Luke Zappia
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/splatter |
| Branch: RELEASE_3_12 |
| Last Commit: 8c83847 |
| Last Changed Date: 2020-12-01 04:45:41 -0400 (Tue, 01 Dec 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:55 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the splatter package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1772/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| splatter 1.14.1 (landing page) Luke Zappia
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: splatter |
| Version: 1.14.1 |
| 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_1.14.1.tar.gz |
| StartedAt: 2021-05-06 06:31:31 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:41:33 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 602.1 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_1.14.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/splatter.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.14.1’
* 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 30.842 0.538 31.421
zinbEstimate 17.592 0.114 17.727
mockBulkeQTL 5.654 0.268 7.203
kersplatEstimate 5.666 0.195 5.867
splatPopEstimate 5.082 0.111 5.199
* 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/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
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
0.265 0.065 0.307
splatter.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 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")'.
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 9 | SKIP 0 | PASS 168 ]
>
> proc.time()
user system elapsed
267.482 7.934 277.162
splatter.Rcheck/splatter-Ex.timings
| name | user | system | elapsed | |
| BASiCSEstimate | 0.000 | 0.001 | 0.001 | |
| BASiCSSimulate | 4.271 | 0.148 | 4.424 | |
| addGeneLengths | 0.931 | 0.023 | 0.956 | |
| compareSCEs | 3.248 | 0.128 | 3.382 | |
| diffSCEs | 2.956 | 0.011 | 2.970 | |
| getParam | 0.000 | 0.000 | 0.001 | |
| getParams | 0.001 | 0.000 | 0.001 | |
| kersplatEstimate | 5.666 | 0.195 | 5.867 | |
| kersplatSample | 2.043 | 0.114 | 2.190 | |
| kersplatSetup | 0.207 | 0.021 | 0.229 | |
| kersplatSimulate | 0.000 | 0.001 | 0.000 | |
| listSims | 0.029 | 0.003 | 0.033 | |
| lun2Estimate | 0 | 0 | 0 | |
| lun2Simulate | 0.883 | 0.031 | 0.915 | |
| lunEstimate | 0.460 | 0.007 | 0.467 | |
| lunSimulate | 0.392 | 0.029 | 0.421 | |
| makeCompPanel | 0.000 | 0.000 | 0.001 | |
| makeDiffPanel | 0 | 0 | 0 | |
| makeOverallPanel | 0.001 | 0.000 | 0.000 | |
| mfaEstimate | 0.156 | 0.011 | 0.168 | |
| mfaSimulate | 1.114 | 0.040 | 1.155 | |
| minimiseSCE | 0.980 | 0.035 | 1.016 | |
| mockBulkMatrix | 0.001 | 0.001 | 0.001 | |
| mockBulkeQTL | 5.654 | 0.268 | 7.203 | |
| mockGFF | 0.003 | 0.000 | 0.003 | |
| mockVCF | 0.288 | 0.003 | 0.292 | |
| newParams | 0.002 | 0.001 | 0.002 | |
| phenoEstimate | 0.842 | 0.017 | 0.859 | |
| phenoSimulate | 1.806 | 0.071 | 1.879 | |
| scDDEstimate | 30.842 | 0.538 | 31.421 | |
| scDDSimulate | 0 | 0 | 0 | |
| setParam | 0.013 | 0.001 | 0.014 | |
| setParams | 0.031 | 0.002 | 0.034 | |
| simpleEstimate | 0.454 | 0.004 | 0.458 | |
| simpleSimulate | 0.523 | 0.004 | 0.529 | |
| sparseDCEstimate | 1.224 | 0.078 | 1.305 | |
| sparseDCSimulate | 1.618 | 0.074 | 1.694 | |
| splatEstimate | 4.478 | 0.097 | 4.582 | |
| splatPopEstimate | 5.082 | 0.111 | 5.199 | |
| splatPopQuantNorm | 0.043 | 0.000 | 0.043 | |
| splatPopSimulate | 0 | 0 | 0 | |
| splatPopSimulateMeans | 0.000 | 0.000 | 0.001 | |
| splatPopSimulateSC | 0 | 0 | 0 | |
| splatSimulate | 0.818 | 0.029 | 0.850 | |
| summariseDiff | 2.867 | 0.033 | 2.904 | |
| zinbEstimate | 17.592 | 0.114 | 17.727 | |
| zinbSimulate | 0.176 | 0.001 | 0.178 | |