Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1870/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scDesign3 1.4.0 (landing page) Dongyuan Song
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
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: 2024-12-20 09:09:57 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 09:15:12 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 315.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scDesign3.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 4.4.2 (2024-10-31) * 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 ... 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 12.072 0.503 12.647 scdesign3 5.369 2.296 4.822 simu_new 4.744 0.405 5.190 * 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.
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)
scDesign3.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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 0.389096 secs Vine Copula Estimation Ends Copula group embryonic day 4 starts Vine Copula Estimation Starts Time difference of 0.074054 secs Vine Copula Estimation Ends Copula group embryonic day 5 starts Vine Copula Estimation Starts Time difference of 0.1183758 secs Vine Copula Estimation Ends Copula group embryonic day 6 starts Vine Copula Estimation Starts Time difference of 0.1212568 secs Vine Copula Estimation Ends Copula group embryonic day 7 starts Vine Copula Estimation Starts Time difference of 0.1393819 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 0.07109094 secs Vine Copula Estimation Ends Copula group 2 starts Vine Copula Estimation Starts Time difference of 0.07843113 secs Vine Copula Estimation Ends Copula group 3 starts Vine Copula Estimation Starts Time difference of 0.100455 secs Vine Copula Estimation Ends Copula group 4 starts Vine Copula Estimation Starts Time difference of 0.04163313 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 122.933 8.864 132.348
scDesign3.Rcheck/scDesign3-Ex.timings
name | user | system | elapsed | |
ba | 0.001 | 0.000 | 0.001 | |
construct_data | 12.072 | 0.503 | 12.647 | |
extract_para | 4.199 | 0.204 | 4.470 | |
fit_copula | 2.841 | 0.101 | 2.988 | |
fit_marginal | 1.501 | 0.070 | 1.587 | |
ga | 0.000 | 0.001 | 0.001 | |
gamlss.ba | 0.000 | 0.000 | 0.001 | |
gamlss.ga | 0.001 | 0.001 | 0.001 | |
perform_lrt | 3.548 | 0.483 | 3.857 | |
scdesign3 | 5.369 | 2.296 | 4.822 | |
simu_new | 4.744 | 0.405 | 5.190 | |
sparse_cov | 0.000 | 0.000 | 0.001 | |