Multiple platform build/check report for BioC 3.20 - CHECK results for PolySTest on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 PolySTest on merida1

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

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PolySTest.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PolySTest_1.0.2.tar.gz

StartedAt: 2024-12-20 07:47:05 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 08:03:49 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 1004.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: PolySTest.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PolySTest.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PolySTest_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PolySTest.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PolySTest/DESCRIPTION’ ... OK
* this is package ‘PolySTest’ version ‘1.0.2’
* 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 ‘PolySTest’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in parse(con): 11:41: unexpected ','
  10:          year="2020",
  11:          doi="10.1074/mcp.RA119.001777"),
                                              ^
* 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 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 ... NOTE
perm_unpaired: no visible binding for global variable ‘NumTests’
permtest_paired: no visible binding for global variable ‘NumTests’
Undefined global functions or variables:
  NumTests
* 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
plotExpression     7.383  0.250   7.730
PolySTest_unpaired 0.796  0.079  49.510
perm_unpaired      0.036  0.016  24.408
rp_unpaired        0.014  0.012  19.036
FindFCandQlim      0.015  0.010  18.516
permtest_paired    0.013  0.009  19.024
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/PolySTest.Rcheck/00check.log’
for details.

Installation output

PolySTest.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PolySTest
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘PolySTest’ ...
** using staged installation
** R
** data
** 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 (PolySTest)

Tests output

PolySTest.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(PolySTest)
> 
> test_check("PolySTest")
Estimating suitable values for FDR and FC cutoff
Estimating suitable values for FDR and FC cutoff
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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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: GenomeInfoDb
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

Plotting number of regulated features
Running limma test
limma completed
Running Miss_Test test
Running Miss test ...
================================================================================
Miss_Test completed
=======tests completed

Unifying q-values across tests ...
Calculating PolySTest FDRs ...
------- Summary of Results --------
Number of differentially regulated features with FDR < 0.01:
|       | PolySTest| limma| Miss_Test| rank_products| permutation_test| t_test|
|:------|---------:|-----:|---------:|-------------:|----------------:|------:|
|B_vs_A |         0|     0|         0|             0|                0|      0|
Running limma test
limma completed
=======tests completed

------- Summary of Results --------
Number of differentially regulated features with FDR < 0.01:
|       | limma| t_test|
|:------|-----:|------:|
|B_vs_A |     0|      0|
Running limma test
limma completed
=======tests completed

Unifying q-values across tests ...
Calculating PolySTest FDRs ...
------- Summary of Results --------
Number of differentially regulated features with FDR < 0.01:
|       | PolySTest| limma| rank_products| t_test|
|:------|---------:|-----:|-------------:|------:|
|B_vs_A |         0|     0|             0|      0|
Running limma test
limma completed
Running Miss_Test test
Running Miss test ...
================================================================================
Miss_Test completed
================================================================================
tests completed
Unifying q-values across tests ...
Calculating PolySTest FDRs ...
------- Summary of Results --------
Number of differentially regulated features with FDR < 0.01:
|       | PolySTest| limma| Miss_Test| rank_products| permutation_test| t_test|
|:------|---------:|-----:|---------:|-------------:|----------------:|------:|
|B_vs_A |         0|     0|         0|             0|                0|      0|
Running limma test
limma completed
================================================================================
tests completed
------- Summary of Results --------
Number of differentially regulated features with FDR < 0.01:
|       | limma| t_test|
|:------|-----:|------:|
|B_vs_A |     0|      0|
Running limma test
limma completed
================================================================================
tests completed
Unifying q-values across tests ...
Calculating PolySTest FDRs ...
------- Summary of Results --------
Number of differentially regulated features with FDR < 0.01:
|       | PolySTest| limma| rank_products| t_test|
|:------|---------:|-----:|-------------:|------:|
|B_vs_A |         0|     0|             0|      0|
All pairwise comparison between conditions:
|Condition A |Condition B |
|:-----------|:-----------|
|TTA.Rep.    |HF.Rep.     |
|TTA.Rep.    |FO.Rep.     |
|TTA.Rep.    |TTA.FO.Rep. |
Running limma test
limma completed
Running Miss_Test test
Running Miss test ...
================================================================================
Miss_Test completed
======================================================tests completed

Unifying q-values across tests ...
Calculating PolySTest FDRs ...
------- Summary of Results --------
Number of differentially regulated features with FDR < 0.01:
|                        | PolySTest| limma| Miss_Test| rank_products| permutation_test| t_test|
|:-----------------------|---------:|-----:|---------:|-------------:|----------------:|------:|
|HF.Rep._vs_TTA.Rep.     |        23|    33|         9|             3|                0|      0|
|FO.Rep._vs_TTA.Rep.     |        20|    39|         8|             4|                0|      0|
|TTA.FO.Rep._vs_TTA.Rep. |         1|     0|         2|             0|                0|      0|
Running limma test
limma completed
Running Miss_Test test
Running Miss test ...
================================================================================
Miss_Test completed
================================================================================
tests completed
Unifying q-values across tests ...
Calculating PolySTest FDRs ...
------- Summary of Results --------
Number of differentially regulated features with FDR < 0.01:
|                        | PolySTest| limma| Miss_Test| rank_products| permutation_test| t_test|
|:-----------------------|---------:|-----:|---------:|-------------:|----------------:|------:|
|HF.Rep._vs_TTA.Rep.     |        34|    49|         7|             3|                0|     16|
|FO.Rep._vs_TTA.Rep.     |        33|    46|         7|             5|                0|     11|
|TTA.FO.Rep._vs_TTA.Rep. |         1|     0|         2|             0|                0|      0|
plotting expression profiles
Making circos plot
Note: 1 point is out of plotting region in sector '1', track '1'.
Note: 1 point is out of plotting region in sector '1', track '1'.
Note: 1 point is out of plotting region in sector '2', track '1'.
Note: 1 point is out of plotting region in sector '2', track '1'.
Note: 1 point is out of plotting region in sector '3', track '1'.
Note: 1 point is out of plotting region in sector '3', track '1'.
plotting expression profiles
Making circos plot
Note: 1 point is out of plotting region in sector '1', track '1'.
Note: 1 point is out of plotting region in sector '1', track '1'.
Note: 1 point is out of plotting region in sector '2', track '1'.
Note: 1 point is out of plotting region in sector '2', track '1'.
Note: 1 point is out of plotting region in sector '3', track '1'.
Note: 1 point is out of plotting region in sector '3', track '1'.
plotting heatmap ...
plotting heatmap ...
Plotting p-values
Plotting upset plots
Plotting volcano plots
Plotting volcano plots
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
 34.225   1.834 493.762

Example timings

PolySTest.Rcheck/PolySTest-Ex.timings

name	user	system	elapsed
FindFCandQlim	0.015	0.010	18.516
FindFCandQlimAlternative	0.003	0.002	0.005
MissValPDistr	0.000	0.001	0.001
MissingStats	0.060	0.005	0.064
MissingStatsDesign	0.224	0.006	0.238
PolySTest_paired	1.528	0.041	1.649
PolySTest_unpaired	0.796	0.079	49.510
RPStats	0.001	0.000	0.001
StatsForPermutTest	0.001	0.000	0.001
check_for_polystest	0.037	0.003	0.041
check_stat_names	0.016	0.004	0.020
create_pairwise_comparisons	0.006	0.001	0.007
get_numthreads	0	0	0
limma_paired	0.031	0.001	0.033
limma_unpaired	0.027	0.006	0.032
liver_example	0.014	0.003	0.017
perm_unpaired	0.036	0.016	24.408
permtest_paired	0.013	0.009	19.024
plotExpression	7.383	0.250	7.730
plotHeatmaply	4.135	0.127	4.264
plotPvalueDistr	0.114	0.007	0.122
plotRegNumber	0.599	0.023	0.628
plotUpset	1.693	0.028	1.799
plotVolcano	0.080	0.008	0.099
rp_unpaired	0.014	0.012	19.036
set_mfrow	0.043	0.002	0.045
ttest_paired	0.039	0.000	0.038
ttest_unpaired	0.062	0.004	0.066
update_conditions_with_lcs	0.392	0.019	0.413