Luke Zappia
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/splatter |
| git_branch: RELEASE_3_16 |
| git_last_commit: 22d3e70 |
| git_last_commit_date: 2023-01-30 05:25:12 -0400 (Mon, 30 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:20 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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 1944/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| splatter 1.22.1 (landing page) Luke Zappia
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: splatter |
| Version: 1.22.1 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings splatter_1.22.1.tar.gz |
| StartedAt: 2023-04-11 00:15:38 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:25:57 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 618.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: splatter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:splatter.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings splatter_1.22.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/splatter.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘splatter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘splatter’ version ‘1.22.1’
* 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 loading without being on the library search path ... 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 26.257 0.231 26.490
mockBulkeQTL 5.121 0.100 5.222
* 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-3.16-bioc/R/bin/R CMD INSTALL splatter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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
0.188 0.015 0.190
splatter.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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
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
181.506 2.826 184.321
splatter.Rcheck/splatter-Ex.timings
| name | user | system | elapsed | |
| BASiCSEstimate | 0 | 0 | 0 | |
| BASiCSSimulate | 4.625 | 0.104 | 4.729 | |
| addGeneLengths | 0.384 | 0.008 | 0.392 | |
| compareSCEs | 2.584 | 0.064 | 2.647 | |
| diffSCEs | 2.439 | 0.039 | 2.479 | |
| getParam | 0.000 | 0.000 | 0.001 | |
| getParams | 0.000 | 0.000 | 0.001 | |
| kersplatEstimate | 3.567 | 0.080 | 3.648 | |
| kersplatSample | 1.845 | 0.120 | 1.966 | |
| kersplatSetup | 0.197 | 0.008 | 0.206 | |
| kersplatSimulate | 0.001 | 0.000 | 0.001 | |
| listSims | 0.02 | 0.00 | 0.02 | |
| lun2Estimate | 0.001 | 0.000 | 0.000 | |
| lun2Simulate | 1.150 | 0.016 | 1.165 | |
| lunEstimate | 0.446 | 0.000 | 0.446 | |
| lunSimulate | 0.324 | 0.020 | 0.344 | |
| makeCompPanel | 0.001 | 0.000 | 0.000 | |
| makeDiffPanel | 0 | 0 | 0 | |
| makeOverallPanel | 0 | 0 | 0 | |
| mfaEstimate | 0.098 | 0.000 | 0.099 | |
| mfaSimulate | 0.446 | 0.004 | 0.450 | |
| minimiseSCE | 0.765 | 0.000 | 0.765 | |
| mockBulkMatrix | 0.001 | 0.000 | 0.000 | |
| mockBulkeQTL | 5.121 | 0.100 | 5.222 | |
| mockEmpiricalSet | 2.352 | 0.246 | 2.597 | |
| mockGFF | 0.003 | 0.000 | 0.003 | |
| mockVCF | 0.105 | 0.000 | 0.105 | |
| newParams | 0.000 | 0.002 | 0.002 | |
| phenoEstimate | 0.557 | 0.009 | 0.567 | |
| phenoSimulate | 0.928 | 0.036 | 0.964 | |
| scDDEstimate | 26.257 | 0.231 | 26.490 | |
| scDDSimulate | 0 | 0 | 0 | |
| setParam | 0.008 | 0.000 | 0.008 | |
| setParams | 0.019 | 0.000 | 0.019 | |
| simpleEstimate | 0.457 | 0.008 | 0.466 | |
| simpleSimulate | 0.462 | 0.008 | 0.469 | |
| sparseDCEstimate | 0.766 | 0.024 | 0.790 | |
| sparseDCSimulate | 0.483 | 0.044 | 0.527 | |
| splatEstimate | 2.573 | 0.048 | 2.622 | |
| splatPopEstimate | 2.659 | 0.040 | 2.699 | |
| splatPopQuantNorm | 0.026 | 0.001 | 0.026 | |
| splatPopSimulate | 0 | 0 | 0 | |
| splatPopSimulateMeans | 0 | 0 | 0 | |
| splatPopSimulateSC | 0 | 0 | 0 | |
| splatSimulate | 0.694 | 0.028 | 0.722 | |
| summariseDiff | 2.429 | 0.004 | 2.433 | |
| zinbEstimate | 1.849 | 0.040 | 1.889 | |
| zinbSimulate | 0.15 | 0.00 | 0.15 | |