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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings pathwayPCA_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pathwayPCA.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘pathwayPCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathwayPCA’ version ‘1.15.0’
* 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 ‘pathwayPCA’ 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 R 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 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
SE2Tidy        18.134  0.670  21.016
ExtractAESPCs   0.711  0.142  14.133
LoadOntoPCs     0.648  0.176   9.661
AESPCA_pVals    0.687  0.049  25.977
SuperPCA_pVals  0.629  0.049  12.820
getPathPCLs     0.524  0.048  11.537
getPathpVals    0.449  0.006  20.337
* 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:
  > library(testthat)
  > library(pathwayPCA)
  > 
  > test_check("pathwayPCA")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 46 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_SE2Tidy.R:11:3'): SE2Tidy transforms data correctly ──────────
  dim(airway_df) not equal to c(8, 64112).
  1/2 mismatches
  [2] 63687 - 64112 == -425
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 46 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Introduction_to_pathwayPCA.Rmd’ using ‘UTF-8’... OK
  ‘Supplement1-Quickstart_Guide.Rmd’ using ‘UTF-8’... OK
  ‘Supplement2-Importing_Data.Rmd’ using ‘UTF-8’... OK
  ‘Supplement3-Create_Omics_Objects.Rmd’ using ‘UTF-8’... OK
  ‘Supplement4-Methods_Walkthrough.Rmd’ using ‘UTF-8’... OK
  ‘Supplement5-Analyse_Results.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/pathwayPCA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL pathwayPCA
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘pathwayPCA’ ...
** 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 (pathwayPCA)

R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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(pathwayPCA)
> 
> test_check("pathwayPCA")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 46 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_SE2Tidy.R:11:3'): SE2Tidy transforms data correctly ──────────
dim(airway_df) not equal to c(8, 64112).
1/2 mismatches
[2] 63687 - 64112 == -425

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 46 ]
Error: Test failures
Execution halted