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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QuartPAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QuartPAC_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/QuartPAC.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QuartPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuartPAC’ version ‘1.38.0’
* 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 ‘QuartPAC’ 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 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 ... NOTE
constructCanonicalNumbering: no visible global function definition for
  ‘start’
getMutations : <anonymous>: no visible global function definition for
  ‘read.table’
getRangeLocInfo: no visible global function definition for ‘aggregate’
quartCluster: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  aggregate capture.output read.table start
Consider adding
  importFrom("stats", "aggregate", "start")
  importFrom("utils", "capture.output", "read.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) getMutations.Rd:36: Lost braces
    36 | To see examples of mutation matrices, please look in the /emph{extdata} folder of the package.
       |                                                               ^
* 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
QuartPAC-package          27.041  0.425  31.002
quartCluster               8.513  0.129  11.997
makeAlignedSuperStructure  7.480  0.141  10.378
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  QuartPAC RUnit Tests - 1 test function, 0 errors, 1 failure
  FAILURE in test_quartCluster: Error in checkEquals(dim(quart_results$ipac)[1], 35) : 
    Mean relative difference: 0.02777778
  
  
  Test files with failing tests
  
     test_quartCluster.R 
       test_quartCluster 
  
  
  Error in BiocGenerics:::testPackage("QuartPAC") : 
    unit tests failed for package QuartPAC
  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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/QuartPAC.Rcheck/00check.log’
for details.