Luke Zappia
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/splatter |
| git_branch: RELEASE_3_13 |
| git_last_commit: 62da653 |
| git_last_commit_date: 2021-05-20 04:36:12 -0400 (Thu, 20 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:53 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1828/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| splatter 1.16.1 (landing page) Luke Zappia
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: splatter |
| Version: 1.16.1 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings splatter_1.16.1.tar.gz |
| StartedAt: 2021-10-14 11:44:03 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 11:51:34 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 451.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: splatter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings splatter_1.16.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/splatter.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.1’
* 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 43.444 1.343 44.786
zinbEstimate 18.969 0.036 19.006
* 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: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL splatter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
0.178 0.061 0.225
splatter.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
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.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: 0.318933
Average acceptance rate among mu[i]'s: 0.442449
Maximum acceptance rate among mu[i]'s: 0.642267
Minimum acceptance rate among delta[i]'s: 0.3818
Average acceptance rate among delta[i]'s: 0.450307
Maximum acceptance rate among delta[i]'s: 0.525867
Acceptance rate for phi (joint): 0.407
Minimum acceptance rate among nu[j]'s: 0.392933
Average acceptance rate among nu[j]'s: 0.446416
Maximum acceptance rate among nu[j]'s: 0.5014
Minimum acceptance rate among theta[k]'s: 0.422333
Average acceptance rate among theta[k]'s: 0.422333
Maximum acceptance rate among theta[k]'s: 0.422333
-----------------------------------------------------
-----------------------------------------------------
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: 0.3176
Average acceptance rate among mu[i]'s: 0.459391
Maximum acceptance rate among mu[i]'s: 0.6118
Minimum acceptance rate among delta[i]'s: 0.381067
Average acceptance rate among delta[i]'s: 0.448929
Maximum acceptance rate among delta[i]'s: 0.522067
Minimum acceptance rate among nu[jk]'s: 0.376667
Average acceptance rate among nu[jk]'s: 0.4292
Maximum acceptance rate among nu[jk]'s: 0.470267
Minimum acceptance rate among theta[k]'s: 0.433533
Average acceptance rate among theta[k]'s: 0.4432
Maximum acceptance rate among theta[k]'s: 0.452867
-----------------------------------------------------
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 167 ]
>
> proc.time()
user system elapsed
180.891 3.816 184.712
splatter.Rcheck/splatter-Ex.timings
| name | user | system | elapsed | |
| BASiCSEstimate | 0 | 0 | 0 | |
| BASiCSSimulate | 4.009 | 0.116 | 4.126 | |
| addGeneLengths | 1.046 | 0.024 | 1.069 | |
| compareSCEs | 3.112 | 0.100 | 3.213 | |
| diffSCEs | 3.234 | 0.024 | 3.257 | |
| getParam | 0.001 | 0.000 | 0.000 | |
| getParams | 0.001 | 0.000 | 0.000 | |
| kersplatEstimate | 3.680 | 0.075 | 3.756 | |
| kersplatSample | 2.638 | 0.060 | 2.699 | |
| kersplatSetup | 0.182 | 0.000 | 0.182 | |
| kersplatSimulate | 0 | 0 | 0 | |
| listSims | 0.017 | 0.000 | 0.017 | |
| lun2Estimate | 0 | 0 | 0 | |
| lun2Simulate | 0.403 | 0.011 | 0.415 | |
| lunEstimate | 1.294 | 0.020 | 1.313 | |
| lunSimulate | 0.402 | 0.020 | 0.422 | |
| makeCompPanel | 0.000 | 0.000 | 0.001 | |
| makeDiffPanel | 0.000 | 0.000 | 0.001 | |
| makeOverallPanel | 0.001 | 0.000 | 0.001 | |
| mfaEstimate | 0.089 | 0.000 | 0.089 | |
| mfaSimulate | 0.470 | 0.012 | 0.482 | |
| minimiseSCE | 0.945 | 0.036 | 0.980 | |
| mockBulkMatrix | 0.001 | 0.000 | 0.000 | |
| mockBulkeQTL | 4.626 | 0.124 | 4.750 | |
| mockGFF | 0.003 | 0.000 | 0.003 | |
| mockVCF | 0.168 | 0.004 | 0.171 | |
| newParams | 0.001 | 0.000 | 0.002 | |
| phenoEstimate | 0.737 | 0.084 | 0.821 | |
| phenoSimulate | 0.950 | 0.032 | 0.983 | |
| scDDEstimate | 43.444 | 1.343 | 44.786 | |
| scDDSimulate | 0 | 0 | 0 | |
| setParam | 0.008 | 0.000 | 0.009 | |
| setParams | 0.016 | 0.004 | 0.020 | |
| simpleEstimate | 0.686 | 0.024 | 0.711 | |
| simpleSimulate | 0.649 | 0.020 | 0.668 | |
| sparseDCEstimate | 1.053 | 0.044 | 1.096 | |
| sparseDCSimulate | 1.869 | 0.512 | 2.382 | |
| splatEstimate | 3.030 | 0.032 | 3.062 | |
| splatPopEstimate | 4.251 | 0.008 | 4.260 | |
| splatPopQuantNorm | 0.025 | 0.000 | 0.025 | |
| splatPopSimulate | 0 | 0 | 0 | |
| splatPopSimulateMeans | 0.001 | 0.000 | 0.000 | |
| splatPopSimulateSC | 0 | 0 | 0 | |
| splatSimulate | 0.939 | 0.000 | 0.938 | |
| summariseDiff | 3.726 | 0.008 | 3.734 | |
| zinbEstimate | 18.969 | 0.036 | 19.006 | |
| zinbSimulate | 0.231 | 0.000 | 0.232 | |