Package: curatedMetagenomicData

Version: 1.14.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.14.1.tar.gz

StartedAt: 2019-10-17 13:02:07 -0400 (Thu, 17 Oct 2019)

EndedAt: 2019-10-17 13:06:17 -0400 (Thu, 17 Oct 2019)

EllapsedTime: 250.1 seconds

RetCode: 0

Status:  OK

CheckDir: curatedMetagenomicData.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘curatedMetagenomicData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedMetagenomicData’ version ‘1.14.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘curatedMetagenomicData’ 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
* 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 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
Examples with CPU or elapsed time > 5s
                        user system elapsed
ExpressionSet2phyloseq 5.196  0.104   5.441
* 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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL curatedMetagenomicData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘curatedMetagenomicData’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* DONE (curatedMetagenomicData)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
> library(curatedMetagenomicData)
Loading required package: AnnotationHub
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

Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    cache

Loading required package: dplyr

Attaching package: 'dplyr'

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

    combine

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

    ident, sql

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

Loading required package: ExperimentHub
                      _           _
  ___ _   _ _ __ __ _| |_ ___  __| |
 / __| | | | '__/ _` | __/ _ \/ _` |
| (__| |_| | | | (_| | ||  __/ (_| |
 \___|\__,_|_|  \__,_|\__\___|\__,_|
 __  __      _                                         _
|  \/  | ___| |_ __ _  __ _  ___ _ __   ___  _ __ ___ (_) ___
| |\/| |/ _ \ __/ _` |/ _` |/ _ \ '_ \ / _ \| '_ ` _ \| |/ __|
| |  | |  __/ || (_| | (_| |  __/ | | | (_) | | | | | | | (__
|_|  |_|\___|\__\__,_|\__, |\___|_| |_|\___/|_| |_| |_|_|\___|
 ____        _        |___/
|  _ \  __ _| |_ __ _
| | | |/ _` | __/ _` |
| |_| | (_| | || (_| |
|____/ \__,_|\__\__,_|

> 
> test_check("curatedMetagenomicData")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 40 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 30.533   0.656  33.853 

name	user	system	elapsed
AsnicarF_2017	3.328	0.127	3.881
BackhedF_2015	2.085	0.024	2.426
Bengtsson-PalmeJ_2015	2.060	0.016	2.394
BritoIL_2016	2.131	0.020	2.427
Castro-NallarE_2015	2.126	0.016	2.442
ChengpingW_2017	1.978	0.024	2.325
ChngKR_2016	1.754	0.028	2.208
CosteaPI_2017	2.095	0.020	3.398
DavidLA_2015	1.814	0.029	2.081
ExpressionSet2MRexperiment	2.791	0.028	2.971
ExpressionSet2phyloseq	5.196	0.104	5.441
FengQ_2015	2.126	0.016	2.314
FerrettiP_2018	2.145	0.016	2.453
HMP_2012	1.870	0.028	2.052
HanniganGD_2017	1.912	0.040	2.138
Heitz-BuschartA_2016	1.954	0.040	2.130
KarlssonFH_2013	2.024	0.020	2.195
KosticAD_2015	2.099	0.040	2.311
LeChatelierE_2013	2.233	0.016	2.435
LiJ_2014	2.345	0.023	2.525
LiJ_2017	2.157	0.020	2.401
LiSS_2016	2.186	0.013	2.361
LiuW_2016	2.183	0.028	2.377
LomanNJ_2013	2.327	0.012	2.500
LoombaR_2017	2.223	0.032	2.422
LouisS_2016	2.459	0.023	2.659
NielsenHB_2014	2.004	0.025	2.355
Obregon-TitoAJ_2015	2.236	0.032	2.551
OhJ_2014	2.189	0.020	2.572
OlmMR_2017	2.188	0.012	2.439
PasolliE_2018	2.141	0.024	2.313
QinJ_2012	2.076	0.024	2.249
QinN_2014	2.255	0.024	2.447
RampelliS_2015	2.464	0.020	2.685
RaymondF_2016	2.071	0.016	2.267
SchirmerM_2016	1.954	0.028	2.211
ShiB_2015	2.007	0.016	2.177
SmitsSA_2017	1.798	0.024	2.023
TettAJ_2016	2.203	0.044	2.417
ThomasAM_2018a	2.169	0.015	2.329
ThomasAM_2018b	2.063	0.028	2.254
VatanenT_2016	2.116	0.020	2.507
VincentC_2016	2.139	0.032	2.357
VogtmannE_2016	2.138	0.016	2.294
WenC_2017	2.203	0.016	2.371
XieH_2016	2.252	0.040	2.440
YuJ_2015	2.170	0.028	2.323
ZellerG_2014	2.130	0.012	2.298
cmdValidVersions	0.000	0.002	0.002
curatedMetagenomicData	4.196	0.045	4.520
getMetaphlanTree	0.376	0.000	0.376
mergeData	4.605	0.032	4.951