Multiple platform build/check report for BioC 3.22 - CHECK results for notameStats on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4902
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4638
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 notameStats on nebbiolo2

To the developers/maintainers of the notameStats package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/notameStats.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: notameStats

Version: 1.0.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:notameStats.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings notameStats_1.0.0.tar.gz

StartedAt: 2025-11-11 02:22:00 -0500 (Tue, 11 Nov 2025)

EndedAt: 2025-11-11 02:26:56 -0500 (Tue, 11 Nov 2025)

EllapsedTime: 295.4 seconds

RetCode: 0

Status: OK

CheckDir: notameStats.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:notameStats.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings notameStats_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/notameStats.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘notameStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘notameStats’ version ‘1.0.0’
* 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 ‘notameStats’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
perform_auc               16.160  2.604   5.384
pls_da                    17.462  0.306  17.768
muvr_analysis             14.522  0.717  15.244
perform_lmer              12.141  1.986   5.102
perform_non_parametric     7.637  4.068   3.832
perform_logistic           7.215  2.165   1.703
pls                        7.958  0.653   8.530
perform_correlation_tests  4.638  2.790   3.039
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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-3.22-bioc/meat/notameStats.Rcheck/00check.log’
for details.

Installation output

notameStats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL notameStats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘notameStats’ ...
** this is package ‘notameStats’ version ‘1.0.0’
** using staged installation
** R
** 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 (notameStats)

Tests output

notameStats.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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(notameStats)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("notameStats")
Running tests in parallel requires the 3rd edition
INFO [2025-11-11 02:26:11] Starting to compute Cohen's D between groups B & A from time change 2 - 1
INFO [2025-11-11 02:26:11] Cohen's D computed.
INFO [2025-11-11 02:26:11] Starting to compute Cohen's D between groups B & A
INFO [2025-11-11 02:26:11] Cohen's D computed.
INFO [2025-11-11 02:26:11] Starting to compute fold changes.
INFO [2025-11-11 02:26:12] Fold changes computed.
INFO [2025-11-11 02:26:12] Starting to compute fold changes.
INFO [2025-11-11 02:26:12] Fold changes computed.
INFO [2025-11-11 02:26:12] Starting linear regression.
INFO [2025-11-11 02:26:13] Linear regression performed.
INFO [2025-11-11 02:26:14] Starting linear regression.
INFO [2025-11-11 02:26:15] Linear regression performed.
INFO [2025-11-11 02:26:15] 
92% of features flagged for low quality
INFO [2025-11-11 02:26:15] Starting linear regression.
INFO [2025-11-11 02:26:16] Linear regression performed.
INFO [2025-11-11 02:26:16] Starting logistic regression
INFO [2025-11-11 02:26:18] Logistic regression performed.
INFO [2025-11-11 02:26:18] Starting logistic regression
INFO [2025-11-11 02:26:20] Logistic regression performed.
INFO [2025-11-11 02:26:20] Starting to compute Cohen's D between groups B & A
INFO [2025-11-11 02:26:20] Cohen's D computed.
INFO [2025-11-11 02:26:20] Starting to compute Cohen's D between groups C & A
INFO [2025-11-11 02:26:21] Cohen's D computed.
INFO [2025-11-11 02:26:21] Starting to compute Cohen's D between groups C & B
INFO [2025-11-11 02:26:21] Cohen's D computed.
INFO [2025-11-11 02:26:21] Starting to compute Cohen's D between groups B & A from time change 2 - 1
INFO [2025-11-11 02:26:22] Cohen's D computed.
INFO [2025-11-11 02:26:22] Starting to compute Cohen's D between groups B & A from time change 3 - 1
INFO [2025-11-11 02:26:22] Cohen's D computed.
INFO [2025-11-11 02:26:22] Starting to compute Cohen's D between groups B & A from time change 3 - 2
INFO [2025-11-11 02:26:22] Cohen's D computed.
INFO [2025-11-11 02:26:22] Starting to compute Cohen's D between groups C & A from time change 2 - 1
INFO [2025-11-11 02:26:22] Cohen's D computed.
INFO [2025-11-11 02:26:22] Starting to compute Cohen's D between groups C & A from time change 3 - 1
INFO [2025-11-11 02:26:22] Cohen's D computed.
INFO [2025-11-11 02:26:22] Starting to compute Cohen's D between groups C & A from time change 3 - 2
INFO [2025-11-11 02:26:23] Cohen's D computed.
INFO [2025-11-11 02:26:23] Starting to compute Cohen's D between groups C & B from time change 2 - 1
INFO [2025-11-11 02:26:23] Cohen's D computed.
INFO [2025-11-11 02:26:23] Starting to compute Cohen's D between groups C & B from time change 3 - 1
INFO [2025-11-11 02:26:23] Cohen's D computed.
INFO [2025-11-11 02:26:23] Starting to compute Cohen's D between groups C & B from time change 3 - 2
INFO [2025-11-11 02:26:23] Cohen's D computed.
INFO [2025-11-11 02:26:23] Starting to compute Cohen's D between groups B & A from time change 2 - 1
INFO [2025-11-11 02:26:24] Cohen's D computed.
INFO [2025-11-11 02:26:24] Starting to compute Cohen's D between groups B & A from time change 3 - 1
INFO [2025-11-11 02:26:24] Cohen's D computed.
INFO [2025-11-11 02:26:24] Starting to compute Cohen's D between groups B & A from time change 3 - 2
INFO [2025-11-11 02:26:24] Cohen's D computed.
INFO [2025-11-11 02:26:24] Starting to compute Cohen's D between groups C & A from time change 2 - 1
INFO [2025-11-11 02:26:24] Cohen's D computed.
INFO [2025-11-11 02:26:24] Starting to compute Cohen's D between groups C & A from time change 3 - 1
INFO [2025-11-11 02:26:24] Cohen's D computed.
INFO [2025-11-11 02:26:25] Starting to compute Cohen's D between groups C & A from time change 3 - 2
INFO [2025-11-11 02:26:25] Cohen's D computed.
INFO [2025-11-11 02:26:25] Starting to compute Cohen's D between groups C & B from time change 2 - 1
INFO [2025-11-11 02:26:25] Cohen's D computed.
INFO [2025-11-11 02:26:25] Starting to compute Cohen's D between groups C & B from time change 3 - 1
INFO [2025-11-11 02:26:25] Cohen's D computed.
INFO [2025-11-11 02:26:25] Starting to compute Cohen's D between groups C & B from time change 3 - 2
INFO [2025-11-11 02:26:25] Cohen's D computed.
INFO [2025-11-11 02:26:25] Starting to compute Cohen's D between groups B & A from time change 2 - 1
INFO [2025-11-11 02:26:26] Cohen's D computed.
INFO [2025-11-11 02:26:26] Starting to compute Cohen's D between groups B & A from time change 3 - 1
INFO [2025-11-11 02:26:26] Cohen's D computed.
INFO [2025-11-11 02:26:26] Starting to compute Cohen's D between groups B & A from time change 3 - 2
INFO [2025-11-11 02:26:26] Cohen's D computed.
INFO [2025-11-11 02:26:26] Starting to compute Cohen's D between groups C & A from time change 2 - 1
INFO [2025-11-11 02:26:26] Cohen's D computed.
INFO [2025-11-11 02:26:26] Starting to compute Cohen's D between groups C & B from time change 2 - 1
INFO [2025-11-11 02:26:27] Cohen's D computed.
INFO [2025-11-11 02:26:27] Starting to compute Cohen's D between groups B & A from time change 2 - 1
INFO [2025-11-11 02:26:27] Cohen's D computed.
INFO [2025-11-11 02:26:27] Starting to compute Cohen's D between groups B & A from time change 3 - 1
INFO [2025-11-11 02:26:27] Cohen's D computed.
INFO [2025-11-11 02:26:27] Starting to compute Cohen's D between groups B & A from time change 3 - 2
INFO [2025-11-11 02:26:27] Cohen's D computed.
INFO [2025-11-11 02:26:27] Starting to compute Cohen's D between groups C & A from time change 2 - 1
INFO [2025-11-11 02:26:28] Cohen's D computed.
INFO [2025-11-11 02:26:28] Starting to compute Cohen's D between groups C & B from time change 2 - 1
INFO [2025-11-11 02:26:28] Cohen's D computed.
INFO [2025-11-11 02:26:28] Starting to compute Cohen's D between groups B & A from time change 3 - 2
INFO [2025-11-11 02:26:28] Cohen's D computed.
INFO [2025-11-11 02:26:28] Starting to compute Cohen's D between groups C & A from time change 2 - 1
INFO [2025-11-11 02:26:28] Cohen's D computed.
INFO [2025-11-11 02:26:28] Starting to compute Cohen's D between groups C & A from time change 3 - 1
INFO [2025-11-11 02:26:29] Cohen's D computed.
INFO [2025-11-11 02:26:29] Starting to compute Cohen's D between groups C & A from time change 3 - 2
INFO [2025-11-11 02:26:29] Cohen's D computed.
INFO [2025-11-11 02:26:29] Starting to compute Cohen's D between groups C & B from time change 2 - 1
INFO [2025-11-11 02:26:29] Cohen's D computed.
INFO [2025-11-11 02:26:29] Starting to compute Cohen's D between groups C & B from time change 3 - 1
INFO [2025-11-11 02:26:29] Cohen's D computed.
INFO [2025-11-11 02:26:29] Starting to compute Cohen's D between groups C & B from time change 3 - 2
INFO [2025-11-11 02:26:29] Cohen's D computed.
INFO [2025-11-11 02:26:30] Starting paired tests for 1 & 2
INFO [2025-11-11 02:26:30] Found 20 complete pairs.
INFO [2025-11-11 02:26:30] Paired tests performed.
INFO [2025-11-11 02:26:30] Starting tests for 1 & 2
INFO [2025-11-11 02:26:30] Tests performed
INFO [2025-11-11 02:26:30] Starting tests for 1 & 3
INFO [2025-11-11 02:26:30] Tests performed
INFO [2025-11-11 02:26:30] Starting tests for 2 & 3
INFO [2025-11-11 02:26:31] Tests performed
INFO [2025-11-11 02:26:31] Starting tests for 1 & 2
INFO [2025-11-11 02:26:31] Tests performed
INFO [2025-11-11 02:26:31] Starting tests for 1 & 3
INFO [2025-11-11 02:26:31] Tests performed
INFO [2025-11-11 02:26:31] Starting tests for 2 & 3
INFO [2025-11-11 02:26:31] Tests performed
INFO [2025-11-11 02:26:32] Starting paired tests for 1 & 2
INFO [2025-11-11 02:26:32] Found 4 complete pairs.
INFO [2025-11-11 02:26:32] Paired tests performed.
INFO [2025-11-11 02:26:32] Starting paired tests for 1 & 3
INFO [2025-11-11 02:26:32] Found 4 complete pairs.
INFO [2025-11-11 02:26:32] Paired tests performed.
INFO [2025-11-11 02:26:32] Starting paired tests for 2 & 3
INFO [2025-11-11 02:26:32] Found 4 complete pairs.
INFO [2025-11-11 02:26:32] Paired tests performed.
INFO [2025-11-11 02:26:32] Starting paired tests for 1 & 2
INFO [2025-11-11 02:26:32] Found 8 complete pairs.
INFO [2025-11-11 02:26:33] Paired tests performed.
INFO [2025-11-11 02:26:33] Starting paired tests for 1 & 3
INFO [2025-11-11 02:26:33] Found 8 complete pairs.
INFO [2025-11-11 02:26:33] Paired tests performed.
INFO [2025-11-11 02:26:33] Starting paired tests for 2 & 3
INFO [2025-11-11 02:26:33] Found 8 complete pairs.
INFO [2025-11-11 02:26:33] Paired tests performed.
INFO [2025-11-11 02:26:33] Starting paired tests for 1 & 2
INFO [2025-11-11 02:26:33] Found 4 complete pairs.
INFO [2025-11-11 02:26:33] Paired tests performed.
INFO [2025-11-11 02:26:33] Starting paired tests for 1 & 3
INFO [2025-11-11 02:26:33] Found 4 complete pairs.
INFO [2025-11-11 02:26:34] Paired tests performed.
INFO [2025-11-11 02:26:34] Starting paired tests for 2 & 3
INFO [2025-11-11 02:26:34] Found 4 complete pairs.
INFO [2025-11-11 02:26:34] Paired tests performed.
INFO [2025-11-11 02:26:34] Starting tests for A & B
INFO [2025-11-11 02:26:35] Tests performed
INFO [2025-11-11 02:26:36] Starting paired tests for 1 & 2
INFO [2025-11-11 02:26:36] Found 20 complete pairs.
INFO [2025-11-11 02:26:36] Paired tests performed.
INFO [2025-11-11 02:26:37] Starting tests for 1 & 2
INFO [2025-11-11 02:26:37] Tests performed
INFO [2025-11-11 02:26:37] Starting tests for 1 & 3
INFO [2025-11-11 02:26:37] Tests performed
INFO [2025-11-11 02:26:37] Starting tests for 2 & 3
INFO [2025-11-11 02:26:38] Tests performed
INFO [2025-11-11 02:26:38] Starting tests for 1 & 2
INFO [2025-11-11 02:26:38] Tests performed
INFO [2025-11-11 02:26:38] Starting tests for 1 & 3
INFO [2025-11-11 02:26:39] Tests performed
INFO [2025-11-11 02:26:39] Starting tests for 2 & 3
INFO [2025-11-11 02:26:39] Tests performed
INFO [2025-11-11 02:26:39] Starting paired tests for 1 & 2
INFO [2025-11-11 02:26:39] Found 4 complete pairs.
INFO [2025-11-11 02:26:39] Paired tests performed.
INFO [2025-11-11 02:26:39] Starting paired tests for 1 & 3
INFO [2025-11-11 02:26:39] Found 4 complete pairs.
INFO [2025-11-11 02:26:40] Paired tests performed.
INFO [2025-11-11 02:26:40] Starting paired tests for 2 & 3
INFO [2025-11-11 02:26:40] Found 4 complete pairs.
INFO [2025-11-11 02:26:40] Paired tests performed.
INFO [2025-11-11 02:26:40] Starting correlation tests.
INFO [2025-11-11 02:26:40] Performing correlation tests for single object
INFO [2025-11-11 02:26:40] Correlation tests performed.
INFO [2025-11-11 02:26:40] Starting correlation tests.
INFO [2025-11-11 02:26:40] Starting correlation tests.
INFO [2025-11-11 02:26:40] Starting correlation tests.
INFO [2025-11-11 02:26:40] Starting correlation tests.
INFO [2025-11-11 02:26:40] Performing correlation tests for two objects
INFO [2025-11-11 02:26:41] Correlation tests performed.
INFO [2025-11-11 02:26:41] Starting correlation tests.
INFO [2025-11-11 02:26:41] Performing correlation tests for two objects
INFO [2025-11-11 02:26:41] Correlation tests performed.
INFO [2025-11-11 02:26:41] Starting paired tests for 1 & 2
INFO [2025-11-11 02:26:41] Found 20 complete pairs.
INFO [2025-11-11 02:26:42] Paired tests performed.
INFO [2025-11-11 02:26:42] Starting tests for A & B
INFO [2025-11-11 02:26:42] Tests performed
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 88 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 88 ]
> 
> proc.time()
   user  system elapsed 
 53.226  36.785  44.725

Example timings

notameStats.Rcheck/notameStats-Ex.timings

name	user	system	elapsed
cohens_d	3.684	0.444	3.793
fit_rf	0.170	0.016	0.186
fold_change	0.342	0.521	0.370
importance_rf	0.204	0.055	0.185
muvr_analysis	14.522	0.717	15.244
perform_auc	16.160	2.604	5.384
perform_correlation_tests	4.638	2.790	3.039
perform_homoscedasticity_tests	3.115	1.507	1.573
perform_kruskal_wallis	2.283	1.212	0.775
perform_lm	2.054	1.233	1.375
perform_lm_anova	3.155	1.640	0.874
perform_lmer	12.141	1.986	5.102
perform_logistic	7.215	2.165	1.703
perform_non_parametric	7.637	4.068	3.832
perform_oneway_anova	1.250	0.914	0.705
perform_permanova	2.173	0.562	1.578
perform_t_test	1.339	2.050	1.738
pls	7.958	0.653	8.530
pls_da	17.462	0.306	17.768
summarize_results	2.465	1.030	1.232
summary_statistics	1.999	1.556	0.934