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CHECK report for UMI4Cats on tokay1

This page was generated on 2021-05-06 12:34:07 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the UMI4Cats package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1920/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
UMI4Cats 1.0.1  (landing page)
Mireia Ramos-Rodriguez
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/UMI4Cats
Branch: RELEASE_3_12
Last Commit: 1f6f3d8
Last Changed Date: 2020-12-29 05:50:42 -0400 (Tue, 29 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: UMI4Cats
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UMI4Cats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings UMI4Cats_1.0.1.tar.gz
StartedAt: 2021-05-06 07:47:34 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:58:22 -0400 (Thu, 06 May 2021)
EllapsedTime: 647.2 seconds
RetCode: 0
Status:   OK   
CheckDir: UMI4Cats.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UMI4Cats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings UMI4Cats_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/UMI4Cats.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'UMI4Cats/DESCRIPTION' ... OK
* this is package 'UMI4Cats' version '1.0.1'
* 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 whether package 'UMI4Cats' 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 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
differentialNbinomWaldTestUMI4C 41.10   2.09   43.19
UMI4C                            5.22   0.31    5.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
differentialNbinomWaldTestUMI4C 39.62   2.03   41.88
UMI4C                            6.22   0.06    6.28
* 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

UMI4Cats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/UMI4Cats_1.0.1.tar.gz && rm -rf UMI4Cats.buildbin-libdir && mkdir UMI4Cats.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=UMI4Cats.buildbin-libdir UMI4Cats_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL UMI4Cats_1.0.1.zip && rm UMI4Cats_1.0.1.tar.gz UMI4Cats_1.0.1.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
100 1965k  100 1965k    0     0  42.2M      0 --:--:-- --:--:-- --:--:-- 43.6M

install for i386

* installing *source* package 'UMI4Cats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'UMI4Cats'
    finding HTML links ... done
    UMI4C-methods                           html  
    finding level-2 HTML links ... done

    UMI4C                                   html  
    UMI4C2dds                               html  
    UMI4Cats                                html  
    addGrouping                             html  
    addStepping                             html  
    alignmentUMI4C                          html  
    calculateAdaptativeTrend                html  
    calculateDomainogram                    html  
    contactsUMI4C                           html  
    counterUMI4C                            html  
    createGeneAnnotation                    html  
    createStatsTable                        html  
    darken                                  html  
    demultiplexFastq                        html  
    deseq2UMI4C                             html  
    differentialNbinomWaldTestUMI4C         html  
    digestGenome                            html  
    dot-getCache                            html  
    dot-getSummaryBam                       html  
    dot-singleAlignmentUMI4C                html  
    dot-singleCounterUMI4C                  html  
    dot-singlePrepUMI4C                     html  
    dot-singleSplitUMI4C                    html  
    dot-smoothMonotone                      html  
    downloadUMI4CexampleData                html  
    ex_ciita_umi4c                          html  
    fisherUMI4C                             html  
    formatPlotsUMI4C                        html  
    geoMeanCoordinates                      html  
    getColors                               html  
    getFactors                              html  
    getNormalizationMatrix                  html  
    getViewpointCoordinates                 html  
    groupSamplesUMI4C                       html  
    nbinomWaldTestUMI4C                     html  
    pipe                                    html  
    plotDifferential                        html  
    plotDomainogram                         html  
    plotGenes                               html  
    plotTrend                               html  
    plotUMI4C                               html  
    prepUMI4C                               html  
    smoothMonotoneUMI4C                     html  
    splitUMI4C                              html  
    statsUMI4C                              html  
    theme                                   html  
    themeXYblank                            html  
    themeXblank                             html  
    themeYblank                             html  
    vstUMI4C                                html  
*** copying figures
** 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 'UMI4Cats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'UMI4Cats' as UMI4Cats_1.0.1.zip
* DONE (UMI4Cats)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'UMI4Cats' successfully unpacked and MD5 sums checked

Tests output

UMI4Cats.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
> library(UMI4Cats)
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

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


> library(BSgenome)
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: rtracklayer
> 
> test_check("UMI4Cats")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
  26.85    1.98   30.62 

UMI4Cats.Rcheck/tests_x64/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-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)
> library(UMI4Cats)
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

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


> library(BSgenome)
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: rtracklayer
> 
> test_check("UMI4Cats")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
  28.98    0.81   31.37 

Example timings

UMI4Cats.Rcheck/examples_i386/UMI4Cats-Ex.timings

nameusersystemelapsed
UMI4C-methods2.760.142.91
UMI4C5.220.315.53
addGrouping2.090.172.26
alignmentUMI4C000
contactsUMI4C0.020.000.02
counterUMI4C000
createGeneAnnotation1.620.271.89
darken000
demultiplexFastq000
differentialNbinomWaldTestUMI4C41.10 2.0943.19
digestGenome3.310.103.40
downloadUMI4CexampleData000
fisherUMI4C2.230.002.23
getViewpointCoordinates2.220.112.33
pipe000
plotDifferential2.690.072.77
plotDomainogram2.220.102.31
plotGenes1.810.031.85
plotTrend0.630.060.69
plotUMI4C3.830.003.82
prepUMI4C000
splitUMI4C000
statsUMI4C0.610.000.61
theme0.090.000.10
themeXYblank0.070.000.06
themeXblank0.090.020.11
themeYblank0.090.010.11

UMI4Cats.Rcheck/examples_x64/UMI4Cats-Ex.timings

nameusersystemelapsed
UMI4C-methods2.270.062.33
UMI4C6.220.066.28
addGrouping1.640.081.72
alignmentUMI4C000
contactsUMI4C000
counterUMI4C000
createGeneAnnotation1.540.031.56
darken000
demultiplexFastq000
differentialNbinomWaldTestUMI4C39.62 2.0341.88
digestGenome4.610.184.78
downloadUMI4CexampleData000
fisherUMI4C2.550.012.56
getViewpointCoordinates0.270.000.27
pipe0.010.000.02
plotDifferential2.550.022.56
plotDomainogram4.530.074.61
plotGenes1.710.021.72
plotTrend0.960.051.01
plotUMI4C4.690.014.71
prepUMI4C000
splitUMI4C000
statsUMI4C1.010.001.02
theme0.110.000.11
themeXYblank0.100.000.09
themeXblank0.110.000.11
themeYblank0.120.000.12