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This page was generated on 2023-11-02 11:41:14 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 1878/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scider 1.0.0  (landing page)
Yunshun Chen
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/scider
git_branch: RELEASE_3_18
git_last_commit: aa4483a
git_last_commit_date: 2023-10-24 11:52:18 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for scider on kunpeng2


To the developers/maintainers of the scider package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scider.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: scider
Version: 1.0.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:scider.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings scider_1.0.0.tar.gz
StartedAt: 2023-11-02 14:07:38 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 14:16:40 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 542.0 seconds
RetCode: 0
Status:   OK  
CheckDir: scider.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:scider.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings scider_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/scider.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘scider/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scider’ 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 ‘scider’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plotCellCompo  22.267  0.148  22.464
allocateCells  17.838  0.265  18.166
spe2PB         15.550  0.036  15.616
plotROI        14.083  0.063  14.175
plotDensCor     9.246  0.040   9.302
plotCorHeatmap  7.505  0.084   7.604
corDensity      7.367  0.068   7.448
findROI         6.381  0.027   6.421
mergeROI        6.252  0.016   6.280
* 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: OK


Installation output

scider.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL scider
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘scider’ ...
** using staged installation
** R
** data
** 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 (scider)

Tests output

scider.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-unknown-linux-gnu (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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(scider)
> 
> test_check("scider")
Assigning cells to ROIs defined by Breast cancer 

No contour detected.
Using bins = 10 to draw contours.
Assigning cells to ROIs defined by Breast cancer 

Assigning cells to contour levels of Breast cancer 

Linking to GEOS 3.9.0, GDAL 3.7.0, PROJ 8.2.1; sf_use_s2() is TRUE
Using bins = 10 to draw contours.
Using bins = 10 to draw contours.
Assigning cells to ROIs defined by Breast cancer, Fibroblasts 

Assigning cells to contour levels of Breast cancer 

Using bins = 10 to draw contours.
Assigning cells to ROIs defined by Breast cancer 

No contour detected.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 78 ]
> 
> proc.time()
   user  system elapsed 
172.290   3.038 177.511 

Example timings

scider.Rcheck/scider-Ex.timings

nameusersystemelapsed
allocateCells17.838 0.26518.166
corDensity7.3670.0687.448
findROI6.3810.0276.421
getContour1.4700.0441.516
gridDensity2.0840.0402.128
mergeROI6.2520.0166.280
plotCellCompo22.267 0.14822.464
plotContour2.0480.0322.084
plotCorHeatmap7.5050.0847.604
plotDensCor9.2460.0409.302
plotDensity2.7390.0602.803
plotROI14.083 0.06314.175
plotSpatial0.5780.0110.590
postSelRegion2.1340.0322.169
selectRegion0.1880.0040.193
spe2PB15.550 0.03615.616
xenium_bc_spe0.1280.0000.128