##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/QuartPAC.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.40.0’
* 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 whether startup messages can be suppressed ... 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 9.425  0.182  15.888
quartCluster     2.634  0.059   5.866
* 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-3.21-bioc/meat/QuartPAC.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL QuartPAC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘QuartPAC’ ...
** this is package ‘QuartPAC’ version ‘1.40.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: In fun(libname, pkgname) :
  Package 'iPAC' is deprecated and will be removed from Bioconductor
  version 3.22
2: In fun(libname, pkgname) :
  Package 'GraphPAC' is deprecated and will be removed from Bioconductor
  version 3.22
3: In fun(libname, pkgname) :
  Package 'SpacePAC' is deprecated and will be removed from Bioconductor
  version 3.22
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'iPAC' is deprecated and will be removed from Bioconductor
  version 3.22
Warning in fun(libname, pkgname) :
  Package 'GraphPAC' is deprecated and will be removed from Bioconductor
  version 3.22
Warning in fun(libname, pkgname) :
  Package 'SpacePAC' is deprecated and will be removed from Bioconductor
  version 3.22
Warning in fun(libname, pkgname) :
  Package 'QuartPAC' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'iPAC' is deprecated and will be removed from Bioconductor
  version 3.22
Warning in fun(libname, pkgname) :
  Package 'GraphPAC' is deprecated and will be removed from Bioconductor
  version 3.22
Warning in fun(libname, pkgname) :
  Package 'SpacePAC' is deprecated and will be removed from Bioconductor
  version 3.22
Warning in fun(libname, pkgname) :
  Package 'QuartPAC' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (QuartPAC)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> BiocGenerics:::testPackage("QuartPAC")

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'pwalign'

The following objects are masked from 'package:Biostrings':

    PairwiseAlignments, PairwiseAlignmentsSingleSubject, aligned,
    alignedPattern, alignedSubject, compareStrings, deletion,
    errorSubstitutionMatrices, indel, insertion, mismatchSummary,
    mismatchTable, nedit, nindel, nucleotideSubstitutionMatrix,
    pairwiseAlignment, pattern, pid, qualitySubstitutionMatrices,
    stringDist, unaligned, writePairwiseAlignments

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'igraph'

The following object is masked from 'package:Biostrings':

    union

The following object is masked from 'package:XVector':

    path

The following object is masked from 'package:IRanges':

    union

The following object is masked from 'package:S4Vectors':

    union

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following objects are masked from 'package:generics':

    components, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'combinat'

The following object is masked from 'package:utils':

    combn


Attaching package: 'data.table'

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

Performing SpacePAC calculations
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.50 
Performing iPAC Calculations
[1] "Running Remapped"
Performing GraphPAC Calculations
Calculating Remapped Clusters.Timing stopped at: 7.231 0.179 10.7
Error in checkEquals(dim(quart_results$ipac)[1], 35) : 
  Mean relative difference: 0.02777778

In addition: Warning messages:
1: In fun(libname, pkgname) :
  Package 'iPAC' is deprecated and will be removed from Bioconductor
  version 3.22
2: In fun(libname, pkgname) :
  Package 'GraphPAC' is deprecated and will be removed from Bioconductor
  version 3.22
3: In fun(libname, pkgname) :
  Package 'SpacePAC' is deprecated and will be removed from Bioconductor
  version 3.22
4: In fun(libname, pkgname) :
  Package 'QuartPAC' is deprecated and will be removed from Bioconductor
  version 3.22


RUNIT TEST PROTOCOL -- Mon Apr 21 21:06:43 2025 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 1 

 
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