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CHECK report for curatedMetagenomicData on malbec2

This page was generated on 2021-01-21 16:01:06 -0500 (Thu, 21 Jan 2021).

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 85/386HostnameOS / ArchINSTALLBUILDCHECK
curatedMetagenomicData 1.21.0
Lucas Schiffer
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/curatedMetagenomicData
Branch: master
Last Commit: 8f99117
Last Changed Date: 2020-10-27 10:20:00 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: curatedMetagenomicData
Version: 1.21.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.21.0.tar.gz
StartedAt: 2021-01-21 11:54:16 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 12:01:49 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 453.3 seconds
RetCode: 0
Status:  OK 
CheckDir: curatedMetagenomicData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘1.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
curatedMetagenomicData     8.388  0.080   9.378
mergeData                  7.722  0.092   8.998
ExpressionSet2phyloseq     6.822  0.148   7.587
ExpressionSet2MRexperiment 5.512  0.032   6.147
AsnicarF_2017              5.058  0.129   6.408
VogtmannE_2016             4.118  0.044   5.033
LouisS_2016                4.067  0.028   5.017
OlmMR_2017                 3.951  0.028   9.446
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/curatedMetagenomicData.Rcheck/00check.log’
for details.



Installation output

curatedMetagenomicData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL curatedMetagenomicData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 Under development (unstable) (2021-01-05 r79797) -- "Unsuffered Consequences"
Copyright (C) 2021 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.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")
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning (test-ExpressionSet2MRexperiment.R:6:3): ExpressionSet2MRexperiment works ──
`data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Backtrace:
 1. curatedMetagenomicData::ExpressionSet2MRexperiment(eset) test-ExpressionSet2MRexperiment.R:6:2
 5. tibble::data_frame(.)

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
 51.119   0.860  59.162 

Example timings

curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings

nameusersystemelapsed
AsnicarF_20175.0580.1296.408
BackhedF_20154.1310.0274.767
Bengtsson-PalmeJ_20154.0250.0394.788
BritoIL_20163.3720.0484.099
Castro-NallarE_20153.9120.0364.587
ChengpingW_20173.8180.0444.375
ChngKR_20163.7420.0284.365
CosteaPI_20173.8890.0404.585
DavidLA_20153.7010.0404.327
DhakanDB_20193.6160.0284.253
ExpressionSet2MRexperiment5.5120.0326.147
ExpressionSet2phyloseq6.8220.1487.587
FengQ_20154.0160.0524.928
FerrettiP_20183.8650.0364.305
GopalakrishnanV_20183.8030.0244.440
HMP_20124.1100.0444.774
HanniganGD_20173.6640.0164.268
HansenLBS_20183.8280.0524.530
Heitz-BuschartA_20164.0360.0324.648
JieZ_20173.9650.0484.631
KarlssonFH_20134.1050.0164.728
KieserS_20183.9330.0604.587
KosticAD_20153.9010.0284.514
LeChatelierE_20133.9990.0244.636
LiJ_20144.0960.0404.623
LiJ_20173.8670.0324.491
LiSS_20164.0170.0404.716
LiuW_20163.7930.0444.266
LomanNJ_20133.9200.0364.547
LoombaR_20173.9500.0364.587
LouisS_20164.0670.0285.017
MatsonV_20183.9960.0244.623
NielsenHB_20144.2120.0414.737
Obregon-TitoAJ_20154.1230.0514.854
OhJ_20144.1260.0284.818
OlmMR_20173.9510.0289.446
PasolliE_20183.8970.0324.520
PehrssonE_20164.2970.0444.930
QinJ_20123.9600.0284.565
QinN_20143.9240.0404.567
RampelliS_20153.7340.0244.507
RaymondF_20163.7870.0124.398
SchirmerM_20163.8870.0324.520
ShiB_20154.1370.0404.802
SmitsSA_20173.7950.0404.444
TettAJ_20163.9340.0364.645
TettAJ_2019_a4.2290.0364.847
TettAJ_2019_b4.1240.0284.734
TettAJ_2019_c3.9410.0244.491
ThomasAM_2018a4.0330.0324.901
ThomasAM_2018b4.0000.0204.607
VatanenT_20163.7700.0524.325
VincentC_20163.7940.0324.322
VogtmannE_20164.1180.0445.033
XieH_20163.9200.0524.604
YeZ_20183.9920.0324.639
YuJ_20153.8850.0404.545
ZeeviD_20154.0900.0324.773
ZellerG_20143.9580.0164.676
cmdValidVersions0.0030.0000.003
curatedMetagenomicData8.3880.0809.378
getMetaphlanTree0.4000.0040.404
mergeData7.7220.0928.998