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CHECK report for metavizr on tokay1

This page was generated on 2020-04-15 12:28:22 -0400 (Wed, 15 Apr 2020).

Package 1009/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metavizr 1.10.0
Hector Corrada Bravo
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/metavizr
Branch: RELEASE_3_10
Last Commit: e8518fa
Last Changed Date: 2019-10-29 13:10:25 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: metavizr
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metavizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings metavizr_1.10.0.tar.gz
StartedAt: 2020-04-15 04:36:23 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:45:24 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 540.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: metavizr.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metavizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings metavizr_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/metavizr.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.10.0'
* 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 'metavizr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-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
replaceNAFeatures 11.65   0.46   12.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
replaceNAFeatures 12.27   0.28   12.56
* 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-3.10-bioc/meat/metavizr.Rcheck/00check.log'
for details.



Installation output

metavizr.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/metavizr_1.10.0.tar.gz && rm -rf metavizr.buildbin-libdir && mkdir metavizr.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metavizr.buildbin-libdir metavizr_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL metavizr_1.10.0.zip && rm metavizr_1.10.0.tar.gz metavizr_1.10.0.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 1239k  100 1239k    0     0  13.9M      0 --:--:-- --:--:-- --:--:-- 14.5M

install for i386

* installing *source* package 'metavizr' ...
** using staged installation
** 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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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-3.10-bioc/tmpdir/RtmpWeTv0N/R.INSTALL231445425f53/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_1.10.0.zip
* DONE (metavizr)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'metavizr' successfully unpacked and MD5 sums checked

Tests output

metavizr.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
Loaded glmnet 3.0-2

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 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  54.68    9.31   57.03 

metavizr.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
Loaded glmnet 3.0-2

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 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  60.37    6.98   60.92 

Example timings

metavizr.Rcheck/examples_i386/metavizr-Ex.timings

nameusersystemelapsed
EpivizMetagenomicsData-class000
EpivizMetagenomicsDataInnerNodes-class000
EpivizMetagenomicsDataTimeSeries-class000
generateSelection000
metavizControl000
replaceNAFeatures11.65 0.4612.11
setMetavizStandalone000
startMetaviz0.190.000.19
startMetavizStandalone0.080.000.08
validateObject0.230.030.26

metavizr.Rcheck/examples_x64/metavizr-Ex.timings

nameusersystemelapsed
EpivizMetagenomicsData-class000
EpivizMetagenomicsDataInnerNodes-class000
EpivizMetagenomicsDataTimeSeries-class000
generateSelection000
metavizControl000
replaceNAFeatures12.27 0.2812.56
setMetavizStandalone000
startMetaviz0.120.000.12
startMetavizStandalone0.070.000.07
validateObject0.140.000.14