Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:44:49 -0400 (Wed, 15 Apr 2020).
Package 1645/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
splatter 1.10.1 Luke Zappia
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: splatter |
Version: 1.10.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings splatter_1.10.1.tar.gz |
StartedAt: 2020-04-15 05:54:06 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 06:01:47 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 460.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: splatter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:splatter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings splatter_1.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/splatter.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘splatter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘splatter’ version ‘1.10.1’ * 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 ... NOTE Unexported object imported by a ':::' call: ‘rlang:::warn_deprecated’ See the note in ?`:::` about the use of this operator. * 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 or elapsed time > 5s user system elapsed scDDEstimate 26.487 0.402 27.205 kersplatEstimate 7.119 0.208 7.385 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.10-bioc/meat/splatter.Rcheck/00check.log’ for details.
splatter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL splatter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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 0.244 0.068 0.285
splatter.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid 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")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum > > 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: 0.21 Average acceptance rate among mu[i]'s: 0.421265 Maximum acceptance rate among mu[i]'s: 0.5352 Minimum acceptance rate among delta[i]'s: 0.391267 Average acceptance rate among delta[i]'s: 0.4489 Maximum acceptance rate among delta[i]'s: 0.541733 Acceptance rate for phi (joint): 0.429067 Minimum acceptance rate among nu[j]'s: 0.384467 Average acceptance rate among nu[j]'s: 0.448498 Maximum acceptance rate among nu[j]'s: 0.499933 Minimum acceptance rate among theta[k]'s: 0.462667 Average acceptance rate among theta[k]'s: 0.462667 Maximum acceptance rate among theta[k]'s: 0.462667 ----------------------------------------------------- ----------------------------------------------------- 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: 0.181267 Average acceptance rate among mu[i]'s: 0.444741 Maximum acceptance rate among mu[i]'s: 0.7594 Minimum acceptance rate among delta[i]'s: 0.375667 Average acceptance rate among delta[i]'s: 0.450051 Maximum acceptance rate among delta[i]'s: 0.5164 Minimum acceptance rate among nu[jk]'s: 0.4146 Average acceptance rate among nu[jk]'s: 0.530309 Maximum acceptance rate among nu[jk]'s: 0.637867 Minimum acceptance rate among theta[k]'s: 0.461733 Average acceptance rate among theta[k]'s: 0.462933 Maximum acceptance rate among theta[k]'s: 0.464133 ----------------------------------------------------- ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 144 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ] > > proc.time() user system elapsed 173.637 14.584 191.892
splatter.Rcheck/splatter-Ex.timings
name | user | system | elapsed | |
BASiCSEstimate | 0 | 0 | 0 | |
BASiCSSimulate | 3.966 | 0.183 | 4.222 | |
addGeneLengths | 0.353 | 0.012 | 0.375 | |
compareSCEs | 3.392 | 0.063 | 3.494 | |
diffSCEs | 3.016 | 0.008 | 3.053 | |
getParam | 0.001 | 0.000 | 0.000 | |
getParams | 0.001 | 0.000 | 0.001 | |
kersplatEstimate | 7.119 | 0.208 | 7.385 | |
kersplatSample | 1.197 | 0.095 | 1.307 | |
kersplatSetup | 0.823 | 0.063 | 0.897 | |
kersplatSimulate | 1.691 | 0.080 | 1.788 | |
listSims | 0.022 | 0.002 | 0.023 | |
lun2Estimate | 0.000 | 0.001 | 0.000 | |
lun2Simulate | 0.291 | 0.006 | 0.299 | |
lunEstimate | 0.355 | 0.002 | 0.358 | |
lunSimulate | 0.278 | 0.004 | 0.283 | |
makeCompPanel | 0 | 0 | 0 | |
makeDiffPanel | 0.001 | 0.000 | 0.000 | |
makeOverallPanel | 0.000 | 0.001 | 0.001 | |
mfaEstimate | 0.168 | 0.009 | 0.180 | |
mfaSimulate | 0.445 | 0.043 | 0.490 | |
newParams | 0.002 | 0.000 | 0.003 | |
phenoEstimate | 0.336 | 0.008 | 0.344 | |
phenoSimulate | 0.693 | 0.034 | 0.733 | |
scDDEstimate | 26.487 | 0.402 | 27.205 | |
scDDSimulate | 0 | 0 | 0 | |
setParam | 0.01 | 0.00 | 0.01 | |
setParams | 0.028 | 0.001 | 0.029 | |
simpleEstimate | 0.331 | 0.006 | 0.337 | |
simpleSimulate | 0.344 | 0.001 | 0.349 | |
sparseDCEstimate | 0.978 | 0.060 | 1.059 | |
sparseDCSimulate | 0.493 | 0.061 | 0.567 | |
splatEstimate | 4.462 | 0.112 | 4.628 | |
splatSimulate | 0.935 | 0.050 | 0.996 | |
summariseDiff | 3.161 | 0.009 | 3.194 | |
zinbEstimate | 3.707 | 0.154 | 3.907 | |
zinbSimulate | 0.076 | 0.001 | 0.080 | |