIGN:::heatmap.test.pos(...)
  
  [ FAIL 1 | WARN 8 | SKIP 0 | PASS 135 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/TBSignatureProfiler.Rcheck/00check.log’
for details.

Installation output

TBSignatureProfiler.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL TBSignatureProfiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘TBSignatureProfiler’ ...
** this is package ‘TBSignatureProfiler’ version ‘1.23.0’
** 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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.140   0.037   0.164

TBSignatureProfiler.Rcheck/tests/spelling.Rout


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.141   0.041   0.171

TBSignatureProfiler.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
Warning: stack imbalance in '::', 52 then 54
Warning: stack imbalance in '<-', 50 then 52

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================================================================================
================================================================================
================================================================================
Saving _problems/test-profile-191.R
================================================================================
[ FAIL 1 | WARN 8 | SKIP 0 | PASS 135 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-profile.R:186:3'): data.frame input ────────────────────────────
Error in `if (nrow(path) <= 1) {     next }`: argument is of length zero
Backtrace:
    ▆
 1. ├─testthat::expect_is(...) at test-profile.R:186:3
 2. │ └─testthat::quasi_label(enquo(object), label)
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─TBSignatureProfiler::runTBsigProfiler(...)
 5.   └─TBSignatureProfiler:::score_algorithm(...)
 6.     └─ASSIGN::assign.wrapper(...)
 7.       └─ASSIGN:::heatmap.test.pos(...)

[ FAIL 1 | WARN 8 | SKIP 0 | PASS 135 ]
Error:
! Test failures.
Execution halted

Example timings

TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings

name	user	system	elapsed
COVIDsignatures	0.009	0.006	0.015
OriginalTrainingData	0.000	0.001	0.001
SignatureQuantitative	3.805	0.218	4.032
TBSPapp	0	0	0
TB_hiv	0.000	0.001	0.001
TB_indian	0.000	0.001	0.000
TBcommon	0.001	0.000	0.000
TBsignatures	0.000	0.001	0.001
TBsignaturesSplit	0.001	0.000	0.000
addTBsignature	0.007	0.002	0.008
bootstrapAUC	10.600	0.606	11.210
common_sigAnnotData	0.000	0.001	0.001
compareAlgs	2.514	0.102	2.618
compareBoxplots	0.931	0.054	0.985
deseq2_norm_rle	0.226	0.017	0.242
distinctColors	0.002	0.000	0.001
evaluateOriginalModel	0.219	0.023	0.241
mkAssay	2.810	0.067	2.877
plotQuantitative	1.670	0.019	1.690
runTBsigProfiler	1.426	0.050	1.476
sigAnnotData	0.001	0.000	0.001
signatureBoxplot	0.832	0.008	0.840
signatureGeneHeatmap	3.488	0.021	3.510
signatureHeatmap	0.685	0.041	0.727
signatureROCplot	0.935	0.005	0.941
signatureROCplot_CI	4.875	0.088	4.964
tableAUC	0.585	0.051	0.636