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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mariner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mariner_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/mariner.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mariner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mariner’ version ‘1.8.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mariner’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘plotgardener:::check_page’ ‘plotgardener:::convert_page’
  ‘plotgardener:::current_viewports’ ‘plotgardener:::defaultUnits’
  ‘plotgardener:::pgEnv’
  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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) mariner-package.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mariner-package.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mariner-package.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mariner-package.Rd:26-28: Lost braces in \itemize; meant \describe ?
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'MatrixSelection.Rd':
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
CountMatrix-class         17.184  2.238  22.854
adjustEnrichment          17.003  1.933  20.922
calcLoopEnrichment        10.231  1.633  12.913
aggPairMcols              10.718  1.128  13.241
aggHicMatrices             9.555  1.878  13.477
changePixelRes             9.432  1.186  12.515
pullHicMatrices            8.723  0.595  12.285
selectPixel                8.663  0.575  11.144
pullHicPixels              7.542  0.491  10.176
counts                     6.578  0.425   8.236
MergedGInteractions-class  6.102  0.368   8.073
getPairClusters            5.592  0.401   7.182
path                       5.339  0.332   6.943
sources                    5.183  0.324   7.185
mergePairs                 4.994  0.353   6.962
selectionMethod            4.792  0.315   6.351
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/mariner.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mariner
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘mariner’ ...
** this is package ‘mariner’ version ‘1.8.1’
** using staged installation
** R
** 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 (mariner)

R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.

> library(testthat)
> library(mariner)
> 
> test_check("mariner")
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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class: InteractionMatrix 
dim: count matrix with 3 interactions and 2 file(s)
metadata(3): binSize norm matrix
assays(1): counts
rownames: NULL
rowData names(0):
colnames(2): FS WT
colData names(2): files fileNames
type: GInteractions
regions: 4
class: InteractionMatrix 
dim: count matrix with 3 interactions and 2 file(s)
metadata(3): binSize norm matrix
assays(1): counts
rownames: NULL
rowData names(0):
colnames(2): FS WT
colData names(2): files fileNames
type: GInteractions
regions: 4
class: InteractionMatrix 
dim: count matrix with 3 interactions and 2 file(s)
metadata(3): binSize norm matrix
assays(1): counts
rownames: NULL
rowData names(0):
colnames(2): FS WT
colData names(2): files fileNames
type: GInteractions
regions: 4
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians


Attaching package: 'data.table'

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

    shift

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

    shift

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

    shift

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

    first, second

see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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'0' = foreground;
'X' = background;
'*' = both;
'-' = unselected
                                 
 X  X  X  X  -  -  -  -  -  -  - 
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 X  X  X  X  -  -  -  -  -  -  - 
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 -  -  -  -  -  0  -  -  -  -  - 
 -  -  -  -  0  0  0  -  -  -  - 
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/ reading and realizing block 5/5 ... ok
\ processing it ... ok

/ reading and realizing block 1/5 ... ok
\ processing it ... ok
/ reading and realizing block 2/5 ... ok
\ processing it ... ok

/ reading and realizing block 3/5 ... ok
\ processing it ... ok
/ reading and realizing block 4/5 ... ok
\ processing it ... ok

see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
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'0' = selected; '- ' = unselected
         
 0  0  0 
 -  -  - 
 0  0  0 
'0' = selected; '- ' = unselected
         
 -  -  - 
 0  0  0 
 -  -  - 
'0' = selected; '- ' = unselected
                           
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'0' = selected; '- ' = unselected
                           
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'0' = foreground;
'X' = background;
'*' = both;
'-' = unselected
                     
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 X  X  X  X  X  X  X 
 X  X  X  0  X  X  X 
 X  X  0  0  0  X  X 
 X  X  X  0  X  X  X 
 X  X  X  X  X  X  X 
 X  X  X  X  X  X  X 
'0' = foreground;
'X' = background;
'*' = both;
'-' = unselected
                                 
 X  X  X  X  -  -  -  -  -  -  - 
 X  X  X  X  -  -  -  -  -  -  - 
 X  X  X  X  -  -  -  -  -  -  - 
 X  X  X  X  -  -  -  -  -  -  - 
 -  -  -  -  -  0  -  -  -  -  - 
 -  -  -  -  0  0  0  -  -  -  - 
 -  -  -  -  -  0  -  -  -  -  - 
 -  -  -  -  -  -  -  X  X  X  X 
 -  -  -  -  -  -  -  X  X  X  X 
 -  -  -  -  -  -  -  X  X  X  X 
 -  -  -  -  -  -  -  X  X  X  X 
/ reading and realizing block 5/5 ... ok
\ processing it ... ok

/ reading and realizing block 3/5 ... ok
\ processing it ... ok
/ reading and realizing block 4/5 ... ok
\ processing it ... ok

/ reading and realizing block 1/5 ... ok
\ processing it ... ok
/ reading and realizing block 2/5 ... ok
\ processing it ... ok

see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
/ Reading and realizing block 1/5 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/5 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 ... OK
\ Processing it ... OK
Loading required package: Matrix

Attaching package: 'Matrix'

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

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep

/ Reading and realizing block 1/10 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/10 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/10 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/10 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/10 ... OK
\ Processing it ... OK
/ Reading and realizing block 6/10 ... OK
\ Processing it ... OK
/ Reading and realizing block 7/10 ... OK
\ Processing it ... OK
/ Reading and realizing block 8/10 ... OK
\ Processing it ... OK
/ Reading and realizing block 9/10 ... OK
\ Processing it ... OK
/ Reading and realizing block 10/10 ... OK
\ Processing it ... OK
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache

Attaching package: 'plotgardener'

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

    c

MatrixPlot[MatrixPlot1]
MatrixPlot[MatrixPlot1]
MatrixPlot[MatrixPlot1]
MatrixPlot[MatrixPlot1]
MatrixPlot[MatrixPlot1]
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
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see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache

Attaching package: 'rlang'

The following object is masked from 'package:data.table':

    :=

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

    exprs

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

    is_false, is_null, is_true


Attaching package: 'assertthat'

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

    has_name

see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
[ FAIL 0 | WARN 0 | SKIP 4 | PASS 899 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test_InteractionArray.R:39:5', 'test_InteractionArray.R:97:5',
  'test_InteractionMatrix.R:74:5', 'test_MergedGInteractions.R:61:5'

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 899 ]
> 
> proc.time()
   user  system elapsed 
456.553  32.601 538.268