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This page was generated on 2024-11-20 12:07 -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 839/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geomeTriD 1.0.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/geomeTriD
git_branch: RELEASE_3_20
git_last_commit: 30e2f2e
git_last_commit_date: 2024-10-29 11:34:09 -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  UNNEEDED, same version is already published
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 geomeTriD on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: geomeTriD
Version: 1.0.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:geomeTriD.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings geomeTriD_1.0.0.tar.gz
StartedAt: 2024-11-20 08:15:37 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 08:26:09 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 632.1 seconds
RetCode: 0
Status:   OK  
CheckDir: geomeTriD.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:geomeTriD.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings geomeTriD_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/geomeTriD.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geomeTriD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geomeTriD’ version ‘1.0.0’
* 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 ‘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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
mdsPlot         5.660  0.108   5.780
loopBouquetPlot 5.021  0.151   5.184
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL geomeTriD
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘geomeTriD’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> 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
This build of rgl does not include OpenGL functions.  Use
 rglwidget() to display results, e.g. via options(rgl.printRglwidget = TRUE).
[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 0 | SKIP 3 | PASS 92 ]

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

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
 54.973   1.142  56.168 

Example timings

geomeTriD.Rcheck/geomeTriD-Ex.timings

nameusersystemelapsed
alignCoor1.6490.0641.719
availableGeometries000
create3dGenomicSignals0.5760.0080.586
extractBackbonePositions0.8570.0120.872
geomeTriD-package0.0010.0000.001
loopBouquetPlot5.0210.1515.184
mdsPlot5.6600.1085.780
rglViewer1.7040.0241.732
smooth3dPoints0.2090.0000.209
threeJsGeometry-class0.0010.0000.000
threeJsViewer-shiny0.0010.0000.001
threeJsViewer0.2780.0001.068
view3dCells0.0270.0010.028
view3dStructure1.3010.0001.304