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This page was generated on 2025-10-18 12:05 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1183/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mariner 1.9.1  (landing page)
Eric Davis
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/mariner
git_branch: devel
git_last_commit: bc589a5
git_last_commit_date: 2025-08-05 09:04:06 -0400 (Tue, 05 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for mariner on lconway

To the developers/maintainers of the mariner package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mariner.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: mariner
Version: 1.9.1
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_1.9.1.tar.gz
StartedAt: 2025-10-17 23:18:11 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 23:33:24 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 912.9 seconds
RetCode: 0
Status:   OK  
CheckDir: mariner.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/mariner.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.9.1’
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
pileupDomains                   12.650  5.089  12.846
adjustEnrichment                12.163  1.055  14.398
CountMatrix-class               10.595  1.655  20.603
pileupBoundaries                 8.716  1.976   9.988
calcLoopEnrichment               8.117  1.899  17.062
pullHicMatrices                  7.362  0.715   9.529
aggHicMatrices                   6.240  1.769   8.626
changePixelRes                   6.205  0.716   8.424
pileupPixels                     5.063  1.163  12.877
selectPixel                      5.707  0.466   7.619
aggMetadata                      4.959  0.482   6.410
pullHicPixels                    4.838  0.395   6.717
InteractionJaggedArray-overlaps  4.534  0.313   5.827
counts                           4.062  0.337   5.392
regularize                       3.868  0.313   5.177
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/mariner.Rcheck/00check.log’
for details.


Installation output

mariner.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘mariner’ ...
** this is package ‘mariner’ version ‘1.9.1’
** 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)

Tests output

mariner.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "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
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
loading from cache
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
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
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: Seqinfo
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
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
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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'0' = foreground;
'X' = background;
'*' = both;
'-' = unselected
                                 
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/ 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
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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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see ?marinerData and browseVignettes('marinerData') for documentation
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'0' = selected; '- ' = unselected
         
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'0' = selected; '- ' = unselected
         
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'0' = selected; '- ' = unselected
                           
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'0' = selected; '- ' = unselected
                           
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'0' = foreground;
'X' = background;
'*' = both;
'-' = unselected
                     
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'0' = foreground;
'X' = background;
'*' = both;
'-' = unselected
                                 
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/ 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

'0' = foreground;
'X' = background;
'*' = both;
'-' = unselected
                                                               
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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

'0' = foreground;
'X' = background;
'*' = both;
'-' = unselected
                                                               
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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

'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

'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

'0' = foreground;
'X' = background;
'*' = both;
'-' = unselected
                                                               
 X  X  X  X  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
 X  X  X  X  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
 X  X  X  X  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
 X  X  X  X  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
 -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
 -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
 -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
 -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
 -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
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 -  -  -  -  -  -  -  -  -  -  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

'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 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

'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 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

'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 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

'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
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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
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
loading from cache
/ 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

/ 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

/ 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


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
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
loading from cache
/ Reading and realizing block 1/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/3 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/3 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/3 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/3 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/3 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/3 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/5 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 4/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 5/5 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 1/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/1 of file 2/2 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/3 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/3 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/3 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/3 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/3 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/3 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 1/3 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 2/3 of file 1/1 ... OK
\ Processing it ... OK
/ Reading and realizing block 3/3 of file 1/1 ... 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: '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
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
[ FAIL 0 | WARN 0 | SKIP 7 | PASS 1010 ]

══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On CRAN (7): 'test_InteractionArray.R:39:5', 'test_InteractionArray.R:97:5',
  'test_InteractionJaggedArray.R:30:5', 'test_InteractionMatrix.R:74:5',
  'test_JaggedArray.R:34:5', 'test_MergedGInteractions.R:61:5',
  'test_regularize.R:91:5'

[ FAIL 0 | WARN 0 | SKIP 7 | PASS 1010 ]
> 
> proc.time()
   user  system elapsed 
337.857  61.431 418.022 

Example timings

mariner.Rcheck/mariner-Ex.timings

nameusersystemelapsed
CountMatrix-class10.595 1.65520.603
GInteractions-accessors0.4040.0170.424
InteractionArray-class0.0890.0020.090
InteractionJaggedArray-class3.2770.2474.587
InteractionJaggedArray-overlaps4.5340.3135.827
InteractionMatrix-class0.0690.0070.076
JaggedArray-class3.1360.2814.355
MatrixSelection-class0.010.000.01
MergedGInteractions-class3.0170.2714.213
adjustEnrichment12.163 1.05514.398
aggHicMatrices6.2401.7698.626
aggMetadata4.9590.4826.410
as_ginteractions0.8490.0120.863
assignToBins1.1030.0311.138
binRanges0.6650.0150.684
calcLoopEnrichment 8.117 1.89917.062
changePixelRes6.2050.7168.424
clusters3.3570.2874.565
counts4.0620.3375.392
hdf5BlockApply0.6080.0440.656
makeRandomGInteractions1.2840.0931.388
mergePairs3.3040.2844.558
path3.5300.2674.788
pileupBoundaries8.7161.9769.988
pileupDomains12.650 5.08912.846
pileupPixels 5.063 1.16312.877
pixelsToMatrices0.7990.1470.957
plotMatrix0.2430.0370.282
pullHicMatrices7.3620.7159.529
pullHicPixels4.8380.3956.717
regularize3.8680.3135.177
removeShortPairs0.1570.0040.163
selectPixel5.7070.4667.619
selection-functions0.1120.0060.119
selectionMethod3.5000.3404.849
sets0.5800.0250.614
shiftRanges0.5300.0180.554
snapToBins1.8410.0461.903
sources3.2970.2544.502