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This page was generated on 2021-10-18 12:04:25 -0400 (Mon, 18 Oct 2021).

CHECK results for zinbwave on riesling1

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zinbwave.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 2059/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zinbwave 1.15.3  (landing page)
Davide Risso
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/zinbwave
git_branch: master
git_last_commit: 712b11d
git_last_commit_date: 2021-09-21 05:41:56 -0400 (Tue, 21 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: zinbwave
Version: 1.15.3
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:zinbwave.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings zinbwave_1.15.3.tar.gz
StartedAt: 2021-10-18 03:41:01 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 03:45:44 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 283.1 seconds
RetCode: 0
Status:   OK  
CheckDir: zinbwave.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:zinbwave.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings zinbwave_1.15.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/zinbwave.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 'zinbwave/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'zinbwave' version '1.15.3'
* 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 'zinbwave' 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
** 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


Installation output

zinbwave.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/zinbwave_1.15.3.tar.gz && rm -rf zinbwave.buildbin-libdir && mkdir zinbwave.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=zinbwave.buildbin-libdir zinbwave_1.15.3.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL zinbwave_1.15.3.zip && rm zinbwave_1.15.3.tar.gz zinbwave_1.15.3.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  109k  100  109k    0     0   458k      0 --:--:-- --:--:-- --:--:--  458k

install for i386

* installing *source* package 'zinbwave' ...
** 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 'zinbwave'
    finding HTML links ... done
    ZinbModel-class                         html  
    computeDevianceResiduals                html  
    computeObservationalWeights             html  
    getAlpha_mu                             html  
    getAlpha_pi                             html  
    getBeta_mu                              html  
    getBeta_pi                              html  
    getEpsilon_W                            html  
    getEpsilon_alpha                        html  
    getEpsilon_beta_mu                      html  
    getEpsilon_beta_pi                      html  
    getEpsilon_gamma_mu                     html  
    getEpsilon_gamma_pi                     html  
    getEpsilon_zeta                         html  
    getGamma_mu                             html  
    getGamma_pi                             html  
    getLogMu                                html  
    getLogitPi                              html  
    getMu                                   html  
    getPhi                                  html  
    getPi                                   html  
    getTheta                                html  
    getV_mu                                 html  
    getV_pi                                 html  
    getW                                    html  
    getX_mu                                 html  
    getX_pi                                 html  
    getZeta                                 html  
    glmWeightedF                            html  
    imputeZeros                             html  
    independentFiltering                    html  
    loglik                                  html  
    nFactors                                html  
    nFeatures                               html  
    nParams                                 html  
    nSamples                                html  
    orthogonalizeTraceNorm                  html  
    penalty                                 html  
    pvalueAdjustment                        html  
    solveRidgeRegression                    html  
    toydata                                 html  
    zinb.loglik                             html  
    zinb.loglik.dispersion                  html  
    zinb.loglik.dispersion.gradient         html  
    zinb.loglik.matrix                      html  
    zinb.loglik.regression                  html  
    zinb.loglik.regression.gradient         html  
    zinb.regression.parseModel              html  
    zinbAIC                                 html  
    zinbFit                                 html  
    zinbInitialize                          html  
    zinbModel                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.14-bioc/meat/zinbwave.buildbin-libdir/00LOCK-zinbwave/00new/zinbwave/help/zinbModel.html
    zinbOptimize                            html  
    zinbOptimizeDispersion                  html  
    zinbSim                                 html  
    zinbsurf                                html  
    zinbwave                                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 'zinbwave' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'zinbwave' as zinbwave_1.15.3.zip
* DONE (zinbwave)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'zinbwave' successfully unpacked and MD5 sums checked

Tests output

zinbwave.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)
> library(zinbwave)
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

Loading required package: SingleCellExperiment
> 
> test_check("zinbwave")
   user  system elapsed 
   0.03    0.00    0.03 
   user  system elapsed 
   0.02    0.00    0.02 
   user  system elapsed 
   0.01    0.00    0.01 
   user  system elapsed 
   0.02    0.00    0.02 
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 219 ]
> 
> proc.time()
   user  system elapsed 
  56.23    0.37   56.57 

zinbwave.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)
> library(zinbwave)
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

Loading required package: SingleCellExperiment
> 
> test_check("zinbwave")
   user  system elapsed 
   0.02    0.00    0.02 
   user  system elapsed 
   0.01    0.00    0.01 
   user  system elapsed 
   0.02    0.00    0.02 
   user  system elapsed 
   0.02    0.00    0.02 
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 219 ]
> 
> proc.time()
   user  system elapsed 
  57.65    0.46   58.10 

Example timings

zinbwave.Rcheck/examples_i386/zinbwave-Ex.timings

nameusersystemelapsed
computeDevianceResiduals0.190.020.20
computeObservationalWeights0.400.020.42
getAlpha_mu000
getAlpha_pi000
getBeta_mu000
getBeta_pi000
getEpsilon_W0.020.000.02
getEpsilon_alpha000
getEpsilon_beta_mu000
getEpsilon_beta_pi000
getEpsilon_gamma_mu000
getEpsilon_gamma_pi000
getEpsilon_zeta000
getGamma_mu000
getGamma_pi0.010.000.01
getLogMu000
getLogitPi000
getMu000
getPhi000
getPi000
getTheta000
getV_mu000
getV_pi0.020.000.02
getW000
getX_mu000
getX_pi000
getZeta000
imputeZeros0.120.000.12
loglik000
nFactors000
nFeatures000
nParams000
nSamples000
orthogonalizeTraceNorm0.000.010.02
penalty000
zinb.loglik000
zinb.loglik.dispersion000
zinbAIC0.130.000.12
zinbFit0.220.000.22
zinbInitialize0.040.000.05
zinbModel000
zinbOptimize0.050.000.05
zinbOptimizeDispersion0.030.000.03
zinbSim0.020.000.01
zinbsurf0.550.000.55
zinbwave0.50.00.5

zinbwave.Rcheck/examples_x64/zinbwave-Ex.timings

nameusersystemelapsed
computeDevianceResiduals0.220.000.22
computeObservationalWeights0.420.040.45
getAlpha_mu000
getAlpha_pi000
getBeta_mu000
getBeta_pi0.020.000.02
getEpsilon_W000
getEpsilon_alpha000
getEpsilon_beta_mu000
getEpsilon_beta_pi000
getEpsilon_gamma_mu000
getEpsilon_gamma_pi000
getEpsilon_zeta000
getGamma_mu0.010.000.01
getGamma_pi000
getLogMu000
getLogitPi000
getMu000
getPhi000
getPi000
getTheta000
getV_mu0.000.010.02
getV_pi000
getW000
getX_mu000
getX_pi000
getZeta000
imputeZeros0.130.000.12
loglik000
nFactors000
nFeatures0.010.000.02
nParams000
nSamples000
orthogonalizeTraceNorm000
penalty000
zinb.loglik000
zinb.loglik.dispersion000
zinbAIC0.140.000.14
zinbFit0.240.000.23
zinbInitialize0.040.000.05
zinbModel000
zinbOptimize0.050.000.05
zinbOptimizeDispersion0.030.000.03
zinbSim0.020.000.01
zinbsurf0.590.000.60
zinbwave0.50.00.5