Eric Davis
| Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-29 12:03 -0400 (Mon, 29 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4833 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 1176/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mariner 1.9.1 (landing page) Eric Davis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. |
| Package: mariner |
| Version: 1.9.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:mariner.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings mariner_1.9.1.tar.gz |
| StartedAt: 2025-09-29 01:21:42 -0400 (Mon, 29 Sep 2025) |
| EndedAt: 2025-09-29 01:35:58 -0400 (Mon, 29 Sep 2025) |
| EllapsedTime: 856.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mariner.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:mariner.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings mariner_1.9.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/mariner.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 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 34.472 0.929 16.034
pullHicMatrices 24.704 0.578 8.269
InteractionJaggedArray-overlaps 19.298 0.295 6.194
JaggedArray-class 18.488 0.085 4.378
InteractionJaggedArray-class 18.380 0.124 4.225
calcLoopEnrichment 15.522 1.858 9.914
pileupPixels 16.075 0.932 6.188
pileupDomains 10.241 3.599 10.070
counts 11.582 0.202 4.922
CountMatrix-class 10.916 0.490 10.919
regularize 9.685 0.157 4.416
aggHicMatrices 7.711 1.248 7.071
pileupBoundaries 6.840 0.630 7.952
changePixelRes 5.409 0.851 7.320
pullHicPixels 5.881 0.241 5.763
selectPixel 5.415 0.159 6.868
aggMetadata 4.839 0.425 5.587
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/mariner.Rcheck/00check.log’
for details.
mariner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL mariner ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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)
mariner.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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
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
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
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
'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
'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
'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
'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
'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
'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
'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
'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
'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
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 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
/ 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
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
953.531 41.358 354.605
mariner.Rcheck/mariner-Ex.timings
| name | user | system | elapsed | |
| CountMatrix-class | 10.916 | 0.490 | 10.919 | |
| GInteractions-accessors | 0.273 | 0.005 | 0.278 | |
| InteractionArray-class | 0.104 | 0.001 | 0.105 | |
| InteractionJaggedArray-class | 18.380 | 0.124 | 4.225 | |
| InteractionJaggedArray-overlaps | 19.298 | 0.295 | 6.194 | |
| InteractionMatrix-class | 0.048 | 0.000 | 0.048 | |
| JaggedArray-class | 18.488 | 0.085 | 4.378 | |
| MatrixSelection-class | 0.009 | 0.000 | 0.010 | |
| MergedGInteractions-class | 2.600 | 0.106 | 3.737 | |
| adjustEnrichment | 34.472 | 0.929 | 16.034 | |
| aggHicMatrices | 7.711 | 1.248 | 7.071 | |
| aggMetadata | 4.839 | 0.425 | 5.587 | |
| as_ginteractions | 0.723 | 0.003 | 0.726 | |
| assignToBins | 0.861 | 0.004 | 0.865 | |
| binRanges | 0.559 | 0.001 | 0.560 | |
| calcLoopEnrichment | 15.522 | 1.858 | 9.914 | |
| changePixelRes | 5.409 | 0.851 | 7.320 | |
| clusters | 2.985 | 0.209 | 4.167 | |
| counts | 11.582 | 0.202 | 4.922 | |
| hdf5BlockApply | 0.433 | 0.008 | 0.441 | |
| makeRandomGInteractions | 1.029 | 0.041 | 1.070 | |
| mergePairs | 2.713 | 0.175 | 3.815 | |
| path | 3.223 | 0.138 | 4.042 | |
| pileupBoundaries | 6.840 | 0.630 | 7.952 | |
| pileupDomains | 10.241 | 3.599 | 10.070 | |
| pileupPixels | 16.075 | 0.932 | 6.188 | |
| pixelsToMatrices | 0.675 | 0.197 | 0.674 | |
| plotMatrix | 0.251 | 0.037 | 0.288 | |
| pullHicMatrices | 24.704 | 0.578 | 8.269 | |
| pullHicPixels | 5.881 | 0.241 | 5.763 | |
| regularize | 9.685 | 0.157 | 4.416 | |
| removeShortPairs | 0.136 | 0.003 | 0.139 | |
| selectPixel | 5.415 | 0.159 | 6.868 | |
| selection-functions | 0.090 | 0.001 | 0.091 | |
| selectionMethod | 2.679 | 0.210 | 3.772 | |
| sets | 0.457 | 0.041 | 0.487 | |
| shiftRanges | 0.471 | 0.042 | 0.513 | |
| snapToBins | 1.409 | 0.089 | 1.498 | |
| sources | 3.641 | 0.226 | 4.180 | |