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CHECK report for metagenomeFeatures on tokay2

This page was generated on 2020-10-17 11:57:03 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE metagenomeFeatures PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1037/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeFeatures 2.8.0
Nathan D. Olson
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/metagenomeFeatures
Branch: RELEASE_3_11
Last Commit: b3e4e05
Last Changed Date: 2020-04-27 14:51:49 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: metagenomeFeatures
Version: 2.8.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings metagenomeFeatures_2.8.0.tar.gz
StartedAt: 2020-10-17 05:49:39 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:52:43 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 183.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: metagenomeFeatures.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagenomeFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings metagenomeFeatures_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/metagenomeFeatures.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metagenomeFeatures/DESCRIPTION' ... OK
* this is package 'metagenomeFeatures' version '2.8.0'
* package encoding: UTF-8
* 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 'metagenomeFeatures' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpSuHbZJ/R.INSTALL1a50240e4a97/metagenomeFeatures/man/mgFeatures-class.Rd:27: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpSuHbZJ/R.INSTALL1a50240e4a97/metagenomeFeatures/man/reexports.Rd:14: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/metagenomeFeatures.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
* 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 ... NOTE
Package in Depends field not imported from: 'Biobase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.select.taxa: no visible binding for global variable 'Keys'
Undefined global functions or variables:
  Keys
* 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
** running examples for arch 'x64' ... OK
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/metagenomeFeatures.Rcheck/00check.log'
for details.



Installation output

metagenomeFeatures.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/metagenomeFeatures_2.8.0.tar.gz && rm -rf metagenomeFeatures.buildbin-libdir && mkdir metagenomeFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagenomeFeatures.buildbin-libdir metagenomeFeatures_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL metagenomeFeatures_2.8.0.zip && rm metagenomeFeatures_2.8.0.tar.gz metagenomeFeatures_2.8.0.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 2642k  100 2642k    0     0  21.4M      0 --:--:-- --:--:-- --:--:-- 22.6M

install for i386

* installing *source* package 'metagenomeFeatures' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'metagenomeFeatures'
    finding HTML links ... done
    MgDb-accessor                           html  
    MgDb-class                              html  
    MgDb-methods                            html  
    annotateFeatures-MgDb-method            html  
    get_gg13.8_85MgDb                       html  
    make_mgdb_sqlite                        html  
    mgFeatures-accessors                    html  
    mgFeatures-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpSuHbZJ/R.INSTALL1a50240e4a97/metagenomeFeatures/man/mgFeatures-class.Rd:27: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    mgFeatures-methods                      html  
    mock_mgF                                html  
    mock_query_df                           html  
    newMgDb                                 html  
    qiita_study_94_gg_ids                   html  
    reexports                               html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpSuHbZJ/R.INSTALL1a50240e4a97/metagenomeFeatures/man/reexports.Rd:14: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
    select-MgDb-method                      html  
    taxa_                                   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 'metagenomeFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagenomeFeatures' as metagenomeFeatures_2.8.0.zip
* DONE (metagenomeFeatures)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'metagenomeFeatures' successfully unpacked and MD5 sums checked

Tests output

metagenomeFeatures.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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)
> 
> test_check("metagenomeFeatures")
Loading required package: metagenomeFeatures
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")'.


Attaching package: 'dplyr'

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

    combine

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

    combine, intersect, setdiff, union

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

== testthat results  ===========================================================
[ OK: 79 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
Warning messages:
1: `as_data_frame()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
2: call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
   8.01    0.45    8.45 

metagenomeFeatures.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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)
> 
> test_check("metagenomeFeatures")
Loading required package: metagenomeFeatures
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")'.


Attaching package: 'dplyr'

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

    combine

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

    combine, intersect, setdiff, union

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

== testthat results  ===========================================================
[ OK: 79 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
Warning messages:
1: `as_data_frame()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
2: call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
   8.81    0.32    9.12 

Example timings

metagenomeFeatures.Rcheck/examples_i386/metagenomeFeatures-Ex.timings

nameusersystemelapsed
MgDb-accessor0.290.000.30
MgDb-class0.080.000.08
MgDb-methods0.100.000.09
annotateFeatures-MgDb-method0.310.030.46
get_gg13.8_85MgDb0.110.020.12
make_mgdb_sqlite000
mgFeatures-accessors0.200.030.24
mgFeatures-class0.050.000.04
mock_mgF000
mock_query_df000
newMgDb0.080.000.08
select-MgDb-method0.310.010.64
taxa_0.100.000.09

metagenomeFeatures.Rcheck/examples_x64/metagenomeFeatures-Ex.timings

nameusersystemelapsed
MgDb-accessor0.160.000.16
MgDb-class0.050.000.04
MgDb-methods0.050.000.05
annotateFeatures-MgDb-method0.380.020.39
get_gg13.8_85MgDb0.070.000.08
make_mgdb_sqlite000
mgFeatures-accessors0.100.000.09
mgFeatures-class0.040.000.05
mock_mgF0.000.010.01
mock_query_df000
newMgDb0.080.000.08
select-MgDb-method0.240.020.25
taxa_0.060.000.06