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 15:06:54 -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: /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_1.16.1.tar.gz |
| StartedAt: 2021-10-15 00:20:14 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:31:22 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 667.3 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_1.16.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/splatter.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.16.1’
* 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 63.091 0.435 63.584
zinbEstimate 20.503 0.093 20.607
kersplatEstimate 6.497 0.208 6.708
mockBulkeQTL 6.398 0.300 6.701
summariseDiff 5.548 0.099 5.649
diffSCEs 5.446 0.016 5.468
BASiCSSimulate 5.218 0.183 5.404
splatEstimate 5.224 0.100 5.326
splatPopEstimate 5.100 0.095 5.202
* 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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
0.288 0.070 0.335
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-apple-darwin17.0 (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: 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
269.571 9.915 279.726
splatter.Rcheck/splatter-Ex.timings
| name | user | system | elapsed | |
| BASiCSEstimate | 0.000 | 0.001 | 0.001 | |
| BASiCSSimulate | 5.218 | 0.183 | 5.404 | |
| addGeneLengths | 1.159 | 0.030 | 1.189 | |
| compareSCEs | 4.554 | 0.082 | 4.641 | |
| diffSCEs | 5.446 | 0.016 | 5.468 | |
| getParam | 0 | 0 | 0 | |
| getParams | 0.001 | 0.000 | 0.001 | |
| kersplatEstimate | 6.497 | 0.208 | 6.708 | |
| kersplatSample | 2.522 | 0.097 | 2.620 | |
| kersplatSetup | 0.228 | 0.036 | 0.265 | |
| kersplatSimulate | 0.000 | 0.000 | 0.001 | |
| listSims | 0.041 | 0.004 | 0.045 | |
| lun2Estimate | 0 | 0 | 0 | |
| lun2Simulate | 1.268 | 0.045 | 1.314 | |
| lunEstimate | 1.046 | 0.007 | 1.054 | |
| lunSimulate | 0.614 | 0.025 | 0.640 | |
| makeCompPanel | 0 | 0 | 0 | |
| makeDiffPanel | 0.000 | 0.001 | 0.001 | |
| makeOverallPanel | 0 | 0 | 0 | |
| mfaEstimate | 0.160 | 0.014 | 0.177 | |
| mfaSimulate | 0.776 | 0.048 | 0.825 | |
| minimiseSCE | 1.535 | 0.045 | 1.581 | |
| mockBulkMatrix | 0.000 | 0.000 | 0.001 | |
| mockBulkeQTL | 6.398 | 0.300 | 6.701 | |
| mockGFF | 0.002 | 0.000 | 0.003 | |
| mockVCF | 0.210 | 0.001 | 0.211 | |
| newParams | 0.001 | 0.001 | 0.002 | |
| phenoEstimate | 1.029 | 0.050 | 1.080 | |
| phenoSimulate | 3.258 | 0.100 | 3.366 | |
| scDDEstimate | 63.091 | 0.435 | 63.584 | |
| scDDSimulate | 0 | 0 | 0 | |
| setParam | 0.012 | 0.001 | 0.013 | |
| setParams | 0.039 | 0.003 | 0.043 | |
| simpleEstimate | 1.123 | 0.007 | 1.131 | |
| simpleSimulate | 1.061 | 0.015 | 1.077 | |
| sparseDCEstimate | 1.737 | 0.132 | 1.872 | |
| sparseDCSimulate | 1.798 | 0.077 | 1.877 | |
| splatEstimate | 5.224 | 0.100 | 5.326 | |
| splatPopEstimate | 5.100 | 0.095 | 5.202 | |
| splatPopQuantNorm | 0.039 | 0.001 | 0.039 | |
| splatPopSimulate | 0.001 | 0.001 | 0.001 | |
| splatPopSimulateMeans | 0.001 | 0.001 | 0.001 | |
| splatPopSimulateSC | 0.000 | 0.001 | 0.001 | |
| splatSimulate | 1.413 | 0.033 | 1.448 | |
| summariseDiff | 5.548 | 0.099 | 5.649 | |
| zinbEstimate | 20.503 | 0.093 | 20.607 | |
| zinbSimulate | 0.356 | 0.001 | 0.358 | |