Lucas Schiffer
| Snapshot Date: 2019-04-16 11:00:05 -0400 (Tue, 16 Apr 2019) |
| URL: https://git.bioconductor.org/packages/curatedMetagenomicData |
| Branch: RELEASE_3_8 |
| Last Commit: a0ee22e |
| Last Changed Date: 2018-11-04 11:59:10 -0400 (Sun, 04 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.8 experimental data |
This page was generated on 2019-04-16 15:26:16 -0400 (Tue, 16 Apr 2019).
| Package 76/360 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| curatedMetagenomicData 1.12.3 Lucas Schiffer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | |
| Package: curatedMetagenomicData |
| Version: 1.12.3 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.12.3.tar.gz |
| StartedAt: 2019-04-16 13:35:44 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 13:37:50 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 125.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: curatedMetagenomicData.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.12.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-data-experiment/meat/curatedMetagenomicData.Rcheck’ * using R version 3.5.3 (2019-03-11) * 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 ‘1.12.3’ * 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 * 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-3.8-bioc/R/bin/R CMD INSTALL curatedMetagenomicData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘curatedMetagenomicData’ ... ** 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 * DONE (curatedMetagenomicData)
curatedMetagenomicData.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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: dplyr
Attaching package: 'dplyr'
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: Biobase
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:dplyr':
combine, intersect, setdiff, union
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ExperimentHub
Loading required package: AnnotationHub
Attaching package: 'AnnotationHub'
The following object is masked from 'package:Biobase':
cache
_ _
___ _ _ _ __ __ _| |_ ___ __| |
/ __| | | | '__/ _` | __/ _ \/ _` |
| (__| |_| | | | (_| | || __/ (_| |
\___|\__,_|_| \__,_|\__\___|\__,_|
__ __ _ _
| \/ | ___| |_ __ _ __ _ ___ _ __ ___ _ __ ___ (_) ___
| |\/| |/ _ \ __/ _` |/ _` |/ _ \ '_ \ / _ \| '_ ` _ \| |/ __|
| | | | __/ || (_| | (_| | __/ | | | (_) | | | | | | | (__
|_| |_|\___|\__\__,_|\__, |\___|_| |_|\___/|_| |_| |_|_|\___|
____ _ |___/
| _ \ __ _| |_ __ _
| | | |/ _` | __/ _` |
| |_| | (_| | || (_| |
|____/ \__,_|\__\__,_|
>
> test_check("curatedMetagenomicData")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 40 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
15.612 0.440 17.884
curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings
| name | user | system | elapsed | |
| AsnicarF_2017 | 1.544 | 0.140 | 2.500 | |
| Bengtsson-PalmeJ_2015 | 0.532 | 0.012 | 1.057 | |
| BritoIL_2016 | 0.388 | 0.008 | 0.539 | |
| Castro-NallarE_2015 | 0.360 | 0.004 | 0.460 | |
| ChngKR_2016 | 0.384 | 0.000 | 0.587 | |
| DavidLA_2015 | 0.476 | 0.008 | 0.765 | |
| ExpressionSet2MRexperiment | 1.560 | 0.000 | 1.829 | |
| ExpressionSet2phyloseq | 3.736 | 0.072 | 3.925 | |
| FengQ_2015 | 0.464 | 0.000 | 0.647 | |
| HMP_2012 | 0.760 | 0.008 | 0.944 | |
| HanniganGD_2017 | 0.328 | 0.004 | 0.449 | |
| Heitz-BuschartA_2016 | 0.340 | 0.004 | 0.418 | |
| KarlssonFH_2013 | 0.344 | 0.004 | 0.571 | |
| KosticAD_2015 | 0.376 | 0.004 | 0.475 | |
| LeChatelierE_2013 | 0.356 | 0.012 | 0.499 | |
| LiJ_2014 | 0.352 | 0.004 | 0.527 | |
| LiJ_2017 | 0.328 | 0.008 | 0.423 | |
| LiSS_2016 | 0.444 | 0.008 | 0.609 | |
| LiuW_2016 | 0.408 | 0.000 | 0.541 | |
| LomanNJ_2013 | 0.332 | 0.008 | 0.416 | |
| LoombaR_2017 | 0.380 | 0.012 | 0.479 | |
| LouisS_2016 | 0.484 | 0.012 | 0.558 | |
| NielsenHB_2014 | 0.492 | 0.004 | 0.568 | |
| Obregon-TitoAJ_2015 | 0.344 | 0.004 | 0.420 | |
| OhJ_2014 | 0.372 | 0.012 | 0.462 | |
| OlmMR_2017 | 0.420 | 0.020 | 0.503 | |
| PasolliE_2018 | 0.384 | 0.004 | 0.461 | |
| QinJ_2012 | 0.436 | 0.000 | 0.536 | |
| QinN_2014 | 0.440 | 0.008 | 0.578 | |
| RampelliS_2015 | 0.428 | 0.008 | 0.519 | |
| RaymondF_2016 | 0.380 | 0.004 | 0.488 | |
| SchirmerM_2016 | 0.780 | 0.020 | 1.115 | |
| ShiB_2015 | 0.352 | 0.000 | 0.428 | |
| SmitsSA_2017 | 0.352 | 0.008 | 0.499 | |
| TettAJ_2016 | 0.400 | 0.020 | 0.526 | |
| ThomasAM_2018a | 0.512 | 0.016 | 0.603 | |
| VatanenT_2016 | 0.520 | 0.008 | 0.649 | |
| VincentC_2016 | 0.476 | 0.012 | 0.573 | |
| VogtmannE_2016 | 0.324 | 0.000 | 0.401 | |
| WenC_2017 | 0.332 | 0.008 | 0.419 | |
| XieH_2016 | 0.336 | 0.004 | 0.447 | |
| YuJ_2015 | 0.328 | 0.004 | 0.393 | |
| ZellerG_2014 | 0.344 | 0.004 | 0.438 | |
| cmdValidVersions | 0.000 | 0.000 | 0.003 | |
| curatedMetagenomicData | 0.792 | 0.020 | 0.960 | |
| getMetaphlanTree | 0.400 | 0.000 | 0.397 | |
| mergeData | 1.000 | 0.012 | 1.175 | |