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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graphite.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graphite_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/graphite.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.46.0’
* 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 ‘graphite’ 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
runClipper         18.876  0.787  25.567
runSPIA             8.851  1.337  13.151
convertIdentifiers  9.343  0.176  14.456
Pathway-class       7.217  0.131  13.294
pathwayGraph        6.727  0.064   8.417
pathways            6.576  0.075   8.039
runTopologyGSA      5.075  0.111   6.929
* 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:
  > test_check("graphite")
  [ FAIL 3 | WARN 8 | SKIP 0 | PASS 92 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_clipper.R:60:3'): pathway "Hippo signaling pathway - multiple species" is altered in the ALL dataset ──
  x$errors has length 2, not length 0.
  ── Failure ('test_clipper.R:61:3'): pathway "Hippo signaling pathway - multiple species" is altered in the ALL dataset ──
  length(x$results) is not more than 1. Difference: -1
  ── Failure ('test_clipper.R:62:3'): pathway "Hippo signaling pathway - multiple species" is altered in the ALL dataset ──
  "Hippo signaling pathway - multiple species" %in% names(x$results) not equal to TRUE.
  1 element mismatch
  
  [ FAIL 3 | WARN 8 | SKIP 0 | PASS 92 ]
  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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graphite
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘graphite’ ...
** using staged installation
** R
** 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 (graphite)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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(graphite)
> 
> test_check("graphite")
[ FAIL 3 | WARN 8 | SKIP 0 | PASS 92 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_clipper.R:60:3'): pathway "Hippo signaling pathway - multiple species" is altered in the ALL dataset ──
x$errors has length 2, not length 0.
── Failure ('test_clipper.R:61:3'): pathway "Hippo signaling pathway - multiple species" is altered in the ALL dataset ──
length(x$results) is not more than 1. Difference: -1
── Failure ('test_clipper.R:62:3'): pathway "Hippo signaling pathway - multiple species" is altered in the ALL dataset ──
"Hippo signaling pathway - multiple species" %in% names(x$results) not equal to TRUE.
1 element mismatch

[ FAIL 3 | WARN 8 | SKIP 0 | PASS 92 ]
Error: Test failures
Execution halted