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This page was generated on 2021-10-23 14:06:47 -0400 (Sat, 23 Oct 2021).

CHECK results for splatter on riesling1

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
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raw results

Package 1861/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
splatter 1.17.4  (landing page)
Luke Zappia
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/splatter
git_branch: master
git_last_commit: 58bb6c9
git_last_commit_date: 2021-10-22 04:10:18 -0400 (Fri, 22 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  YES
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: splatter
Version: 1.17.4
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:splatter.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings splatter_1.17.4.tar.gz
StartedAt: 2021-10-23 08:38:20 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 08:51:52 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 811.4 seconds
RetCode: 0
Status:   OK  
CheckDir: splatter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:splatter.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings splatter_1.17.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/splatter.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'splatter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'splatter' version '1.17.4'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
scDDEstimate     25.88   0.11   25.98
splatPopEstimate  6.47   0.06    6.53
kersplatEstimate  6.19   0.08    6.26
splatEstimate     5.74   0.06    5.80
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
scDDEstimate     26.87   0.10   26.98
kersplatEstimate  6.02   0.14    6.16
splatEstimate     5.02   0.11    5.13
splatPopEstimate  5.02   0.07    5.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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


Installation output

splatter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/splatter_1.17.4.tar.gz && rm -rf splatter.buildbin-libdir && mkdir splatter.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=splatter.buildbin-libdir splatter_1.17.4.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL splatter_1.17.4.zip && rm splatter_1.17.4.tar.gz splatter_1.17.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 50 1364k   50  685k    0     0  2277k      0 --:--:-- --:--:-- --:--:-- 2269k
100 1364k  100 1364k    0     0  3304k      0 --:--:-- --:--:-- --:--:-- 3296k

install for i386

* installing *source* package 'splatter' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'splatter'
    finding HTML links ... done
    BASiCSEstimate                          html  
    BASiCSParams                            html  
    BASiCSSimulate                          html  
    KersplatParams                          html  
    Lun2Params                              html  
    LunParams                               html  
    MFAParams                               html  
    Params                                  html  
    PhenoParams                             html  
    SCDDParams                              html  
    SimpleParams                            html  
    SparseDCParams                          html  
    SplatParams                             html  
    SplatPopParams                          html  
    ZINBParams                              html  
    addFeatureStats                         html  
    finding level-2 HTML links ... done

    addGeneLengths                          html  
    bridge                                  html  
    bringItemsForward                       html  
    checkDependencies                       html  
    co.var                                  html  
    compareSCEs                             html  
    diffSCEs                                html  
    expandParams                            html  
    getBetaStepProbs                        html  
    getCounts                               html  
    getLNormFactors                         html  
    getParam                                html  
    getParams                               html  
    getPathOrder                            html  
    kersplatEstBCV                          html  
    kersplatEstLib                          html  
    kersplatEstMean                         html  
    kersplatEstimate                        html  
    kersplatGenNetwork                      html  
    kersplatSample                          html  
    kersplatSelectRegs                      html  
    kersplatSetup                           html  
    kersplatSimAmbientCounts                html  
    kersplatSimCellCounts                   html  
    kersplatSimCellMeans                    html  
    kersplatSimCounts                       html  
    kersplatSimGeneMeans                    html  
    kersplatSimLibSizes                     html  
    kersplatSimPaths                        html  
    kersplatSimulate                        html  
    listSims                                html  
    logistic                                html  
    lun2Estimate                            html  
    lun2Simulate                            html  
    lunEstimate                             html  
    lunSimulate                             html  
    makeCompPanel                           html  
    makeDiffPanel                           html  
    makeOverallPanel                        html  
    mfaEstimate                             html  
    mfaSimulate                             html  
    minimiseSCE                             html  
    mockBulkMatrix                          html  
    mockBulkeQTL                            html  
    mockEmpiricalSet                        html  
    mockGFF                                 html  
    mockVCF                                 html  
    newParams                               html  
    phenoEstimate                           html  
    phenoSimulate                           html  
    rbindMatched                            html  
    sampleDensity                           html  
    scDDEstimate                            html  
    scDDSimulate                            html  
    selectFit                               html  
    setParam                                html  
    setParamUnchecked                       html  
    setParams                               html  
    setParamsUnchecked                      html  
    showDFs                                 html  
    showPP                                  html  
    showValues                              html  
    simpleEstimate                          html  
    simpleSimulate                          html  
    sparseDCEstimate                        html  
    sparseDCSimulate                        html  
    sparsifyMatrices                        html  
    splatEstBCV                             html  
    splatEstDropout                         html  
    splatEstLib                             html  
    splatEstMean                            html  
    splatEstOutlier                         html  
    splatEstimate                           html  
    splatPopAssignMeans                     html  
    splatPopCleanSCE                        html  
    splatPopConditionEffects                html  
    splatPopConditionalEffects              html  
    splatPopDesignBatches                   html  
    splatPopDesignConditions                html  
    splatPopEstimate                        html  
    splatPopEstimateEffectSize              html  
    splatPopEstimateMeanCV                  html  
    splatPopGroupEffects                    html  
    splatPopParseEmpirical                  html  
    splatPopParseGenes                      html  
    splatPopParseVCF                        html  
    splatPopQuantNorm                       html  
    splatPopQuantNormKey                    html  
    splatPopSimBatchEffects                 html  
    splatPopSimConditionalEffects           html  
    splatPopSimEffects                      html  
    splatPopSimGeneMeans                    html  
    splatPopSimMeans                        html  
    splatPopSimulate                        html  
    splatPopSimulateMeans                   html  
    splatPopSimulateSC                      html  
    splatPopSimulateSample                  html  
    splatPopeQTLEffects                     html  
    splatSimBCVMeans                        html  
    splatSimBatchCellMeans                  html  
    splatSimBatchEffects                    html  
    splatSimCellMeans                       html  
    splatSimDE                              html  
    splatSimDropout                         html  
    splatSimGeneMeans                       html  
    splatSimLibSizes                        html  
    splatSimTrueCounts                      html  
    splatSimulate                           html  
    splatter                                html  
    summariseDiff                           html  
    summariseKS                             html  
    summariseStats                          html  
    tidyStatSumm                            html  
    winsorize                               html  
    zinbEstimate                            html  
    zinbSimulate                            html  
** 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

install for x64

* installing *source* package 'splatter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'splatter' as splatter_1.17.4.zip
* DONE (splatter)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'splatter' successfully unpacked and MD5 sums checked

Tests output

splatter.Rcheck/tests_i386/spelling.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   0.12    0.03    0.14 

splatter.Rcheck/tests_x64/spelling.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   0.10    0.04    0.14 

splatter.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 171 ]
> 
> proc.time()
   user  system elapsed 
 172.40    4.39  176.78 

splatter.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 171 ]
> 
> proc.time()
   user  system elapsed 
 167.84    9.10  176.92 

Example timings

splatter.Rcheck/examples_i386/splatter-Ex.timings

nameusersystemelapsed
BASiCSEstimate000
BASiCSSimulate2.970.083.05
addGeneLengths0.420.000.42
compareSCEs2.230.012.25
diffSCEs2.440.002.44
getParam000
getParams000
kersplatEstimate6.190.086.26
kersplatSample1.530.031.57
kersplatSetup0.170.000.17
kersplatSimulate000
listSims0.030.000.03
lun2Estimate000
lun2Simulate0.750.050.80
lunEstimate0.50.00.5
lunSimulate0.350.000.34
makeCompPanel000
makeDiffPanel000
makeOverallPanel000
mfaEstimate0.050.030.08
mfaSimulate0.470.010.49
minimiseSCE0.810.040.84
mockBulkMatrix000
mockBulkeQTL3.270.263.53
mockEmpiricalSet1.870.081.96
mockGFF000
mockVCF0.080.000.07
newParams000
phenoEstimate0.560.020.58
phenoSimulate1.470.011.49
scDDEstimate25.88 0.1125.98
scDDSimulate000
setParam0.010.000.02
setParams0.020.000.01
simpleEstimate0.560.000.56
simpleSimulate0.520.000.52
sparseDCEstimate0.680.020.70
sparseDCSimulate1.390.031.42
splatEstimate5.740.065.80
splatPopEstimate6.470.066.53
splatPopQuantNorm0.010.000.02
splatPopSimulate000
splatPopSimulateMeans000
splatPopSimulateSC000
splatSimulate0.740.030.76
summariseDiff2.470.002.47
zinbEstimate1.670.021.69
zinbSimulate0.150.000.16

splatter.Rcheck/examples_x64/splatter-Ex.timings

nameusersystemelapsed
BASiCSEstimate000
BASiCSSimulate3.060.173.24
addGeneLengths0.910.030.94
compareSCEs2.510.072.58
diffSCEs2.530.032.56
getParam000
getParams000
kersplatEstimate6.020.146.16
kersplatSample1.590.041.64
kersplatSetup0.130.020.14
kersplatSimulate000
listSims0.020.000.02
lun2Estimate000
lun2Simulate0.480.020.50
lunEstimate0.50.00.5
lunSimulate0.860.030.89
makeCompPanel000
makeDiffPanel000
makeOverallPanel000
mfaEstimate0.040.030.08
mfaSimulate0.490.000.49
minimiseSCE0.860.030.89
mockBulkMatrix000
mockBulkeQTL3.830.314.14
mockEmpiricalSet1.950.172.14
mockGFF000
mockVCF0.090.000.09
newParams000
phenoEstimate0.610.000.61
phenoSimulate1.660.041.69
scDDEstimate26.87 0.1026.98
scDDSimulate000
setParam0.020.000.02
setParams0.020.000.01
simpleEstimate0.510.000.52
simpleSimulate0.520.000.52
sparseDCEstimate0.680.030.72
sparseDCSimulate1.410.021.42
splatEstimate5.020.115.13
splatPopEstimate5.020.075.10
splatPopQuantNorm0.010.000.01
splatPopSimulate000
splatPopSimulateMeans000
splatPopSimulateSC000
splatSimulate0.750.040.78
summariseDiff3.280.033.32
zinbEstimate1.580.031.61
zinbSimulate0.170.000.17