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This page was generated on 2022-04-13 12:06:52 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for metavizr on tokay2


To the developers/maintainers of the metavizr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metavizr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1107/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metavizr 1.18.0  (landing page)
Hector Corrada Bravo
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/metavizr
git_branch: RELEASE_3_14
git_last_commit: e961e56
git_last_commit_date: 2021-10-26 12:34:56 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: metavizr
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metavizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings metavizr_1.18.0.tar.gz
StartedAt: 2022-04-12 22:33:39 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 22:41:52 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 493.5 seconds
RetCode: 0
Status:   OK  
CheckDir: metavizr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metavizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings metavizr_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/metavizr.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.18.0'
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
replaceNAFeatures 7.19   0.45    7.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
replaceNAFeatures 10.38   0.37   10.75
* 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

metavizr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/metavizr_1.18.0.tar.gz && rm -rf metavizr.buildbin-libdir && mkdir metavizr.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metavizr.buildbin-libdir metavizr_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL metavizr_1.18.0.zip && rm metavizr_1.18.0.tar.gz metavizr_1.18.0.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
 15 1240k   15  197k    0     0   742k      0  0:00:01 --:--:--  0:00:01  742k
100 1240k  100 1240k    0     0  1373k      0 --:--:-- --:--:-- --:--:-- 1373k

install for i386

* installing *source* package 'metavizr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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  
    startMetavizStandalone                  html  
    validateObject                          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 'metavizr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metavizr' as metavizr_1.18.0.zip
* DONE (metavizr)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'metavizr' successfully unpacked and MD5 sums checked

Tests output

metavizr.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

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

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 4.1-3
Loading required package: RColorBrewer
Loading required package: data.table
Loading required package: digest
> 
> test_check("metavizr")
[ FAIL 0 | WARN 68 | SKIP 0 | PASS 21 ]

[ FAIL 0 | WARN 68 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
  35.37    3.73   39.06 

metavizr.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

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

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 4.1-3
Loading required package: RColorBrewer
Loading required package: data.table
Loading required package: digest
> 
> test_check("metavizr")
[ FAIL 0 | WARN 68 | SKIP 0 | PASS 21 ]

[ FAIL 0 | WARN 68 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
  36.68    1.01   37.59 

Example timings

metavizr.Rcheck/examples_i386/metavizr-Ex.timings

nameusersystemelapsed
EpivizMetagenomicsData-class000
EpivizMetagenomicsDataInnerNodes-class000
EpivizMetagenomicsDataTimeSeries-class000
generateSelection000
metavizControl000
replaceNAFeatures7.190.457.64
setMetavizStandalone000
startMetaviz0.090.000.09
startMetavizStandalone0.070.000.06
validateObject0.140.000.14

metavizr.Rcheck/examples_x64/metavizr-Ex.timings

nameusersystemelapsed
EpivizMetagenomicsData-class000
EpivizMetagenomicsDataInnerNodes-class000
EpivizMetagenomicsDataTimeSeries-class000
generateSelection000
metavizControl000
replaceNAFeatures10.38 0.3710.75
setMetavizStandalone000
startMetaviz0.120.000.13
startMetavizStandalone0.080.000.07
validateObject0.110.020.13