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CHECK report for curatedMetagenomicData on malbec2

This page was generated on 2020-10-15 20:45:45 -0400 (Thu, 15 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE curatedMetagenomicData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 83/391HostnameOS / ArchINSTALLBUILDCHECK
curatedMetagenomicData 1.18.2
Lucas Schiffer
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/curatedMetagenomicData
Branch: RELEASE_3_11
Last Commit: 0e7bbc8
Last Changed Date: 2020-06-08 15:10:29 -0400 (Mon, 08 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: curatedMetagenomicData
Version: 1.18.2
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.18.2.tar.gz
StartedAt: 2020-10-15 13:12:01 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 13:17:55 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 353.6 seconds
RetCode: 0
Status:  OK 
CheckDir: curatedMetagenomicData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.18.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.18.2’
* 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 (user + system) or elapsed time > 5s
                        user system elapsed
ExpressionSet2phyloseq 5.478  0.092   5.873
mergeData              5.423  0.032   5.859
curatedMetagenomicData 5.083  0.064   5.778
DavidLA_2015           2.542  0.048   8.224
* 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-3.11-bioc/R/bin/R CMD INSTALL curatedMetagenomicData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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 
 39.563   0.719  42.662 

Example timings

curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings

nameusersystemelapsed
AsnicarF_20173.8840.1484.703
BackhedF_20152.7270.0322.960
Bengtsson-PalmeJ_20152.6170.0362.889
BritoIL_20162.6200.0283.553
Castro-NallarE_20152.6090.0202.815
ChengpingW_20172.6310.0243.048
ChngKR_20162.7650.0243.519
CosteaPI_20172.9930.0243.218
DavidLA_20152.5420.0488.224
DhakanDB_20192.6080.0242.835
ExpressionSet2MRexperiment4.0290.0324.366
ExpressionSet2phyloseq5.4780.0925.873
FengQ_20152.7250.0322.952
FerrettiP_20182.7200.0283.195
GopalakrishnanV_20182.9760.0443.514
HMP_20122.5470.0042.785
HanniganGD_20172.5970.0443.203
HansenLBS_20182.7830.0353.402
Heitz-BuschartA_20162.7120.0273.873
JieZ_20172.6010.0153.491
KarlssonFH_20132.6210.0283.340
KieserS_20182.7820.0363.787
KosticAD_20152.5510.0323.149
LeChatelierE_20132.6100.0283.318
LiJ_20142.5770.0362.938
LiJ_20172.5030.0283.002
LiSS_20162.5800.0243.236
LiuW_20162.7980.0643.468
LomanNJ_20132.6190.0212.930
LoombaR_20172.7260.0323.153
LouisS_20162.7320.0433.055
MatsonV_20182.7030.0213.073
NielsenHB_20142.6640.0313.398
Obregon-TitoAJ_20152.7490.0243.533
OhJ_20142.8390.0203.178
OlmMR_20172.8430.0163.533
PasolliE_20182.7290.0163.066
PehrssonE_20162.7260.0243.117
QinJ_20122.6030.0282.829
QinN_20142.7780.0403.003
RampelliS_20152.8520.0493.172
RaymondF_20162.6610.0354.045
SchirmerM_20162.8100.0083.219
ShiB_20152.7840.0173.040
SmitsSA_20172.6770.0362.931
TettAJ_20162.7560.0283.007
TettAJ_2019_a2.7860.0323.038
TettAJ_2019_b2.7890.0483.107
TettAJ_2019_c2.7750.0322.986
ThomasAM_2018a2.9650.0363.323
ThomasAM_2018b2.3000.0242.553
VatanenT_20162.4520.0362.758
VincentC_20162.6880.0203.083
VogtmannE_20162.6830.0282.921
XieH_20162.5480.0202.852
YeZ_20182.7220.0403.040
YuJ_20152.8890.0283.244
ZeeviD_20152.8260.0403.120
ZellerG_20142.7030.0122.991
cmdValidVersions0.0040.0000.003
curatedMetagenomicData5.0830.0645.778
getMetaphlanTree0.3330.0080.341
mergeData5.4230.0325.859