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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PolySTest.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PolySTest_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PolySTest.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘PolySTest/DESCRIPTION’ ... OK
* this is package ‘PolySTest’ version ‘1.1.0’
* 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 ‘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 ... 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 ... 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
PolySTest_unpaired 0.327  0.018  20.896
perm_unpaired      0.029  0.006  11.166
rp_unpaired        0.009  0.012   8.354
FindFCandQlim      0.012  0.005   7.830
permtest_paired    0.007  0.002   9.013
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/PolySTest.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL PolySTest
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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.

> # 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
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: 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 
 16.477   1.328 206.915