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CHECK report for zinbwave on tokay2

This page was generated on 2018-10-17 08:44:06 -0400 (Wed, 17 Oct 2018).

Package 1560/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zinbwave 1.2.0
Davide Risso
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/zinbwave
Branch: RELEASE_3_7
Last Commit: 6fe1e59
Last Changed Date: 2018-04-30 10:35:47 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: zinbwave
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:zinbwave.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings zinbwave_1.2.0.tar.gz
StartedAt: 2018-10-17 05:29:18 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:57:37 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1699.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: zinbwave.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:zinbwave.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings zinbwave_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/zinbwave.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.2.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/glmWeightedF.Rd:35: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/glmWeightedF.Rd:52: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/independentFiltering.Rd:19: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbFit.Rd:56: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbFit.Rd:81: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbInitialize.Rd:19: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbOptimize.Rd:28: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbOptimizeDispersion.Rd:27: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbwave.Rd:58: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbwave.Rd:98: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/zinbwave.Rcheck/00install.out' for details.
* 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 or elapsed time > 5s
                       user system elapsed
zinbFit                0.68   0.12  263.09
zinbwave               0.57   0.13  124.99
zinbOptimize           0.13   0.16  119.61
zinbOptimizeDispersion 0.14   0.12   85.25
zinbInitialize         0.11   0.06   93.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
zinbwave               0.69   0.19  130.17
zinbFit                0.64   0.17  261.49
zinbOptimize           0.22   0.17  121.41
zinbInitialize         0.12   0.08   95.02
zinbOptimizeDispersion 0.12   0.05   87.95
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/zinbwave.Rcheck/00check.log'
for details.



Installation output

zinbwave.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/zinbwave_1.2.0.tar.gz && rm -rf zinbwave.buildbin-libdir && mkdir zinbwave.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=zinbwave.buildbin-libdir zinbwave_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL zinbwave_1.2.0.zip && rm zinbwave_1.2.0.tar.gz zinbwave_1.2.0.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 97257  100 97257    0     0  1478k      0 --:--:-- --:--:-- --:--:-- 1666k

install for i386

* installing *source* package 'zinbwave' ...
** 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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/glmWeightedF.Rd:35: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/glmWeightedF.Rd:52: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
    imputeZeros                             html  
    independentFiltering                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/independentFiltering.Rd:19: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
    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  
    zinbBIC                                 html  
    zinbFit                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbFit.Rd:56: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbFit.Rd:81: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    zinbInitialize                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbInitialize.Rd:19: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    zinbModel                               html  
    zinbOptimize                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbOptimize.Rd:28: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    zinbOptimizeDispersion                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbOptimizeDispersion.Rd:27: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    zinbSim                                 html  
    zinbwave                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbwave.Rd:58: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYjRYf3/R.INSTALL1d2c36f868a5/zinbwave/man/zinbwave.Rd:98: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'zinbwave' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'zinbwave' as zinbwave_1.2.0.zip
* DONE (zinbwave)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'zinbwave' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

zinbwave.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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: 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

Loading required package: SingleCellExperiment
> 
> test_check("zinbwave")
   user  system elapsed 
   0.03    0.00    0.03 
   user  system elapsed 
   0.00    0.02    0.02 
   user  system elapsed 
   0.05    0.00    0.04 
   user  system elapsed 
      0       0       0 
== testthat results  ===========================================================
OK: 110 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  33.89    0.70   34.57 

zinbwave.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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: 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

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 
   0.03    0.00    0.03 
   user  system elapsed 
   0.02    0.00    0.01 
== testthat results  ===========================================================
OK: 110 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  35.39    0.48   35.85 

Example timings

zinbwave.Rcheck/examples_i386/zinbwave-Ex.timings

nameusersystemelapsed
getAlpha_mu000
getAlpha_pi000
getBeta_mu0.010.000.01
getBeta_pi000
getEpsilon_W000
getEpsilon_alpha000
getEpsilon_beta_mu000
getEpsilon_beta_pi000
getEpsilon_gamma_mu000
getEpsilon_gamma_pi0.020.000.02
getEpsilon_zeta000
getGamma_mu000
getGamma_pi0.020.000.01
getLogMu000
getLogitPi000
getMu0.010.000.02
getPhi000
getPi000
getTheta0.020.000.01
getV_mu000
getV_pi000
getW000
getX_mu000
getX_pi000
getZeta000
loglik0.020.000.01
orthogonalizeTraceNorm000
penalty000
zinb.loglik000
zinb.loglik.dispersion000
zinbFit 0.68 0.12263.09
zinbInitialize 0.11 0.0693.22
zinbModel0.010.000.02
zinbOptimize 0.13 0.16119.61
zinbOptimizeDispersion 0.14 0.1285.25
zinbSim0.060.000.06
zinbwave 0.57 0.13124.99

zinbwave.Rcheck/examples_x64/zinbwave-Ex.timings

nameusersystemelapsed
getAlpha_mu000
getAlpha_pi000
getBeta_mu000
getBeta_pi000
getEpsilon_W000
getEpsilon_alpha000
getEpsilon_beta_mu000
getEpsilon_beta_pi000
getEpsilon_gamma_mu000
getEpsilon_gamma_pi000
getEpsilon_zeta0.020.000.02
getGamma_mu000
getGamma_pi000
getLogMu000
getLogitPi000
getMu000
getPhi0.020.000.01
getPi000
getTheta000
getV_mu000
getV_pi000
getW000
getX_mu0.010.000.02
getX_pi000
getZeta000
loglik000
orthogonalizeTraceNorm000
penalty0.000.020.01
zinb.loglik000
zinb.loglik.dispersion000
zinbFit 0.64 0.17261.49
zinbInitialize 0.12 0.0895.02
zinbModel0.020.000.01
zinbOptimize 0.22 0.17121.41
zinbOptimizeDispersion 0.12 0.0587.95
zinbSim0.050.010.07
zinbwave 0.69 0.19130.17