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CHECK report for metagenomeSeq on tokay2

This page was generated on 2019-10-16 12:27:45 -0400 (Wed, 16 Oct 2019).

Package 964/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeSeq 1.26.3
Joseph N. Paulson
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/metagenomeSeq
Branch: RELEASE_3_9
Last Commit: 8de127d
Last Changed Date: 2019-08-04 12:53:02 -0400 (Sun, 04 Aug 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: metagenomeSeq
Version: 1.26.3
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metagenomeSeq_1.26.3.tar.gz
StartedAt: 2019-10-16 05:04:49 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:13:43 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 534.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: metagenomeSeq.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metagenomeSeq_1.26.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metagenomeSeq/DESCRIPTION' ... OK
* this is package 'metagenomeSeq' version '1.26.3'
* 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 'metagenomeSeq' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitFeatureModelResults.Rd:16: missing link 'fitFeatureModelResults'
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitFeatureModelResults.Rd:17: missing link 'fitZigResults'
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitZigResults.Rd:16: missing link 'fitFeatureModelResults'
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitZigResults.Rd:17: missing link 'fitZigResults'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.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 ... WARNING
Missing link or links in documentation object 'MRihw-fitFeatureModelResults.Rd':
  'fitFeatureModelResults' 'fitZigResults'

Missing link or links in documentation object 'MRihw-fitZigResults.Rd':
  'fitFeatureModelResults' 'fitZigResults'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'MRcoefs':
  'IHWcov'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
wrenchNorm  19.00   1.02   20.02
MRfulltable  1.36   0.10    6.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
wrenchNorm  22.36   0.34   22.71
MRfulltable  1.69   0.16    6.95
* 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: 3 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck/00check.log'
for details.



Installation output

metagenomeSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/metagenomeSeq_1.26.3.tar.gz && rm -rf metagenomeSeq.buildbin-libdir && mkdir metagenomeSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagenomeSeq.buildbin-libdir metagenomeSeq_1.26.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL metagenomeSeq_1.26.3.zip && rm metagenomeSeq_1.26.3.tar.gz metagenomeSeq_1.26.3.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  949k  100  949k    0     0  12.0M      0 --:--:-- --:--:-- --:--:-- 13.2M

install for i386

* installing *source* package 'metagenomeSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'MRihw' with signature '"fitFeatureModelResults"': no definition for class "fitFeatureModelResults"
in method for 'MRihw' with signature '"fitZigResults"': no definition for class "fitZigResults"
** help
*** installing help indices
  converting help for package 'metagenomeSeq'
    finding HTML links ... done
    MRcoefs                                 html  
    MRcounts                                html  
    MRexperiment-class                      html  
    MRexperiment2biom                       html  
    MRfulltable                             html  
    MRihw-fitFeatureModelResults            html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitFeatureModelResults.Rd:16: missing link 'fitFeatureModelResults'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitFeatureModelResults.Rd:17: missing link 'fitZigResults'
    MRihw-fitZigResults                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitZigResults.Rd:16: missing link 'fitFeatureModelResults'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6BNxsQ/R.INSTALLc8833803c53/metagenomeSeq/man/MRihw-fitZigResults.Rd:17: missing link 'fitZigResults'
    MRihw                                   html  
    MRtable                                 html  
    aggregateBySample                       html  
    aggregateByTaxonomy                     html  
    biom2MRexperiment                       html  
    calcNormFactors                         html  
    calcPosComponent                        html  
    calcShrinkParameters                    html  
    calcStandardError                       html  
    calcZeroAdjustment                      html  
    calcZeroComponent                       html  
    calculateEffectiveSamples               html  
    correctIndices                          html  
    correlationTest                         html  
    cumNorm                                 html  
    cumNormMat                              html  
    cumNormStat                             html  
    cumNormStatFast                         html  
    doCountMStep                            html  
    doEStep                                 html  
    doZeroMStep                             html  
    expSummary                              html  
    exportMat                               html  
    exportStats                             html  
    extractMR                               html  
    filterData                              html  
    fitDO                                   html  
    fitFeatureModel                         html  
    fitFeatureModelResults-class            html  
    fitLogNormal                            html  
    fitMultipleTimeSeries                   html  
    fitPA                                   html  
    fitSSTimeSeries                         html  
    fitTimeSeries                           html  
    fitZeroLogNormal                        html  
    fitZig                                  html  
    fitZigResults-class                     html  
    getCountDensity                         html  
    getEpsilon                              html  
    getNegativeLogLikelihoods               html  
    getPi                                   html  
    getZ                                    html  
    isItStillActive                         html  
    libSize-set                             html  
    libSize                                 html  
    loadBiom                                html  
    loadMeta                                html  
    loadMetaQ                               html  
    loadPhenoData                           html  
    lungData                                html  
    makeLabels                              html  
    mergeMRexperiments                      html  
    mergeTable                              html  
    metagenomeSeq-deprecated                html  
    metagenomeSeq-package                   html  
    mouseData                               html  
    newMRexperiment                         html  
    normFactors-set                         html  
    normFactors                             html  
    plotBubble                              html  
    plotClassTimeSeries                     html  
    plotCorr                                html  
    plotFeature                             html  
    plotGenus                               html  
    plotMRheatmap                           html  
    plotOTU                                 html  
    plotOrd                                 html  
    plotRare                                html  
    plotTimeSeries                          html  
    posteriorProbs                          html  
    returnAppropriateObj                    html  
    ssFit                                   html  
    ssIntervalCandidate                     html  
    ssPerm                                  html  
    ssPermAnalysis                          html  
    trapz                                   html  
    ts2MRexperiment                         html  
    uniqueFeatures                          html  
    wrenchNorm                              html  
    zigControl                              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 'metagenomeSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagenomeSeq' as metagenomeSeq_1.26.3.zip
* DONE (metagenomeSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'metagenomeSeq' successfully unpacked and MD5 sums checked

Tests output

metagenomeSeq.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
> packageVersion("metagenomeSeq")
[1] '1.26.3'
> # As suggested for opt-out option on testing by users, 
> # recommended by CRAN: http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests 
> # and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # >library(testthat)
> # >library(yourpackage)
> # >test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, 
> # and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # >library(testthat)
> # >test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to 
> # R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, 
> # but now you have the flexibility as requested by CRAN maintainers.
> test_check("metagenomeSeq")
Loading required package: metagenomeSeq
Loading required package: Biobase
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, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-18

Loading required package: RColorBrewer
== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 124.10    5.93  130.15 

metagenomeSeq.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
> packageVersion("metagenomeSeq")
[1] '1.26.3'
> # As suggested for opt-out option on testing by users, 
> # recommended by CRAN: http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests 
> # and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # >library(testthat)
> # >library(yourpackage)
> # >test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, 
> # and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # >library(testthat)
> # >test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to 
> # R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, 
> # but now you have the flexibility as requested by CRAN maintainers.
> test_check("metagenomeSeq")
Loading required package: metagenomeSeq
Loading required package: Biobase
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, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-18

Loading required package: RColorBrewer
== testthat results  ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 131.90    2.48  134.36 

Example timings

metagenomeSeq.Rcheck/examples_i386/metagenomeSeq-Ex.timings

nameusersystemelapsed
MRcoefs1.610.171.78
MRcounts0.690.090.80
MRexperiment-class000
MRfulltable1.360.106.37
MRtable1.130.061.20
aggregateBySample0.290.020.32
aggregateByTaxonomy0.250.030.28
biom2MRexperiment0.300.010.31
calcNormFactors0.610.030.64
correctIndices0.170.000.17
correlationTest0.480.040.52
cumNorm0.580.060.64
cumNormMat0.570.030.59
cumNormStat0.870.000.88
cumNormStatFast0.480.030.51
expSummary0.130.020.14
exportMat1.360.682.05
exportStats0.620.100.72
extractMR1.210.371.58
filterData0.180.020.20
fitDO0.660.043.39
fitFeatureModel1.310.081.39
fitLogNormal2.130.102.22
fitMultipleTimeSeries2.030.042.19
fitPA0.560.104.26
fitSSTimeSeries0.640.040.69
fitTimeSeries0.520.050.56
fitZig2.650.112.77
libSize-set0.410.030.44
libSize0.340.080.42
loadBiom0.040.000.03
loadMeta0.070.000.20
loadMetaQ000
loadPhenoData0.050.000.11
makeLabels000
mergeMRexperiments2.20.32.5
newMRexperiment0.040.000.03
normFactors-set0.370.040.43
normFactors0.360.020.37
plotBubble0.450.013.67
plotClassTimeSeries1.140.271.40
plotCorr0.670.050.72
plotFeature0.190.010.21
plotGenus0.240.020.25
plotMRheatmap2.340.152.50
plotOTU0.240.040.27
plotOrd0.320.040.37
plotRare0.180.000.17
plotTimeSeries0.920.111.04
posteriorProbs1.900.061.96
returnAppropriateObj0.360.040.40
ssFit000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis000
trapz000
ts2MRexperiment1.830.172.00
uniqueFeatures0.100.060.15
wrenchNorm19.00 1.0220.02
zigControl000

metagenomeSeq.Rcheck/examples_x64/metagenomeSeq-Ex.timings

nameusersystemelapsed
MRcoefs1.780.161.94
MRcounts0.710.090.80
MRexperiment-class000
MRfulltable1.690.166.95
MRtable1.760.111.88
aggregateBySample0.170.040.22
aggregateByTaxonomy0.170.020.19
biom2MRexperiment0.330.000.32
calcNormFactors0.530.040.58
correctIndices0.110.020.13
correlationTest0.220.060.28
cumNorm0.730.110.84
cumNormMat0.780.020.80
cumNormStat1.190.031.22
cumNormStatFast0.610.010.62
expSummary0.200.000.21
exportMat1.661.052.70
exportStats0.440.050.48
extractMR1.390.311.71
filterData0.310.010.32
fitDO0.560.103.77
fitFeatureModel1.230.031.26
fitLogNormal2.820.233.05
fitMultipleTimeSeries2.140.112.25
fitPA0.620.084.59
fitSSTimeSeries0.470.060.53
fitTimeSeries0.560.050.61
fitZig2.280.142.42
libSize-set0.360.050.41
libSize0.360.010.38
loadBiom0.030.000.03
loadMeta0.020.000.02
loadMetaQ000
loadPhenoData0.030.000.03
makeLabels000
mergeMRexperiments2.360.282.64
newMRexperiment0.030.000.03
normFactors-set0.360.030.39
normFactors0.380.020.39
plotBubble0.340.032.77
plotClassTimeSeries1.300.151.45
plotCorr0.670.070.74
plotFeature0.140.010.15
plotGenus0.190.030.22
plotMRheatmap2.400.082.48
plotOTU0.280.030.32
plotOrd0.540.020.54
plotRare0.230.000.24
plotTimeSeries1.730.081.81
posteriorProbs2.640.082.72
returnAppropriateObj0.440.060.50
ssFit000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis000
trapz000
ts2MRexperiment2.300.172.47
uniqueFeatures0.220.030.25
wrenchNorm22.36 0.3422.71
zigControl000