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CHECK report for curatedMetagenomicData on malbec1

This page was generated on 2018-04-12 12:50:14 -0400 (Thu, 12 Apr 2018).

Package 67/326HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
curatedMetagenomicData 1.8.1
Lucas Schiffer
Snapshot Date: 2018-04-12 07:35:06 -0400 (Thu, 12 Apr 2018)
URL: https://git.bioconductor.org/packages/curatedMetagenomicData
Branch: RELEASE_3_6
Last Commit: eb4d02d
Last Changed Date: 2018-01-18 15:44:01 -0400 (Thu, 18 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: curatedMetagenomicData
Version: 1.8.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings curatedMetagenomicData_1.8.1.tar.gz
StartedAt: 2018-04-12 09:51:43 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 09:54:11 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 148.0 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-3.6-bioc/R/bin/R CMD check --no-vignettes --timings curatedMetagenomicData_1.8.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.1’
* 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 ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    help   2.7Mb
* 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
.onLoad: no visible binding for global variable ‘run_date’
.onLoad: no visible binding for global variable ‘study’
.onLoad: no visible binding for global variable ‘data_type’
.onLoad: no visible binding for global variable ‘body_site’
Undefined global functions or variables:
  body_site data_type run_date study
* 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 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-data-experiment/meat/curatedMetagenomicData.Rcheck/00check.log’
for details.



Installation output

curatedMetagenomicData.Rcheck/00install.out

* installing *source* package ‘curatedMetagenomicData’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
> 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, 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: ExperimentHub
Loading required package: AnnotationHub

Attaching package: 'AnnotationHub'

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

    cache

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

> 
> test_check("curatedMetagenomicData")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 30 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.916   0.928  14.013 

Example timings

curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings

nameusersystemelapsed
AsnicarF_20171.0320.0561.403
BritoIL_20160.2640.0120.364
Castro-NallarE_20150.2760.0040.395
ChngKR_20160.1400.0000.247
ExpressionSet2MRexperiment1.2920.0241.593
ExpressionSet2phyloseq3.5960.2844.384
FengQ_20150.1560.0040.231
HMP_20120.5080.0040.994
HanniganGD_20170.1200.0000.225
Heitz-BuschartA_20160.1200.0040.202
KarlssonFH_20130.1360.0000.220
LeChatelierE_20130.1760.0160.265
LiJ_20140.1440.0000.235
LiuW_20160.1240.0000.192
LomanNJ_20130.1160.0040.192
NielsenHB_20140.1520.0000.219
Obregon-TitoAJ_20150.1200.0000.204
OhJ_20140.1480.0040.229
QinJ_20120.1520.0000.225
QinN_20140.1560.0000.225
RampelliS_20150.1120.0040.186
RaymondF_20160.1200.0000.193
SchirmerM_20160.1440.0040.222
TettAJ_20160.1200.0000.201
VatanenT_20160.1640.0040.227
VincentC_20160.1320.0040.219
VogtmannE_20160.2080.0080.288
XieH_20160.1520.0000.217
YuJ_20150.1280.0080.212
ZellerG_20140.2400.0120.330
cmdValidVersions0.0040.0000.003
curatedMetagenomicData3.1240.0683.630
getMetaphlanTree0.9520.6161.571
mergeData0.6160.0240.780