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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:Rtpca.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Rtpca_1.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Rtpca.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rtpca/DESCRIPTION’ ... OK
* this is package ‘Rtpca’ version ‘1.18.1’
* 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 ‘Rtpca’ 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 ... NOTE
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getRandomProteinPairs: no visible binding for global variable ‘pair’
Undefined global functions or variables:
  pair
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  class(p1) not equal to c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg").
  Lengths differ: 2 is not 5
  ── Failure ('test-plotPPiProfiles.R:56:1'): (code run outside of `test_that()`) ──
  class(p2) not equal to c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg").
  Lengths differ: 2 is not 5
  ── Failure ('test-plotPPiRoc.R:20:1'): (code run outside of `test_that()`) ─────
  class(p) not equal to c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg").
  Lengths differ: 2 is not 5
  ── Failure ('test-plotTpcaVolcano.R:31:1'): (code run outside of `test_that()`) ──
  class(p) not equal to c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg").
  Lengths differ: 2 is not 5
  
  [ FAIL 5 | WARN 1 | SKIP 0 | PASS 33 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Rtpca.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL Rtpca
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘Rtpca’ ...
** this is package ‘Rtpca’ version ‘1.18.1’
** 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 (Rtpca)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(Rtpca)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidyr

Attaching package: 'tidyr'

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

    matches

> 
> test_check("Rtpca")
[ FAIL 5 | WARN 1 | SKIP 0 | PASS 33 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotDiffTpcaVolcano.R:47:1'): (code run outside of `test_that()`) ──
class(p) not equal to c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg").
Lengths differ: 2 is not 5
── Failure ('test-plotPPiProfiles.R:38:1'): (code run outside of `test_that()`) ──
class(p1) not equal to c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg").
Lengths differ: 2 is not 5
── Failure ('test-plotPPiProfiles.R:56:1'): (code run outside of `test_that()`) ──
class(p2) not equal to c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg").
Lengths differ: 2 is not 5
── Failure ('test-plotPPiRoc.R:20:1'): (code run outside of `test_that()`) ─────
class(p) not equal to c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg").
Lengths differ: 2 is not 5
── Failure ('test-plotTpcaVolcano.R:31:1'): (code run outside of `test_that()`) ──
class(p) not equal to c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg").
Lengths differ: 2 is not 5

[ FAIL 5 | WARN 1 | SKIP 0 | PASS 33 ]
Error: Test failures
Execution halted