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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PhosR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PhosR_1.9.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘PhosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhosR’ version ‘1.9.1’
* 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 ... 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 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 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 ... 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
siteAnnotate           42.197  0.032  45.475
kinaseSubstratePred    40.922  0.068  43.417
kinaseSubstrateScore   28.006  0.012  30.476
minmax                 27.428  0.016  31.109
standardise            15.034  0.008  17.360
kinaseSubstrateProfile 14.230  0.000  15.500
matANOVA               14.176  0.008  15.855
plotQC                  6.148  0.047   7.323
* 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'): 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘PhosR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘PhosR.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-19-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-20-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-28-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-29-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-32-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-33-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-48-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-49-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-50-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-50-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/vign_test/PhosR/vignettes/PhosR_files/figure-html/unnamed-chunk-50-3.png" but not available.
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/PhosR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PhosR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘PhosR’ ...
** 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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(PhosR)
> 
> test_check("PhosR")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-pathwayAnalysis.R:74'): 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