Lucas Schiffer
| Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021) |
| URL: https://git.bioconductor.org/packages/curatedMetagenomicData |
| Branch: RELEASE_3_12 |
| Last Commit: 0af9806 |
| Last Changed Date: 2020-10-27 10:20:00 -0400 (Tue, 27 Oct 2020) |
| Back to Build/check report for BioC 3.12 experimental data |
|
This page was generated on 2021-05-06 14:10:07 -0400 (Thu, 06 May 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 85/398 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| curatedMetagenomicData 1.20.0 (landing page) Lucas Schiffer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | |||||||
| Package: curatedMetagenomicData |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.20.0.tar.gz |
| StartedAt: 2021-05-06 11:50:13 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 11:58:10 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 477.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: curatedMetagenomicData.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.20.0’
* 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 ... 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
mergeData 8.580 0.076 9.520
curatedMetagenomicData 7.972 0.072 8.923
ExpressionSet2phyloseq 6.776 0.068 7.304
AsnicarF_2017 5.312 0.184 33.220
TettAJ_2019_c 4.816 0.048 5.463
LoombaR_2017 4.764 0.056 5.373
ExpressionSet2MRexperiment 4.740 0.036 5.578
TettAJ_2016 4.464 0.040 5.147
QinN_2014 3.612 0.028 5.378
* 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-3.12-bioc/R/bin/R CMD INSTALL curatedMetagenomicData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
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")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 40 ]
>
> proc.time()
user system elapsed
51.856 0.836 57.669
curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings
| name | user | system | elapsed | |
| AsnicarF_2017 | 5.312 | 0.184 | 33.220 | |
| BackhedF_2015 | 4.252 | 0.048 | 4.773 | |
| Bengtsson-PalmeJ_2015 | 4.240 | 0.028 | 4.716 | |
| BritoIL_2016 | 3.848 | 0.044 | 4.423 | |
| Castro-NallarE_2015 | 3.532 | 0.036 | 4.190 | |
| ChengpingW_2017 | 4.500 | 0.032 | 4.979 | |
| ChngKR_2016 | 3.780 | 0.020 | 4.478 | |
| CosteaPI_2017 | 3.956 | 0.048 | 4.737 | |
| DavidLA_2015 | 3.636 | 0.020 | 4.166 | |
| DhakanDB_2019 | 3.764 | 0.032 | 4.264 | |
| ExpressionSet2MRexperiment | 4.740 | 0.036 | 5.578 | |
| ExpressionSet2phyloseq | 6.776 | 0.068 | 7.304 | |
| FengQ_2015 | 3.992 | 0.064 | 4.828 | |
| FerrettiP_2018 | 3.560 | 0.048 | 4.032 | |
| GopalakrishnanV_2018 | 4.000 | 0.040 | 4.541 | |
| HMP_2012 | 3.788 | 0.024 | 4.233 | |
| HanniganGD_2017 | 3.756 | 0.020 | 4.288 | |
| HansenLBS_2018 | 4.012 | 0.016 | 4.541 | |
| Heitz-BuschartA_2016 | 3.984 | 0.040 | 4.619 | |
| JieZ_2017 | 3.708 | 0.036 | 4.169 | |
| KarlssonFH_2013 | 3.936 | 0.020 | 4.620 | |
| KieserS_2018 | 3.708 | 0.016 | 4.238 | |
| KosticAD_2015 | 3.468 | 0.040 | 3.986 | |
| LeChatelierE_2013 | 3.912 | 0.020 | 4.457 | |
| LiJ_2014 | 4.096 | 0.024 | 4.890 | |
| LiJ_2017 | 4.152 | 0.056 | 4.644 | |
| LiSS_2016 | 4.284 | 0.036 | 4.746 | |
| LiuW_2016 | 4.092 | 0.024 | 4.531 | |
| LomanNJ_2013 | 3.700 | 0.024 | 4.177 | |
| LoombaR_2017 | 4.764 | 0.056 | 5.373 | |
| LouisS_2016 | 3.580 | 0.036 | 4.145 | |
| MatsonV_2018 | 4.088 | 0.032 | 4.821 | |
| NielsenHB_2014 | 3.752 | 0.032 | 4.262 | |
| Obregon-TitoAJ_2015 | 3.912 | 0.036 | 4.442 | |
| OhJ_2014 | 3.728 | 0.052 | 4.591 | |
| OlmMR_2017 | 4.212 | 0.028 | 4.749 | |
| PasolliE_2018 | 3.700 | 0.044 | 4.359 | |
| PehrssonE_2016 | 3.760 | 0.032 | 4.290 | |
| QinJ_2012 | 3.964 | 0.028 | 4.559 | |
| QinN_2014 | 3.612 | 0.028 | 5.378 | |
| RampelliS_2015 | 3.928 | 0.048 | 4.479 | |
| RaymondF_2016 | 3.696 | 0.020 | 4.145 | |
| SchirmerM_2016 | 3.924 | 0.036 | 4.520 | |
| ShiB_2015 | 3.984 | 0.036 | 4.458 | |
| SmitsSA_2017 | 3.708 | 0.040 | 4.214 | |
| TettAJ_2016 | 4.464 | 0.040 | 5.147 | |
| TettAJ_2019_a | 3.740 | 0.036 | 4.195 | |
| TettAJ_2019_b | 4.484 | 0.024 | 4.943 | |
| TettAJ_2019_c | 4.816 | 0.048 | 5.463 | |
| ThomasAM_2018a | 3.816 | 0.032 | 4.308 | |
| ThomasAM_2018b | 3.636 | 0.032 | 4.166 | |
| VatanenT_2016 | 3.712 | 0.032 | 4.275 | |
| VincentC_2016 | 3.816 | 0.044 | 4.466 | |
| VogtmannE_2016 | 3.844 | 0.028 | 4.409 | |
| XieH_2016 | 3.944 | 0.032 | 4.427 | |
| YeZ_2018 | 3.960 | 0.044 | 4.560 | |
| YuJ_2015 | 3.784 | 0.036 | 4.354 | |
| ZeeviD_2015 | 4.408 | 0.040 | 4.981 | |
| ZellerG_2014 | 3.912 | 0.056 | 4.448 | |
| cmdValidVersions | 0.004 | 0.000 | 0.005 | |
| curatedMetagenomicData | 7.972 | 0.072 | 8.923 | |
| getMetaphlanTree | 0.392 | 0.004 | 0.394 | |
| mergeData | 8.580 | 0.076 | 9.520 | |