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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1150/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mariner 1.6.0  (landing page)
Eric Davis
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/mariner
git_branch: RELEASE_3_20
git_last_commit: 1aa9d93
git_last_commit_date: 2024-10-29 11:20:50 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'plotgardener' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for mariner on teran2

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: 1.6.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mariner.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mariner_1.6.0.tar.gz
StartedAt: 2024-11-20 05:12:50 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 05:21:52 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 541.5 seconds
RetCode: 0
Status:   OK  
CheckDir: mariner.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mariner.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mariner_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/mariner.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mariner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mariner’ version ‘1.6.0’
* 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 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 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 ... 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
adjustEnrichment   9.277  0.712  11.215
CountMatrix-class  5.447  0.364   8.162
aggPairMcols       3.949  0.362   5.364
calcLoopEnrichment 3.314  0.830   5.545
aggHicMatrices     3.131  0.977   5.584
pullHicPixels      3.186  0.073   5.118
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/mariner.Rcheck/00check.log’
for details.


Installation output

mariner.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL mariner
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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)

Tests output

mariner.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, saveRDS, setdiff, 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
downloading 1 resources
retrieving 1 resource
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?marinerData and browseVignettes('marinerData') for documentation
downloading 1 resources
retrieving 1 resource
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
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' = 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  -  - 
 -  0  0  0  -  -  0  -  - 
 -  0  -  0  -  -  0  -  - 
 -  0  -  0  -  0  0  0  - 
 -  -  -  -  -  -  -  -  - 
 -  -  -  -  -  -  -  -  - 
'0' = selected; '- ' = unselected
                           
 0  0  0  0  0  0  0  0  0 
 0  0  0  0  0  0  0  0  0 
 0  -  0  -  0  -  -  -  0 
 0  -  0  -  0  0  -  0  0 
 0  -  -  -  0  0  -  0  0 
 0  -  0  -  0  0  -  0  0 
 0  -  0  -  0  -  -  -  0 
 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 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
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
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 
154.819   9.162 193.639 

Example timings

mariner.Rcheck/mariner-Ex.timings

nameusersystemelapsed
CountMatrix-class5.4470.3648.162
GInteractions-accessors0.1840.0070.191
InteractionArray-class0.0580.0000.059
InteractionMatrix-class0.0420.0010.042
MatrixSelection-class0.0070.0010.007
MergedGInteractions-class1.6240.0762.882
adjustEnrichment 9.277 0.71211.215
aggHicMatrices3.1310.9775.584
aggPairMcols3.9490.3625.364
as_ginteractions0.4470.0000.448
binPairs0.5210.0040.525
binRanges0.4960.0000.497
calcLoopEnrichment3.3140.8305.545
changePixelRes2.8950.3754.874
counts2.3170.0763.514
getPairClusters2.1090.0883.350
hdf5BlockApply0.2870.0120.299
mergePairs1.8070.0792.986
path1.7020.0582.852
pixelsToMatrices0.3090.0060.316
plotMatrix0.1180.0040.124
pullHicMatrices3.0480.1034.792
pullHicPixels3.1860.0735.118
removeShortPairs0.0870.0000.089
selectPixel2.8000.1004.849
selection-functions0.0630.0030.066
selectionMethod1.6310.0513.032
shiftRanges0.2450.0030.249
snapToBins0.9190.0030.926
sources2.0390.0583.209
subsetBySource0.2400.0060.238