Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:51 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the splatter package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/splatter.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1937/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
splatter 1.23.1 (landing page) Luke Zappia
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: splatter |
Version: 1.23.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings splatter_1.23.1.tar.gz |
StartedAt: 2023-02-28 16:22:58 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 16:38:19 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 920.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: splatter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings splatter_1.23.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/splatter.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘splatter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘splatter’ version ‘1.23.1’ * 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 ‘splatter’ 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 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 scDDEstimate 39.957 0.524 40.482 mockBulkeQTL 6.430 0.204 6.635 BASiCSSimulate 5.425 0.324 5.748 kersplatEstimate 5.089 0.147 5.238 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘splatPop.Rmd’ using ‘UTF-8’... OK ‘splat_params.Rmd’ using ‘UTF-8’... OK ‘splatter.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
splatter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL splatter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘splatter’ ... ** 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 (splatter)
splatter.Rcheck/tests/spelling.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.200 0.030 0.215
splatter.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 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. > # setting R_TESTS to empty string because of > # https://github.com/hadley/testthat/issues/144 > # revert this when that issue in R is fixed. > Sys.setenv("R_TESTS" = "") > > library(testthat) > library(splatter) 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, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' 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 > > test_check("splatter") ----------------------------------------------------- MCMC sampler has been started: 20000 iterations to go. ----------------------------------------------------- ----------------------------------------------------- End of Burn-in period. ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- All 20000 MCMC iterations have been completed. ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- Please see below a summary of the overall acceptance rates. ----------------------------------------------------- Minimum acceptance rate among mu[i]'s: 0.216267 Average acceptance rate among mu[i]'s: 0.447751 Maximum acceptance rate among mu[i]'s: 0.581867 Minimum acceptance rate among delta[i]'s: 0.373467 Average acceptance rate among delta[i]'s: 0.446514 Maximum acceptance rate among delta[i]'s: 0.498 Acceptance rate for phi (joint): 0.455867 Minimum acceptance rate among nu[j]'s: 0.3964 Average acceptance rate among nu[j]'s: 0.450696 Maximum acceptance rate among nu[j]'s: 0.506933 Minimum acceptance rate among theta[k]'s: 0.431867 Average acceptance rate among theta[k]'s: 0.431867 Maximum acceptance rate among theta[k]'s: 0.431867 ----------------------------------------------------- ----------------------------------------------------- MCMC sampler has been started: 20000 iterations to go. ----------------------------------------------------- ----------------------------------------------------- End of Burn-in period. ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- All 20000 MCMC iterations have been completed. ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- Please see below a summary of the overall acceptance rates. ----------------------------------------------------- Minimum acceptance rate among mu[i]'s: 0.167067 Average acceptance rate among mu[i]'s: 0.436682 Maximum acceptance rate among mu[i]'s: 0.578267 Minimum acceptance rate among delta[i]'s: 0.395933 Average acceptance rate among delta[i]'s: 0.454213 Maximum acceptance rate among delta[i]'s: 0.515067 Minimum acceptance rate among nu[jk]'s: 0.370533 Average acceptance rate among nu[jk]'s: 0.451502 Maximum acceptance rate among nu[jk]'s: 0.492467 Minimum acceptance rate among theta[k]'s: 0.4586 Average acceptance rate among theta[k]'s: 0.464833 Maximum acceptance rate among theta[k]'s: 0.471067 ----------------------------------------------------- [ FAIL 0 | WARN 14 | SKIP 0 | PASS 184 ] [ FAIL 0 | WARN 14 | SKIP 0 | PASS 184 ] > > proc.time() user system elapsed 335.761 3.938 339.691
splatter.Rcheck/splatter-Ex.timings
name | user | system | elapsed | |
BASiCSEstimate | 0 | 0 | 0 | |
BASiCSSimulate | 5.425 | 0.324 | 5.748 | |
addGeneLengths | 0.443 | 0.008 | 0.450 | |
compareSCEs | 3.401 | 0.083 | 3.485 | |
diffSCEs | 3.345 | 0.021 | 3.365 | |
getParam | 0 | 0 | 0 | |
getParams | 0 | 0 | 0 | |
kersplatEstimate | 5.089 | 0.147 | 5.238 | |
kersplatSample | 2.192 | 0.164 | 2.356 | |
kersplatSetup | 0.244 | 0.000 | 0.244 | |
kersplatSimulate | 0 | 0 | 0 | |
listSims | 0.032 | 0.000 | 0.032 | |
lun2Estimate | 0 | 0 | 0 | |
lun2Simulate | 0.469 | 0.003 | 0.473 | |
lunEstimate | 1.319 | 0.064 | 1.384 | |
lunSimulate | 0.398 | 0.008 | 0.405 | |
makeCompPanel | 0 | 0 | 0 | |
makeDiffPanel | 0 | 0 | 0 | |
makeOverallPanel | 0 | 0 | 0 | |
mfaEstimate | 0.106 | 0.008 | 0.116 | |
mfaSimulate | 0.619 | 0.008 | 0.627 | |
minimiseSCE | 1.857 | 0.044 | 1.902 | |
mockBulkMatrix | 0.000 | 0.000 | 0.001 | |
mockBulkeQTL | 6.430 | 0.204 | 6.635 | |
mockEmpiricalSet | 3.754 | 0.212 | 3.967 | |
mockGFF | 0.003 | 0.000 | 0.003 | |
mockVCF | 0.147 | 0.004 | 0.151 | |
newParams | 0.002 | 0.000 | 0.002 | |
phenoEstimate | 0.743 | 0.024 | 0.767 | |
phenoSimulate | 1.430 | 0.048 | 1.478 | |
scDDEstimate | 39.957 | 0.524 | 40.482 | |
scDDSimulate | 0 | 0 | 0 | |
setParam | 0.012 | 0.000 | 0.013 | |
setParams | 0.032 | 0.000 | 0.032 | |
simpleEstimate | 0.644 | 0.004 | 0.647 | |
simpleSimulate | 0.595 | 0.004 | 0.599 | |
sparseDCEstimate | 1.366 | 0.044 | 1.413 | |
sparseDCSimulate | 2.068 | 0.108 | 2.175 | |
splatEstimate | 3.973 | 0.052 | 4.026 | |
splatPopEstimate | 4.009 | 0.028 | 4.036 | |
splatPopQuantNorm | 0.040 | 0.000 | 0.039 | |
splatPopSimulate | 0 | 0 | 0 | |
splatPopSimulateMeans | 0 | 0 | 0 | |
splatPopSimulateSC | 0 | 0 | 0 | |
splatSimulate | 2.384 | 0.060 | 2.443 | |
summariseDiff | 3.383 | 0.036 | 3.419 | |
zinbEstimate | 2.881 | 0.056 | 2.936 | |
zinbSimulate | 0.221 | 0.000 | 0.222 | |