Back to Multiple platform build/check report for BioC 3.8 experimental data

CHECK report for curatedMetagenomicData on malbec1

This page was generated on 2019-04-16 15:26:16 -0400 (Tue, 16 Apr 2019).

Package 76/360HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
curatedMetagenomicData 1.12.3
Lucas Schiffer
Snapshot Date: 2019-04-16 11:00:05 -0400 (Tue, 16 Apr 2019)
URL: https://git.bioconductor.org/packages/curatedMetagenomicData
Branch: RELEASE_3_8
Last Commit: a0ee22e
Last Changed Date: 2018-11-04 11:59:10 -0400 (Sun, 04 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: curatedMetagenomicData
Version: 1.12.3
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.12.3.tar.gz
StartedAt: 2019-04-16 13:35:44 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 13:37:50 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 125.5 seconds
RetCode: 0
Status:  OK 
CheckDir: curatedMetagenomicData.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.12.3.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.8-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.3’
* 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
* 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


Installation output

curatedMetagenomicData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL curatedMetagenomicData
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘curatedMetagenomicData’ ...
** 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
* DONE (curatedMetagenomicData)

Tests output

curatedMetagenomicData.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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: dplyr

Attaching package: 'dplyr'

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: 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:dplyr':

    combine, intersect, setdiff, union

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")'.

Loading required package: ExperimentHub
Loading required package: AnnotationHub

Attaching package: 'AnnotationHub'

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

    cache

                      _           _
  ___ _   _ _ __ __ _| |_ ___  __| |
 / __| | | | '__/ _` | __/ _ \/ _` |
| (__| |_| | | | (_| | ||  __/ (_| |
 \___|\__,_|_|  \__,_|\__\___|\__,_|
 __  __      _                                         _
|  \/  | ___| |_ __ _  __ _  ___ _ __   ___  _ __ ___ (_) ___
| |\/| |/ _ \ __/ _` |/ _` |/ _ \ '_ \ / _ \| '_ ` _ \| |/ __|
| |  | |  __/ || (_| | (_| |  __/ | | | (_) | | | | | | | (__
|_|  |_|\___|\__\__,_|\__, |\___|_| |_|\___/|_| |_| |_|_|\___|
 ____        _        |___/
|  _ \  __ _| |_ __ _
| | | |/ _` | __/ _` |
| |_| | (_| | || (_| |
|____/ \__,_|\__\__,_|

> 
> test_check("curatedMetagenomicData")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 40 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 15.612   0.440  17.884 

Example timings

curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings

nameusersystemelapsed
AsnicarF_20171.5440.1402.500
Bengtsson-PalmeJ_20150.5320.0121.057
BritoIL_20160.3880.0080.539
Castro-NallarE_20150.3600.0040.460
ChngKR_20160.3840.0000.587
DavidLA_20150.4760.0080.765
ExpressionSet2MRexperiment1.5600.0001.829
ExpressionSet2phyloseq3.7360.0723.925
FengQ_20150.4640.0000.647
HMP_20120.7600.0080.944
HanniganGD_20170.3280.0040.449
Heitz-BuschartA_20160.3400.0040.418
KarlssonFH_20130.3440.0040.571
KosticAD_20150.3760.0040.475
LeChatelierE_20130.3560.0120.499
LiJ_20140.3520.0040.527
LiJ_20170.3280.0080.423
LiSS_20160.4440.0080.609
LiuW_20160.4080.0000.541
LomanNJ_20130.3320.0080.416
LoombaR_20170.3800.0120.479
LouisS_20160.4840.0120.558
NielsenHB_20140.4920.0040.568
Obregon-TitoAJ_20150.3440.0040.420
OhJ_20140.3720.0120.462
OlmMR_20170.4200.0200.503
PasolliE_20180.3840.0040.461
QinJ_20120.4360.0000.536
QinN_20140.4400.0080.578
RampelliS_20150.4280.0080.519
RaymondF_20160.3800.0040.488
SchirmerM_20160.7800.0201.115
ShiB_20150.3520.0000.428
SmitsSA_20170.3520.0080.499
TettAJ_20160.4000.0200.526
ThomasAM_2018a0.5120.0160.603
VatanenT_20160.5200.0080.649
VincentC_20160.4760.0120.573
VogtmannE_20160.3240.0000.401
WenC_20170.3320.0080.419
XieH_20160.3360.0040.447
YuJ_20150.3280.0040.393
ZellerG_20140.3440.0040.438
cmdValidVersions0.0000.0000.003
curatedMetagenomicData0.7920.0200.960
getMetaphlanTree0.4000.0000.397
mergeData1.0000.0121.175