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) |
| Back to Build/check report for BioC 3.10 experimental data |
This page was generated on 2020-04-14 17:46:25 -0400 (Tue, 14 Apr 2020).
| Package 84/384 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| curatedMetagenomicData 1.16.1 Lucas Schiffer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| 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 |
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### Running command:
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### /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
###
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* 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
curatedMetagenomicData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL curatedMetagenomicData ### ############################################################################## ############################################################################## * 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)
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
curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings
| name | user | system | elapsed | |
| AsnicarF_2017 | 4.936 | 0.148 | 8.868 | |
| BackhedF_2015 | 3.076 | 0.024 | 4.006 | |
| Bengtsson-PalmeJ_2015 | 3.160 | 0.032 | 4.338 | |
| BritoIL_2016 | 2.700 | 0.024 | 3.376 | |
| Castro-NallarE_2015 | 2.256 | 0.012 | 3.484 | |
| ChengpingW_2017 | 2.352 | 0.044 | 2.646 | |
| ChngKR_2016 | 2.180 | 0.028 | 2.416 | |
| CosteaPI_2017 | 2.276 | 0.040 | 2.521 | |
| DavidLA_2015 | 2.940 | 0.024 | 3.396 | |
| DhakanDB_2019 | 2.364 | 0.012 | 2.602 | |
| ExpressionSet2MRexperiment | 3.412 | 0.024 | 3.683 | |
| ExpressionSet2phyloseq | 5.460 | 0.112 | 5.802 | |
| FengQ_2015 | 2.376 | 0.020 | 2.636 | |
| FerrettiP_2018 | 2.360 | 0.016 | 2.550 | |
| GopalakrishnanV_2018 | 2.356 | 0.024 | 2.613 | |
| HMP_2012 | 2.276 | 0.028 | 2.491 | |
| HanniganGD_2017 | 2.288 | 0.020 | 2.984 | |
| HansenLBS_2018 | 2.440 | 0.036 | 7.746 | |
| Heitz-BuschartA_2016 | 2.368 | 0.012 | 2.906 | |
| JieZ_2017 | 2.284 | 0.028 | 2.553 | |
| KarlssonFH_2013 | 2.276 | 0.024 | 2.661 | |
| KieserS_2018 | 3.152 | 0.028 | 3.416 | |
| KosticAD_2015 | 2.656 | 0.016 | 2.886 | |
| LeChatelierE_2013 | 2.648 | 0.028 | 3.221 | |
| LiJ_2014 | 3.500 | 0.016 | 3.723 | |
| LiJ_2017 | 3.412 | 0.024 | 3.638 | |
| LiSS_2016 | 3.056 | 0.044 | 3.297 | |
| LiuW_2016 | 2.280 | 0.028 | 2.558 | |
| LomanNJ_2013 | 2.380 | 0.016 | 2.589 | |
| LoombaR_2017 | 2.412 | 0.036 | 2.659 | |
| LouisS_2016 | 2.340 | 0.032 | 2.565 | |
| MatsonV_2018 | 2.284 | 0.032 | 2.564 | |
| NielsenHB_2014 | 2.320 | 0.020 | 2.557 | |
| Obregon-TitoAJ_2015 | 2.292 | 0.036 | 2.539 | |
| OhJ_2014 | 2.376 | 0.024 | 2.583 | |
| OlmMR_2017 | 2.332 | 0.016 | 2.575 | |
| PasolliE_2018 | 2.508 | 0.032 | 2.969 | |
| PehrssonE_2016 | 3.204 | 0.028 | 3.445 | |
| QinJ_2012 | 2.636 | 0.028 | 2.837 | |
| QinN_2014 | 2.660 | 0.016 | 2.915 | |
| RampelliS_2015 | 2.768 | 0.016 | 3.000 | |
| RaymondF_2016 | 2.612 | 0.016 | 2.859 | |
| SchirmerM_2016 | 2.392 | 0.008 | 2.601 | |
| ShiB_2015 | 2.560 | 0.020 | 2.837 | |
| SmitsSA_2017 | 2.368 | 0.024 | 2.617 | |
| TettAJ_2016 | 3.768 | 0.008 | 3.943 | |
| TettAJ_2019_a | 3.104 | 0.020 | 3.343 | |
| TettAJ_2019_b | 2.392 | 0.024 | 2.624 | |
| TettAJ_2019_c | 2.420 | 0.056 | 2.651 | |
| ThomasAM_2018a | 2.456 | 0.016 | 2.658 | |
| ThomasAM_2018b | 2.996 | 0.016 | 3.264 | |
| VatanenT_2016 | 2.572 | 0.016 | 2.761 | |
| VincentC_2016 | 3.204 | 0.032 | 3.409 | |
| VogtmannE_2016 | 2.340 | 0.024 | 2.665 | |
| XieH_2016 | 2.200 | 0.016 | 2.413 | |
| YeZ_2018 | 2.296 | 0.032 | 2.727 | |
| YuJ_2015 | 3.068 | 0.012 | 3.340 | |
| ZeeviD_2015 | 2.912 | 0.044 | 3.179 | |
| ZellerG_2014 | 2.420 | 0.032 | 7.719 | |
| cmdValidVersions | 0.004 | 0.000 | 0.003 | |
| curatedMetagenomicData | 4.616 | 0.048 | 5.028 | |
| getMetaphlanTree | 0.400 | 0.000 | 0.399 | |
| mergeData | 5.616 | 0.044 | 6.039 | |