##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:PhosR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PhosR_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PhosR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhosR’ version ‘1.19.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PhosR’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’
  ‘SummarizedExperiment:::.SummarizedExperiment.charbound’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
abundPlot: no visible binding for global variable ‘.’
Undefined global functions or variables:
  .
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PhosphoExperiment-operate.Rd: SummarizedExperiment-class
  PhosphoExperiment.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
siteAnnotate           40.444  0.195  45.560
kinaseSubstratePred    38.655  0.259  40.592
minmax                 26.626  0.095  29.272
kinaseSubstrateScore   26.016  0.132  28.014
kinaseSubstrateProfile 15.459  0.116  15.613
standardise            14.581  0.000  14.884
matANOVA               14.366  0.051  15.704
plotQC                  5.959  0.040   6.189
* 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(PhosR)
  > 
  > test_check("PhosR")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-pathwayAnalysis.R:74:5'): Case B.2: Expected output ──────────
  `result1` not identical to pathwayOverrepresent(geneSet, annotation, universe, alter1).
  1/12 mismatches
  x[3]: "0.100641107506833"
  y[3]: "0.100641107506832"
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
  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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/PhosR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL PhosR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘PhosR’ ...
** this is package ‘PhosR’ version ‘1.19.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (PhosR)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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(PhosR)
> 
> test_check("PhosR")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-pathwayAnalysis.R:74:5'): Case B.2: Expected output ──────────
`result1` not identical to pathwayOverrepresent(geneSet, annotation, universe, alter1).
1/12 mismatches
x[3]: "0.100641107506833"
y[3]: "0.100641107506832"

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
Error: Test failures
Execution halted