Luke Zappia
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/splatter |
| Branch: RELEASE_3_10 |
| Last Commit: 39a9ae7 |
| Last Changed Date: 2020-02-14 10:01:37 -0400 (Fri, 14 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
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 | |