##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:mariner.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings mariner_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/mariner.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘mariner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mariner’ version ‘1.1.0’
* package encoding: UTF-8
* 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 ‘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 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 loading without being on the library search path ... 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
adjustEnrichment          12.139  0.851  18.294
CountMatrix-class         12.333  0.371  22.588
aggPairMcols               6.854  0.990  12.672
calcLoopEnrichment         6.639  0.715  13.834
changePixelRes             6.131  1.003  13.195
aggHicMatrices             5.503  1.229  13.991
pullHicMatrices            5.608  0.172  13.084
selectPixel                5.568  0.096  12.535
pullHicPixels              4.671  0.115  12.566
counts                     3.924  0.176   8.202
getPairClusters            3.462  0.143   7.956
path                       3.423  0.087   8.366
mergePairs                 3.232  0.065   7.916
sources                    3.072  0.091   7.586
selectionMethod            2.931  0.060   7.202
MergedGInteractions-class  2.748  0.075   8.295
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘introduction_to_mariner.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/mariner.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL mariner
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘mariner’ ...
** 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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(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
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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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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
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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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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/ 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
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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
                                 
 X  X  X  X  -  -  -  -  -  -  - 
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/ 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

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

Attaching package: 'S4Arrays'

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
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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 ═══════════════════════════════════════════════════════════════
• On CRAN (4)

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 899 ]
> 
> proc.time()
   user  system elapsed 
295.366  12.165 414.225