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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 846/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geomeTriD 1.3.16  (landing page)
Jianhong Ou
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/geomeTriD
git_branch: devel
git_last_commit: 832ae3f
git_last_commit_date: 2025-07-23 01:45:10 -0400 (Wed, 23 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for geomeTriD on kjohnson3

To the developers/maintainers of the geomeTriD package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geomeTriD.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: geomeTriD
Version: 1.3.16
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geomeTriD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geomeTriD_1.3.16.tar.gz
StartedAt: 2025-08-08 19:36:35 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 19:39:14 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 158.9 seconds
RetCode: 0
Status:   OK  
CheckDir: geomeTriD.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geomeTriD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geomeTriD_1.3.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/geomeTriD.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geomeTriD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geomeTriD’ version ‘1.3.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 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 ‘geomeTriD’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

geomeTriD.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘geomeTriD’ ...
** this is package ‘geomeTriD’ version ‘1.3.16’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (geomeTriD)

Tests output

geomeTriD.Rcheck/tests/runTests.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> options(rgl.useNULL=TRUE)
> require("geomeTriD") || stop("unable to load Package:geomeTriD")
Loading required package: geomeTriD
[1] TRUE
> require(rgl) || stop("unable to load rgl")
Loading required package: rgl
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> 
> x <- readRDS(system.file("extdata", "4DNFI1UEG1HD.chr21.FLAMINGO.res.rds",
+   package = "geomeTriD"
+ ))
> gi <- readRDS(system.file("extdata", "gi.rds", package = "trackViewer"))
> test_check("geomeTriD")
[ FAIL 0 | WARN 20 | SKIP 3 | PASS 110 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_create3dGenomicSignals.R:1:1',
  'test_signalCalculation.R:1:1', 'test_signalCalculation.R:23:1'

[ FAIL 0 | WARN 20 | SKIP 3 | PASS 110 ]
> 
> proc.time()
   user  system elapsed 
 14.634   0.380  15.050 

Example timings

geomeTriD.Rcheck/geomeTriD-Ex.timings

nameusersystemelapsed
SDC0.0000.0010.001
SRD0.0010.0000.001
alignCoor0.8770.0150.894
autoK0.0010.0000.001
availableGeometries000
cellClusters0.2060.0100.217
create3dGenomicSignals0.1400.0070.151
createTADGeometries0.2930.0090.302
extractBackbonePositions0.1790.0050.184
fill_NA000
gaussianBlur000
geomeTriD-package0.0010.0000.001
loopBouquetPlot0.8650.0290.900
mdsPlot1.2070.0251.240
pointCluster0.0170.0000.017
rglViewer0.8510.0040.864
smooth3dPoints0.0570.0030.060
spatialDistanceMatrix0.9680.2081.178
threeJsGeometry-class000
threeJsViewer-shiny000
threeJsViewer0.0690.0080.182
view3dCells0.0060.0020.009
view3dStructure0.2680.0100.277