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CHECK report for metavizr on tokay2

This page was generated on 2019-04-09 12:30:58 -0400 (Tue, 09 Apr 2019).

Package 953/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metavizr 1.7.1
Hector Corrada Bravo
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/metavizr
Branch: master
Last Commit: c559084
Last Changed Date: 2018-12-03 16:22:47 -0400 (Mon, 03 Dec 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: metavizr
Version: 1.7.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metavizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metavizr_1.7.1.tar.gz
StartedAt: 2019-04-09 04:07:53 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:23:47 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 953.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: metavizr.Rcheck
Warnings: 1

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:metavizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metavizr_1.7.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metavizr.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metavizr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metavizr' version '1.7.1'
* 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 'metavizr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetaviz.Rd:5: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetaviz.Rd:21: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetaviz.Rd:18: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetaviz.Rd:30: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetavizStandalone.Rd:5: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetavizStandalone.Rd:22: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metavizr.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                        user system elapsed
EpivizMetagenomicsDataTimeSeries-class 22.18   4.38   22.30
replaceNAFeatures                       7.78   0.26    8.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                        user system elapsed
EpivizMetagenomicsDataTimeSeries-class 22.40   4.86   22.56
replaceNAFeatures                       7.75   0.25    8.00
* 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-3.9-bioc/meat/metavizr.Rcheck/00check.log'
for details.



Installation output

metavizr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/metavizr_1.7.1.tar.gz && rm -rf metavizr.buildbin-libdir && mkdir metavizr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metavizr.buildbin-libdir metavizr_1.7.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL metavizr_1.7.1.zip && rm metavizr_1.7.1.tar.gz metavizr_1.7.1.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 1185k  100 1185k    0     0  8006k      0 --:--:-- --:--:-- --:--:-- 8405k

install for i386

* installing *source* package 'metavizr' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'git2r::as.data.frame' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::head' by 'git2r::head' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::merge' by 'git2r::merge' when loading 'epivizrStandalone'
** help
*** installing help indices
  converting help for package 'metavizr'
    finding HTML links ... done
    EpivizMetagenomicsData-class            html  
    EpivizMetagenomicsDataInnerNodes-class
                                            html  
    EpivizMetagenomicsDataTimeSeries-class
                                            html  
    MetavizApp-class                        html  
    MetavizGraph-class                      html  
    MetavizGraphInnerNodes-class            html  
    buildMetavizGraph                       html  
    buildMetavizGraphInnerNodes             html  
    generateSelection                       html  
    metavizControl                          html  
    register-MRexperiment-method            html  
    register-phyloseq-method                html  
    finding level-2 HTML links ... done

    replaceNAFeatures                       html  
    setMetavizStandalone                    html  
    startMetaviz                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetaviz.Rd:5: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetaviz.Rd:21: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetaviz.Rd:18: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetaviz.Rd:30: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
    startMetavizStandalone                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetavizStandalone.Rd:5: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8kpt73/R.INSTALL1d9c46e56dca/metavizr/man/startMetavizStandalone.Rd:22: file link 'MetavizApp' in package 'metavizr' does not exist and so has been treated as a topic
    validateObject                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'git2r::as.data.frame' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::head' by 'git2r::head' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::merge' by 'git2r::merge' when loading 'epivizrStandalone'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'git2r::as.data.frame' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::head' by 'git2r::head' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::merge' by 'git2r::merge' when loading 'epivizrStandalone'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'metavizr' ...
** testing if installed package can be loaded
Warning: replacing previous import 'S4Vectors::merge' by 'git2r::merge' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::head' by 'git2r::head' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'git2r::as.data.frame' when loading 'epivizrStandalone'
* MD5 sums
packaged installation of 'metavizr' as metavizr_1.7.1.zip
* DONE (metavizr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'metavizr' successfully unpacked and MD5 sums checked

Tests output

metavizr.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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)
> library(metavizr)
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, colMeans, colSums, 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, rowMeans, rowSums,
    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 2.0-16

Loading required package: RColorBrewer
Loading required package: data.table
Loading required package: digest
Warning messages:
1: replacing previous import 'S4Vectors::as.data.frame' by 'git2r::as.data.frame' when loading 'epivizrStandalone' 
2: replacing previous import 'S4Vectors::head' by 'git2r::head' when loading 'epivizrStandalone' 
3: replacing previous import 'S4Vectors::merge' by 'git2r::merge' when loading 'epivizrStandalone' 
> 
> test_check("metavizr")
== testthat results  ===========================================================
OK: 21 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 238.29   25.06  240.50 

metavizr.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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)
> library(metavizr)
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, colMeans, colSums, 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, rowMeans, rowSums,
    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 2.0-16

Loading required package: RColorBrewer
Loading required package: data.table
Loading required package: digest
Warning messages:
1: replacing previous import 'S4Vectors::merge' by 'git2r::merge' when loading 'epivizrStandalone' 
2: replacing previous import 'S4Vectors::head' by 'git2r::head' when loading 'epivizrStandalone' 
3: replacing previous import 'S4Vectors::as.data.frame' by 'git2r::as.data.frame' when loading 'epivizrStandalone' 
> 
> test_check("metavizr")
== testthat results  ===========================================================
OK: 21 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 257.00   23.95  257.56 

Example timings

metavizr.Rcheck/examples_i386/metavizr-Ex.timings

nameusersystemelapsed
EpivizMetagenomicsData-class000
EpivizMetagenomicsDataInnerNodes-class000
EpivizMetagenomicsDataTimeSeries-class22.18 4.3822.30
generateSelection000
metavizControl000
replaceNAFeatures7.780.268.04
setMetavizStandalone000
startMetaviz0.190.000.19
startMetavizStandalone0.100.000.11
validateObject0.240.000.24

metavizr.Rcheck/examples_x64/metavizr-Ex.timings

nameusersystemelapsed
EpivizMetagenomicsData-class000
EpivizMetagenomicsDataInnerNodes-class000
EpivizMetagenomicsDataTimeSeries-class22.40 4.8622.56
generateSelection000
metavizControl000
replaceNAFeatures7.750.258.00
setMetavizStandalone000
startMetaviz0.130.000.12
startMetavizStandalone0.060.000.07
validateObject0.110.020.12