Luke Zappia
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/splatter |
| Branch: RELEASE_3_9 |
| Last Commit: 0195bb5 |
| Last Changed Date: 2019-05-02 11:54:05 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:59:27 -0400 (Wed, 16 Oct 2019).
| Package 1569/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| splatter 1.8.0 Luke Zappia
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: splatter |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2019-10-16 07:05:42 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:12:45 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 423.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: splatter.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/splatter.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.0’
* 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 ‘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 or elapsed time > 5s
user system elapsed
BASiCSSimulate 4.716 0.394 5.111
* 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: OK
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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
0.346 0.137 0.426
splatter.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 0.324333
Average acceptance rate among mu[i]'s: 0.457085
Maximum acceptance rate among mu[i]'s: 0.612467
Minimum acceptance rate among delta[i]'s: 0.347933
Average acceptance rate among delta[i]'s: 0.447136
Maximum acceptance rate among delta[i]'s: 0.5156
Acceptance rate for phi (joint): 0.467667
Minimum acceptance rate among nu[j]'s: 0.396333
Average acceptance rate among nu[j]'s: 0.450798
Maximum acceptance rate among nu[j]'s: 0.489
Minimum acceptance rate among theta[k]'s: 0.4536
Average acceptance rate among theta[k]'s: 0.4536
Maximum acceptance rate among theta[k]'s: 0.4536
-----------------------------------------------------
-----------------------------------------------------
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: 0.296667
Average acceptance rate among mu[i]'s: 0.441319
Maximum acceptance rate among mu[i]'s: 0.6038
Minimum acceptance rate among delta[i]'s: 0.369
Average acceptance rate among delta[i]'s: 0.449998
Maximum acceptance rate among delta[i]'s: 0.514267
Minimum acceptance rate among nu[jk]'s: 0.398133
Average acceptance rate among nu[jk]'s: 0.456478
Maximum acceptance rate among nu[jk]'s: 0.520733
Minimum acceptance rate among theta[k]'s: 0.451467
Average acceptance rate among theta[k]'s: 0.453867
Maximum acceptance rate among theta[k]'s: 0.456267
-----------------------------------------------------
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 140 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
134.163 8.668 144.801
splatter.Rcheck/splatter-Ex.timings
| name | user | system | elapsed | |
| BASiCSEstimate | 0.001 | 0.001 | 0.000 | |
| BASiCSSimulate | 4.716 | 0.394 | 5.111 | |
| addGeneLengths | 0.353 | 0.004 | 0.356 | |
| compareSCEs | 2.297 | 0.163 | 2.461 | |
| diffSCEs | 1.938 | 0.007 | 1.945 | |
| getParam | 0.001 | 0.000 | 0.001 | |
| getParams | 0.001 | 0.000 | 0.001 | |
| listSims | 0.016 | 0.002 | 0.019 | |
| lun2Estimate | 0.000 | 0.001 | 0.001 | |
| lun2Simulate | 0.368 | 0.041 | 0.410 | |
| lunEstimate | 0.125 | 0.010 | 0.135 | |
| lunSimulate | 1.029 | 0.068 | 1.097 | |
| makeCompPanel | 0.000 | 0.001 | 0.000 | |
| makeDiffPanel | 0.000 | 0.001 | 0.001 | |
| makeOverallPanel | 0.000 | 0.000 | 0.001 | |
| mfaEstimate | 0.225 | 0.019 | 0.246 | |
| mfaSimulate | 1.278 | 0.136 | 1.416 | |
| newParams | 0.003 | 0.000 | 0.003 | |
| phenoEstimate | 0.224 | 0.014 | 0.239 | |
| phenoSimulate | 0.956 | 0.074 | 1.031 | |
| scDDEstimate | 0.000 | 0.001 | 0.001 | |
| scDDSimulate | 0 | 0 | 0 | |
| setParam | 0.011 | 0.000 | 0.012 | |
| setParams | 0.025 | 0.002 | 0.027 | |
| simpleEstimate | 0.396 | 0.012 | 0.409 | |
| simpleSimulate | 1.114 | 0.021 | 1.136 | |
| sparseDCEstimate | 2.948 | 1.085 | 4.035 | |
| sparseDCSimulate | 1.243 | 0.162 | 1.405 | |
| splatEstimate | 1.578 | 0.100 | 1.678 | |
| splatSimulate | 1.468 | 0.150 | 1.618 | |
| summariseDiff | 2.106 | 0.078 | 2.183 | |
| zinbEstimate | 0 | 0 | 0 | |
| zinbSimulate | 2.210 | 0.111 | 2.321 | |