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This page was generated on 2024-11-20 12:06 -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 1870/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDesign3 1.4.0  (landing page)
Dongyuan Song
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/scDesign3
git_branch: RELEASE_3_20
git_last_commit: 0c3d1ba
git_last_commit_date: 2024-10-29 11:25:28 -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 scDesign3 on lconway

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: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDesign3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDesign3_1.4.0.tar.gz
StartedAt: 2024-11-20 02:21:19 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 02:27:15 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 355.7 seconds
RetCode: 0
Status:   OK  
CheckDir: scDesign3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDesign3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDesign3_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scDesign3.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDesign3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDesign3’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘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
construct_data 5.081  0.222   5.333
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/scDesign3.Rcheck/00check.log’
for details.


Installation output

scDesign3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scDesign3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘scDesign3’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.

> library(testthat)
> library(scDesign3)
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
> 
> test_check("scDesign3")
Loading required package: SingleCellExperiment
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: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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: GenomeInfoDb
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

Convert Residuals to Uniform
Converting End
Copula group embryonic day 3 starts
Vine Copula Estimation Starts
Time difference of 0.1326468 secs
Vine Copula Estimation Ends
Copula group embryonic day 4 starts
Vine Copula Estimation Starts
Time difference of 0.02235198 secs
Vine Copula Estimation Ends
Copula group embryonic day 5 starts
Vine Copula Estimation Starts
Time difference of 0.04520392 secs
Vine Copula Estimation Ends
Copula group embryonic day 6 starts
Vine Copula Estimation Starts
Time difference of 0.04896998 secs
Vine Copula Estimation Ends
Copula group embryonic day 7 starts
Vine Copula Estimation Starts
Time difference of 0.05110097 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
Input Data Construction End
Start Marginal Fitting
Marginal Fitting End
Start Copula Fitting
Convert Residuals to Uniform
Converting End
Copula group 1 starts
Vine Copula Estimation Starts
Time difference of 0.04228091 secs
Vine Copula Estimation Ends
Copula group 2 starts
Vine Copula Estimation Starts
Time difference of 0.04434395 secs
Vine Copula Estimation Ends
Copula group 3 starts
Vine Copula Estimation Starts
Time difference of 0.04780793 secs
Vine Copula Estimation Ends
Copula group 4 starts
Vine Copula Estimation Starts
Time difference of 0.02288985 secs
Vine Copula Estimation Ends
Copula Fitting End
Start Parameter Extraction
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
New Data Generating End
[ FAIL 0 | WARN 12 | SKIP 1 | PASS 0 ]

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

[ FAIL 0 | WARN 12 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 46.900   5.040  49.208 

Example timings

scDesign3.Rcheck/scDesign3-Ex.timings

nameusersystemelapsed
ba000
construct_data5.0810.2225.333
extract_para1.8630.1191.989
fit_copula1.1400.0751.218
fit_marginal0.7030.0520.755
ga000
gamlss.ba000
gamlss.ga0.0010.0000.000
perform_lrt1.6620.2761.847
scdesign32.3611.1422.202
simu_new1.7050.1371.862
sparse_cov000