Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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

Package 2136/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TBSignatureProfiler 1.16.0  (landing page)
Aubrey R. Odom
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/TBSignatureProfiler
git_branch: RELEASE_3_19
git_last_commit: 5f3c2c3
git_last_commit_date: 2024-04-30 11:23:30 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    NA  

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: 1.16.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TBSignatureProfiler_1.16.0.tar.gz
StartedAt: 2024-10-17 05:47:32 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 05:50:44 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 191.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TBSignatureProfiler.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TBSignatureProfiler_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ version ‘1.16.0’
* 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 ... NOTE
checkRd: (-1) COVIDsignatures.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) TBcommon.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) TBsignatures.Rd:12: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) TBsignatures.Rd:77: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) TBsignatures.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) TBsignatures.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runTBsigProfiler.Rd:51: Lost braces
    51 | be of the form <algorithm>_<signature>. It must be set to code{TRUE} if the
       |                                                               ^
* 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 10.051  0.888  10.942
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘packagecoverage.R’
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/TBSignatureProfiler.Rcheck/00check.log’
for details.

Installation output

TBSignatureProfiler.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL TBSignatureProfiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘TBSignatureProfiler’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TBSignatureProfiler)

Tests output

TBSignatureProfiler.Rcheck/tests/packagecoverage.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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 
  0.155   0.030   0.173

TBSignatureProfiler.Rcheck/tests/spelling.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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)
NULL
> 
> proc.time()
   user  system elapsed 
  0.153   0.034   0.177

TBSignatureProfiler.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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")

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

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[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
================================================================================
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
================================================================================
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
================================================================================
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
================================================================================
================================================================================
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 136 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 136 ]
> 
> proc.time()
   user  system elapsed 
 59.072   1.736  60.805

Example timings

TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings

nameusersystemelapsed
COVIDsignatures0.0110.0040.015
OriginalTrainingData0.0010.0000.001
SignatureQuantitative3.0460.1473.193
TBSPapp0.0010.0000.001
TB_hiv0.0000.0010.001
TB_indian0.0000.0010.001
TBcommon0.0000.0000.001
TBsignatures0.0000.0000.001
TBsignaturesSplit0.0000.0010.000
addTBsignature0.0040.0060.009
bootstrapAUC10.051 0.88810.942
common_sigAnnotData0.0010.0000.001
compareAlgs1.4620.0471.509
compareBoxplots1.5590.1161.675
deseq2_norm_rle0.2340.0200.254
distinctColors0.0010.0000.001
evaluateOriginalModel0.2030.0000.203
mkAssay2.5240.0842.608
plotQuantitative1.3470.0601.407
runTBsigProfiler0.3250.0400.365
sigAnnotData0.0010.0000.001
signatureBoxplot0.6880.0080.696
signatureGeneHeatmap3.3290.0383.367
signatureHeatmap0.5950.0320.628
signatureROCplot0.6530.0120.665
signatureROCplot_CI4.7340.0724.807
tableAUC0.5000.0080.508