Package: metagenomeFeatures

Version: 2.0.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:metagenomeFeatures.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings metagenomeFeatures_2.0.0.tar.gz

StartedAt: 2018-10-16 01:49:28 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 01:50:42 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 74.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: metagenomeFeatures.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:metagenomeFeatures.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings metagenomeFeatures_2.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/metagenomeFeatures.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeFeatures/DESCRIPTION’ ... OK
* this is package ‘metagenomeFeatures’ version ‘2.0.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: subclass "QualityScaledDNAStringSet" of class "DNAStringSet" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: replacing previous import ‘lazyeval::is_formula’ by ‘purrr::is_formula’ when loading ‘metagenomeFeatures’
  Warning: replacing previous import ‘lazyeval::is_atomic’ by ‘purrr::is_atomic’ when loading ‘metagenomeFeatures’
See ‘/home/biocbuild/bbs-3.7-bioc/meat/metagenomeFeatures.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
* 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 ... NOTE
.select: no visible binding for global variable ‘identifier’
.select.taxa: no visible binding for global variable ‘Keys’
.select.taxa: no visible binding for global variable ‘.’
get_gg13.8_85MgDb: no visible binding for global variable ‘metadata’
Undefined global functions or variables:
  . Keys identifier metadata
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'mgFeatures'
All user-level objects in a package (including S4 classes and methods)
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 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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/metagenomeFeatures.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL metagenomeFeatures
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘metagenomeFeatures’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘lazyeval::is_formula’ by ‘purrr::is_formula’ when loading ‘metagenomeFeatures’
Warning: replacing previous import ‘lazyeval::is_atomic’ by ‘purrr::is_atomic’ when loading ‘metagenomeFeatures’
Warning: subclass "QualityScaledDNAStringSet" of class "DNAStringSet" is not local and cannot be updated for new inheritance information; consider setClassUnion()
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘lazyeval::is_formula’ by ‘purrr::is_formula’ when loading ‘metagenomeFeatures’
Warning: replacing previous import ‘lazyeval::is_atomic’ by ‘purrr::is_atomic’ when loading ‘metagenomeFeatures’
* DONE (metagenomeFeatures)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames,
    dirname, 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")'.


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 FAILED: 0
Warning messages:
1: replacing previous import 'lazyeval::is_formula' by 'purrr::is_formula' when loading 'metagenomeFeatures' 
2: replacing previous import 'lazyeval::is_atomic' by 'purrr::is_atomic' when loading 'metagenomeFeatures' 
3: call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  4.224   0.148   4.371 

name	user	system	elapsed
MgDb-class	0.132	0.000	0.152
annotateFeatures-MgDb-method	0.372	0.004	0.405
get_gg13.8_85MgDb	0.184	0.000	0.186
make_mgdb_sqlite	0	0	0
mgDb_	0.088	0.000	0.087
mgF_	0.060	0.008	0.066
mgFeatures-class	0.000	0.000	0.002
mgFeatures	0.080	0.000	0.082
mock_mgF	0.004	0.000	0.001
mock_query_df	0.000	0.000	0.001
newMgDb	0.072	0.004	0.073
select-MgDb-method	0.200	0.000	0.203
taxa_	0.052	0.000	0.052