Multiple platform build/check report for BioC 3.13 - CHECK results for NewWave on tokay2

Package: NewWave

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NewWave.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NewWave_1.2.0.tar.gz

StartedAt: 2021-10-15 02:44:45 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:50:09 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 323.8 seconds

RetCode: 0

Status: OK

CheckDir: NewWave.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NewWave.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NewWave_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/NewWave.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 'NewWave/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NewWave' version '1.2.0'
* 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 'NewWave' 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
** running examples for arch 'x64' ... OK
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/NewWave_1.2.0.tar.gz && rm -rf NewWave.buildbin-libdir && mkdir NewWave.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NewWave.buildbin-libdir NewWave_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL NewWave_1.2.0.zip && rm NewWave_1.2.0.tar.gz NewWave_1.2.0.zip
###
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  % 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 31155  100 31155    0     0   260k      0 --:--:-- --:--:-- --:--:--  262k

install for i386

* installing *source* package 'NewWave' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NewWave'
    finding HTML links ... done
    delayed_initialization                  html  
    delayed_optimization                    html  
    initialization                          html  
    nb.loglik.matrix                        html  
    newAIC                                  html  
    newAlpha                                html  
    newBIC                                  html  
    newBeta                                 html  
    newEpsilon_W                            html  
    newEpsilon_alpha                        html  
    newEpsilon_beta                         html  
    newEpsilon_gamma                        html  
    newEpsilon_zeta                         html  
    newFit                                  html  
    newGamma                                html  
    newLogMu                                html  
    newMu                                   html  
    newPhi                                  html  
    newSim                                  html  
    newTheta                                html  
    newV                                    html  
    newW                                    html  
    newWave                                 html  
    newX                                    html  
    newZeta                                 html  
    newloglik                               html  
    newmodel-class                          html  
    newmodel                                html  
    newpenalty                              html  
    numberFactors                           html  
    numberFeatures                          html  
    numberParams                            html  
    numberSamples                           html  
    optimization                            html  
    setup                                   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 'NewWave' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NewWave' as NewWave_1.2.0.zip
* DONE (NewWave)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'NewWave' successfully unpacked and MD5 sums checked


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)
> library(NewWave)
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

> Sys.setenv("R_TESTS" = "")
> test_check("NewWave")
Time of setup
   user  system elapsed 
   0.03    0.00    0.47 
Time of initialization
   user  system elapsed 
   0.00    0.00    0.03 
Time of dispersion optimization
   user  system elapsed 
      0       0       0 
Time of right optimization
   user  system elapsed 
   0.00    0.00    0.13 
Time of left optimization
   user  system elapsed 
      0       0       0 
Time of dispersion optimization
   user  system elapsed 
      0       0       0 
Time of right optimization
   user  system elapsed 
   0.00    0.00    0.01 
Time of left optimization
   user  system elapsed 
   0.00    0.00    0.02 
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 53 ]
> 
> proc.time()
   user  system elapsed 
  13.25    1.54   57.62


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)
> library(NewWave)
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

> Sys.setenv("R_TESTS" = "")
> test_check("NewWave")
Time of setup
   user  system elapsed 
   0.02    0.00    0.58 
Time of initialization
   user  system elapsed 
   0.00    0.00    0.03 
Time of dispersion optimization
   user  system elapsed 
   0.01    0.00    0.02 
Time of right optimization
   user  system elapsed 
   0.00    0.00    0.14 
Time of left optimization
   user  system elapsed 
   0.00    0.00    0.02 
Time of dispersion optimization
   user  system elapsed 
   0.02    0.00    0.01 
Time of right optimization
   user  system elapsed 
   0.00    0.00    0.02 
Time of left optimization
   user  system elapsed 
   0.00    0.00    0.01 
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 53 ]
> 
> proc.time()
   user  system elapsed 
  13.28    0.57   57.25

name	user	system	elapsed
newAIC	0	0	0
newAlpha	0	0	0
newBIC	0.02	0.01	0.03
newBeta	0	0	0
newEpsilon_W	0	0	0
newEpsilon_alpha	0.00	0.02	0.02
newEpsilon_beta	0	0	0
newEpsilon_gamma	0	0	0
newEpsilon_zeta	0	0	0
newFit	0.28	0.08	2.50
newGamma	0	0	0
newLogMu	0	0	0
newMu	0	0	0
newPhi	0	0	0
newSim	0.02	0.00	0.01
newTheta	0	0	0
newV	0	0	0
newW	0	0	0
newWave	0.67	0.00	1.76
newX	0	0	0
newZeta	0	0	0
newloglik	0	0	0
newmodel	0.02	0.00	0.02
newpenalty	0	0	0
numberFactors	0	0	0
numberFeatures	0	0	0
numberParams	0	0	0
numberSamples	0.01	0.00	0.02

name	user	system	elapsed
newAIC	0	0	0
newAlpha	0	0	0
newBIC	0.04	0.00	0.03
newBeta	0	0	0
newEpsilon_W	0	0	0
newEpsilon_alpha	0	0	0
newEpsilon_beta	0.01	0.00	0.02
newEpsilon_gamma	0	0	0
newEpsilon_zeta	0	0	0
newFit	0.28	0.03	2.67
newGamma	0	0	0
newLogMu	0	0	0
newMu	0	0	0
newPhi	0	0	0
newSim	0.02	0.00	0.01
newTheta	0	0	0
newV	0	0	0
newW	0	0	0
newWave	0.61	0.05	1.72
newX	0	0	0
newZeta	0	0	0
newloglik	0	0	0
newmodel	0	0	0
newpenalty	0.01	0.00	0.02
numberFactors	0	0	0
numberFeatures	0	0	0
numberParams	0	0	0
numberSamples	0	0	0

CHECK results for NewWave on tokay2

Summary

Command output

Installation output

Tests output

Example timings