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CHECK report for curatedMetagenomicData on malbec1

This page was generated on 2020-04-14 17:46:25 -0400 (Tue, 14 Apr 2020).

Package 84/384HostnameOS / ArchINSTALLBUILDCHECK
curatedMetagenomicData 1.16.1
Lucas Schiffer
Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/curatedMetagenomicData
Branch: RELEASE_3_10
Last Commit: dfb57a7
Last Changed Date: 2020-03-24 10:21:43 -0400 (Tue, 24 Mar 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: curatedMetagenomicData
Version: 1.16.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.16.1.tar.gz
StartedAt: 2020-04-14 13:37:01 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 13:42:34 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 332.7 seconds
RetCode: 0
Status:  OK 
CheckDir: curatedMetagenomicData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.1’
* 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
mergeData              5.616  0.044   6.039
ExpressionSet2phyloseq 5.460  0.112   5.802
AsnicarF_2017          4.936  0.148   8.868
curatedMetagenomicData 4.616  0.048   5.028
HansenLBS_2018         2.440  0.036   7.746
ZellerG_2014           2.420  0.032   7.719
* 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-3.10-bioc/R/bin/R CMD INSTALL curatedMetagenomicData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.10-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)

Tests output

curatedMetagenomicData.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 40.044   0.724  43.945 

Example timings

curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings

nameusersystemelapsed
AsnicarF_20174.9360.1488.868
BackhedF_20153.0760.0244.006
Bengtsson-PalmeJ_20153.1600.0324.338
BritoIL_20162.7000.0243.376
Castro-NallarE_20152.2560.0123.484
ChengpingW_20172.3520.0442.646
ChngKR_20162.1800.0282.416
CosteaPI_20172.2760.0402.521
DavidLA_20152.9400.0243.396
DhakanDB_20192.3640.0122.602
ExpressionSet2MRexperiment3.4120.0243.683
ExpressionSet2phyloseq5.4600.1125.802
FengQ_20152.3760.0202.636
FerrettiP_20182.3600.0162.550
GopalakrishnanV_20182.3560.0242.613
HMP_20122.2760.0282.491
HanniganGD_20172.2880.0202.984
HansenLBS_20182.4400.0367.746
Heitz-BuschartA_20162.3680.0122.906
JieZ_20172.2840.0282.553
KarlssonFH_20132.2760.0242.661
KieserS_20183.1520.0283.416
KosticAD_20152.6560.0162.886
LeChatelierE_20132.6480.0283.221
LiJ_20143.5000.0163.723
LiJ_20173.4120.0243.638
LiSS_20163.0560.0443.297
LiuW_20162.2800.0282.558
LomanNJ_20132.3800.0162.589
LoombaR_20172.4120.0362.659
LouisS_20162.3400.0322.565
MatsonV_20182.2840.0322.564
NielsenHB_20142.3200.0202.557
Obregon-TitoAJ_20152.2920.0362.539
OhJ_20142.3760.0242.583
OlmMR_20172.3320.0162.575
PasolliE_20182.5080.0322.969
PehrssonE_20163.2040.0283.445
QinJ_20122.6360.0282.837
QinN_20142.6600.0162.915
RampelliS_20152.7680.0163.000
RaymondF_20162.6120.0162.859
SchirmerM_20162.3920.0082.601
ShiB_20152.5600.0202.837
SmitsSA_20172.3680.0242.617
TettAJ_20163.7680.0083.943
TettAJ_2019_a3.1040.0203.343
TettAJ_2019_b2.3920.0242.624
TettAJ_2019_c2.4200.0562.651
ThomasAM_2018a2.4560.0162.658
ThomasAM_2018b2.9960.0163.264
VatanenT_20162.5720.0162.761
VincentC_20163.2040.0323.409
VogtmannE_20162.3400.0242.665
XieH_20162.2000.0162.413
YeZ_20182.2960.0322.727
YuJ_20153.0680.0123.340
ZeeviD_20152.9120.0443.179
ZellerG_20142.4200.0327.719
cmdValidVersions0.0040.0000.003
curatedMetagenomicData4.6160.0485.028
getMetaphlanTree0.4000.0000.399
mergeData5.6160.0446.039