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This page was generated on 2021-09-17 15:06:03 -0400 (Fri, 17 Sep 2021).

CHECK results for dittoSeq on tokay2

To the developers/maintainers of the dittoSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dittoSeq.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.

raw results

Package 511/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dittoSeq 1.4.2  (landing page)
Daniel Bunis
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/dittoSeq
git_branch: RELEASE_3_13
git_last_commit: ddf92b8
git_last_commit_date: 2021-09-07 14:26:15 -0400 (Tue, 07 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: dittoSeq
Version: 1.4.2
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dittoSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dittoSeq_1.4.2.tar.gz
StartedAt: 2021-09-16 22:24:44 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 22:38:28 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 824.8 seconds
RetCode: 0
Status:   OK  
CheckDir: dittoSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dittoSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dittoSeq_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/dittoSeq.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 'dittoSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dittoSeq' version '1.4.2'
* 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 'dittoSeq' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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
multi_dittoDimPlotVaryCells 8.27   0.06    8.33
dittoHex                    8.28   0.03    8.31
dittoPlot                   7.94   0.15    8.08
dittoDimPlot                7.00   0.14    7.14
dittoHeatmap                6.61   0.29    6.92
multi_dittoPlot             6.08   0.00    6.07
dittoFreqPlot               4.79   0.39    5.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
multi_dittoDimPlotVaryCells 10.03   0.03   10.06
dittoPlot                    8.02   0.00    8.01
dittoHex                     7.30   0.06    7.36
dittoDimPlot                 7.21   0.06    7.28
dittoHeatmap                 6.90   0.05    6.96
dittoFreqPlot                5.33   0.00    5.33
multi_dittoPlot              5.24   0.02    5.25
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

dittoSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/dittoSeq_1.4.2.tar.gz && rm -rf dittoSeq.buildbin-libdir && mkdir dittoSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dittoSeq.buildbin-libdir dittoSeq_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL dittoSeq_1.4.2.zip && rm dittoSeq_1.4.2.tar.gz dittoSeq_1.4.2.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  930k  100  930k    0     0  2050k      0 --:--:-- --:--:-- --:--:-- 2050k

install for i386

* installing *source* package 'dittoSeq' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dittoSeq'
    finding HTML links ... done
    Darken                                  html  
    Lighten                                 html  
    Simulate                                html  
    addDimReduction                         html  
    finding level-2 HTML links ... done

    addPrcomp                               html  
    demux.SNP.summary                       html  
    demux.calls.summary                     html  
    demuxlet.example                        html  
    dittoBarPlot                            html  
    dittoColors                             html  
    dittoDimPlot                            html  
    dittoDotPlot                            html  
    dittoFreqPlot                           html  
    dittoHeatmap                            html  
    dittoHex                                html  
    dittoPlot                               html  
    dittoPlotVarsAcrossGroups               html  
    dittoScatterPlot                        html  
    dittoSeq                                html  
    gene                                    html  
    getGenes                                html  
    getMetas                                html  
    getReductions                           html  
    importDemux                             html  
    importDittoBulk                         html  
    isBulk                                  html  
    isGene                                  html  
    isMeta                                  html  
    meta                                    html  
    metaLevels                              html  
    multi_dittoDimPlot                      html  
    multi_dittoDimPlotVaryCells             html  
    multi_dittoPlot                         html  
    setBulk                                 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 'dittoSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dittoSeq' as dittoSeq_1.4.2.zip
* DONE (dittoSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'dittoSeq' successfully unpacked and MD5 sums checked

Tests output

dittoSeq.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.

> library(testthat)
> test_check("dittoSeq")
Loading required package: dittoSeq
Loading required package: ggplot2
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

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

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 715 ]
> 
> proc.time()
   user  system elapsed 
 211.59    2.85  214.46 

dittoSeq.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.

> library(testthat)
> test_check("dittoSeq")
Loading required package: dittoSeq
Loading required package: ggplot2
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

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

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 715 ]
> 
> proc.time()
   user  system elapsed 
 200.23    1.23  201.46 

Example timings

dittoSeq.Rcheck/examples_i386/dittoSeq-Ex.timings

nameusersystemelapsed
Darken0.000.020.01
Lighten000
Simulate2.810.082.89
addDimReduction1.580.031.61
addPrcomp1.610.001.61
demux.SNP.summary2.170.032.20
demux.calls.summary2.540.032.58
dittoBarPlot3.190.053.46
dittoColors0.040.000.04
dittoDimPlot7.000.147.14
dittoDotPlot3.170.023.19
dittoFreqPlot4.790.395.19
dittoHeatmap6.610.296.92
dittoHex8.280.038.31
dittoPlot7.940.158.08
dittoPlotVarsAcrossGroups4.080.094.17
dittoScatterPlot4.810.004.82
gene3.010.083.09
getGenes1.530.031.56
getMetas1.400.011.43
getReductions1.550.041.57
importDemux2.260.042.31
importDittoBulk1.220.021.24
isBulk1.310.001.31
isGene1.330.011.34
isMeta1.130.021.14
meta1.280.031.32
metaLevels1.270.021.28
multi_dittoDimPlot4.150.004.16
multi_dittoDimPlotVaryCells8.270.068.33
multi_dittoPlot6.080.006.07
setBulk1.670.001.68

dittoSeq.Rcheck/examples_x64/dittoSeq-Ex.timings

nameusersystemelapsed
Darken0.000.020.02
Lighten000
Simulate2.700.032.74
addDimReduction1.660.031.68
addPrcomp2.110.032.14
demux.SNP.summary2.230.002.24
demux.calls.summary2.660.032.69
dittoBarPlot3.280.083.36
dittoColors0.000.030.03
dittoDimPlot7.210.067.28
dittoDotPlot2.780.002.78
dittoFreqPlot5.330.005.33
dittoHeatmap6.900.056.96
dittoHex7.300.067.36
dittoPlot8.020.008.01
dittoPlotVarsAcrossGroups3.610.053.66
dittoScatterPlot4.620.004.62
gene2.810.313.13
getGenes1.360.021.37
getMetas1.500.031.53
getReductions1.620.021.64
importDemux2.390.002.39
importDittoBulk1.970.032.00
isBulk1.310.001.31
isGene1.330.031.36
isMeta1.230.011.25
meta1.300.021.31
metaLevels1.230.001.23
multi_dittoDimPlot4.690.004.69
multi_dittoDimPlotVaryCells10.03 0.0310.06
multi_dittoPlot5.240.025.25
setBulk1.510.011.54