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CHECK report for metagenomeFeatures on veracruz1

This page was generated on 2018-04-12 13:41:41 -0400 (Thu, 12 Apr 2018).

Package 823/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeFeatures 1.10.0
Nathan D. Olson
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/metagenomeFeatures
Branch: RELEASE_3_6
Last Commit: af71628
Last Changed Date: 2017-10-30 12:41:05 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: metagenomeFeatures
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeFeatures_1.10.0.tar.gz
StartedAt: 2018-04-12 06:06:13 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 06:10:18 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 244.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: metagenomeFeatures.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metagenomeFeatures_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/metagenomeFeatures.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeFeatures/DESCRIPTION’ ... OK
* this is package ‘metagenomeFeatures’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘metagenomeFeatures’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    extdata   6.7Mb
* 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
* 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 loading without being on the library search path ... 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 ... NOTE
.mgDb_annotateFeatures: no visible binding for global variable
  ‘db_keys’
.select.taxa: no visible binding for global variable ‘Keys’
.select.taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘index’
vignette_pheno_data: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  . Keys db_keys index read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘msd16s_metagenomeAnnotation’ ‘msd16s_query_df’
Undocumented data sets:
  ‘msd16s_metagenomeAnnotation’ ‘msd16s_query_df’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/metagenomeFeatures.Rcheck/00check.log’
for details.



Installation output

metagenomeFeatures.Rcheck/00install.out

* installing *source* package ‘metagenomeFeatures’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagenomeFeatures)

Tests output

metagenomeFeatures.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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

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: 90 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.371   0.326  11.831 

Example timings

metagenomeFeatures.Rcheck/metagenomeFeatures-Ex.timings

nameusersystemelapsed
MgDb-class0.2200.0100.236
aggregate_taxa1.6200.0481.693
annotateFeatures-MgDb-method0.5440.0200.586
annotateMRexp_fData-MgDb-method0.0010.0000.001
get_demoMgDb0.0830.0050.088
get_mockMgDb0.0820.0050.086
mgF_meta0.0240.0030.027
mgF_seq0.1300.0020.134
mgF_taxa0.0250.0010.030
mgF_tree0.0240.0010.025
mgFeatures-class0.0020.0010.003
mgQuery0.0020.0010.003
mgdb_meta0.4410.0060.455
mgdb_seq0.1320.0040.136
mgdb_taxa0.4340.0280.471
mgdb_tree0.1050.0080.115
mock_mgF0.0010.0000.003
mock_query_df0.0020.0010.003
select-MgDb-method0.7260.0310.764
taxa_columns0.0740.0020.076
taxa_keys0.1200.0040.127
taxa_keytypes0.0800.0030.084
taxa_levels0.1180.0130.133