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This page was generated on 2025-06-19 12:04 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4810
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4528
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 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 1878/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDesign3 1.7.0  (landing page)
Dongyuan Song
Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025)
git_url: https://git.bioconductor.org/packages/scDesign3
git_branch: devel
git_last_commit: d25bf88
git_last_commit_date: 2025-04-15 13:24:32 -0400 (Tue, 15 Apr 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped

CHECK results for scDesign3 on palomino8

To the developers/maintainers of the scDesign3 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scDesign3.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: scDesign3
Version: 1.7.0
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scDesign3.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings scDesign3_1.7.0.tar.gz
StartedAt: 2025-06-19 06:21:48 -0400 (Thu, 19 Jun 2025)
EndedAt: 2025-06-19 06:26:49 -0400 (Thu, 19 Jun 2025)
EllapsedTime: 301.3 seconds
RetCode: 0
Status:   OK  
CheckDir: scDesign3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scDesign3.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings scDesign3_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/scDesign3.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scDesign3/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scDesign3' version '1.7.0'
* 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 whether package 'scDesign3' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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
scdesign3      11.16   0.19   46.69
simu_new        8.26   0.13    8.39
perform_lrt     7.39   0.28   14.47
construct_data  6.25   0.41    6.66
extract_para    6.17   0.17    6.34
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.22-bioc/meat/scDesign3.Rcheck/00check.log'
for details.

Installation output

scDesign3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL scDesign3
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'scDesign3' ...
** this is package 'scDesign3' version '1.7.0'
** using staged installation
** R
** data
** 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 (scDesign3)

Tests output

scDesign3.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(scDesign3)
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
> 
> test_check("scDesign3")
Loading required namespace: SingleCellExperiment
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Convert Residuals to Uniform
Converting End
Copula group embryonic day 3 starts
Vine Copula Estimation Starts
Time difference of 0.2304752 secs
Vine Copula Estimation Ends
Copula group embryonic day 4 starts
Vine Copula Estimation Starts
Time difference of 0.03755116 secs
Vine Copula Estimation Ends
Copula group embryonic day 5 starts
Vine Copula Estimation Starts
Time difference of 0.06833601 secs
Vine Copula Estimation Ends
Copula group embryonic day 6 starts
Vine Copula Estimation Starts
Time difference of 0.08039498 secs
Vine Copula Estimation Ends
Copula group embryonic day 7 starts
Vine Copula Estimation Starts
Time difference of 0.1049159 secs
Vine Copula Estimation Ends
Use the empirical quantile matrices from the original data; do not fit copula. This will make the result FIXED.
Empirical quantile group embryonic day 3 starts
Empirical quantile group embryonic day 4 starts
Empirical quantile group embryonic day 5 starts
Empirical quantile group embryonic day 6 starts
Empirical quantile group embryonic day 7 starts
Convert Residuals to Multivariate Gaussian
Converting End
Copula group embryonic day 3 starts
Copula group embryonic day 4 starts
Copula group embryonic day 5 starts
Copula group embryonic day 6 starts
Copula group embryonic day 7 starts
Use Copula to sample a multivariate quantile matrix
Sample Copula group embryonic day 3 starts
Sample Copula group embryonic day 4 starts
Sample Copula group embryonic day 5 starts
Sample Copula group embryonic day 6 starts
Sample Copula group embryonic day 7 starts
Multivariate quantile matrix is provided
Use Copula to sample a multivariate quantile matrix
Sample Copula group embryonic day 3 starts
Sample Copula group embryonic day 4 starts
Sample Copula group embryonic day 5 starts
Sample Copula group embryonic day 6 starts
Sample Copula group embryonic day 7 starts
Input Data Construction Start
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Input Data Construction End
Start Marginal Fitting
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Marginal Fitting End
Start Copula Fitting
Convert Residuals to Uniform
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Loading required namespace: SingleCellExperiment

Loading required namespace: SingleCellExperiment

Converting End
Copula group 1 starts
Vine Copula Estimation Starts
Time difference of 0.04229712 secs
Vine Copula Estimation Ends
Copula group 2 starts
Vine Copula Estimation Starts
Time difference of 0.06624508 secs
Vine Copula Estimation Ends
Copula group 3 starts
Vine Copula Estimation Starts
Time difference of 0.08582211 secs
Vine Copula Estimation Ends
Copula group 4 starts
Vine Copula Estimation Starts
Time difference of 0.04076886 secs
Vine Copula Estimation Ends
Copula Fitting End
Start Parameter Extraction
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Parameter
Extraction End
Start Generate New Data
Use Copula to sample a multivariate quantile matrix
Sample Copula group 1 starts
Sample Copula group 2 starts
Sample Copula group 3 starts
Sample Copula group 4 starts
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Use Copula to sample a multivariate quantile matrix
Sample Copula group 1 starts
Sample Copula group 2 starts
Sample Copula group 3 starts
Sample Copula group 4 starts
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
New Data Generating End
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-scDesign3.R:4:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  56.64    2.70  118.50

Example timings

scDesign3.Rcheck/scDesign3-Ex.timings

nameusersystemelapsed
ba000
construct_data6.250.416.66
extract_para6.170.176.34
fit_copula4.290.154.44
fit_marginal2.390.112.50
ga000
gamlss.ba000
gamlss.ga000
perform_lrt 7.39 0.2814.47
scdesign311.16 0.1946.69
simu_new8.260.138.39
sparse_cov000