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This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1116/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mariner 1.0.0  (landing page)
Eric Davis
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/mariner
git_branch: RELEASE_3_17
git_last_commit: 7f2a96d
git_last_commit_date: 2023-04-25 11:44:49 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for mariner on kjohnson2


To the developers/maintainers of the mariner package:
- 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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2023-10-18 04:40:47 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 04:58:19 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 1052.5 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mariner.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mariner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mariner’ version ‘1.0.0’
* 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 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
CountMatrix-class         13.466  2.182  32.560
adjustEnrichment          10.958  0.786  18.792
calcLoopEnrichment         7.855  0.884  15.028
changePixelRes             6.993  0.619  13.583
aggHicMatrices             6.460  0.919  12.810
selectPixel                6.276  0.369  11.855
pullHicMatrices            5.635  0.357  10.925
aggPairMcols               5.462  0.405  10.247
pullHicPixels              5.371  0.312  10.565
counts                     4.581  0.283   8.594
mergePairs                 4.352  0.291   7.654
path                       3.874  0.215   7.011
getPairClusters            3.820  0.229   7.438
MergedGInteractions-class  3.513  0.251   6.970
sources                    3.422  0.192   7.078
selectionMethod            3.032  0.195   6.578
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mariner.Rcheck/00check.log’
for details.



Installation output

mariner.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)

Tests output

mariner.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
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
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
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
'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

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

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


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
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
[ 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 
258.804  14.336 432.137 

Example timings

mariner.Rcheck/mariner-Ex.timings

nameusersystemelapsed
CountMatrix-class13.466 2.18232.560
GInteractions-accessors0.4840.0190.670
InteractionArray-class0.1170.0020.173
InteractionMatrix-class0.0870.0010.137
MatrixSelection-class0.0250.0030.044
MergedGInteractions-class3.5130.2516.970
adjustEnrichment10.958 0.78618.792
aggHicMatrices 6.460 0.91912.810
aggPairMcols 5.462 0.40510.247
as_ginteractions0.9780.0171.483
binPairs1.1510.0341.787
binRanges0.8400.0201.327
calcLoopEnrichment 7.855 0.88415.028
changePixelRes 6.993 0.61913.583
counts4.5810.2838.594
getPairClusters3.8200.2297.438
hdf5BlockApply0.6330.0481.035
mergePairs4.3520.2917.654
path3.8740.2157.011
pixelsToMatrices0.7500.0201.179
plotMatrix0.2060.0080.327
pullHicMatrices 5.635 0.35710.925
pullHicPixels 5.371 0.31210.565
removeShortPairs0.1500.0040.234
selectPixel 6.276 0.36911.855
selection-functions0.2860.0460.497
selectionMethod3.0320.1956.578
shiftRanges0.5420.0160.839
snapToBins1.8670.0332.889
sources3.4220.1927.078
subsetBySource0.6060.0210.949