Lucas Schiffer
| Snapshot Date: 2018-10-16 07:35:22 -0400 (Tue, 16 Oct 2018) |
| URL: https://git.bioconductor.org/packages/curatedMetagenomicData |
| Branch: RELEASE_3_7 |
| Last Commit: c9bc731 |
| Last Changed Date: 2018-07-13 16:07:17 -0400 (Fri, 13 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 experimental data |
This page was generated on 2018-10-16 14:19:34 -0400 (Tue, 16 Oct 2018).
| Package 71/342 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| curatedMetagenomicData 1.10.2 Lucas Schiffer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |
| Package: curatedMetagenomicData |
| Version: 1.10.2 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.10.2.tar.gz |
| StartedAt: 2018-10-16 10:48:10 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 10:50:33 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 143.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: curatedMetagenomicData.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:curatedMetagenomicData.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings curatedMetagenomicData_1.10.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.2’
* 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 or elapsed time > 5s
user system elapsed
curatedMetagenomicData 0.584 0.016 6
* 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-3.7-bioc/R/bin/R CMD INSTALL curatedMetagenomicData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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: 33 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
11.012 0.344 13.960
curatedMetagenomicData.Rcheck/curatedMetagenomicData-Ex.timings
| name | user | system | elapsed | |
| AsnicarF_2017 | 1.108 | 0.104 | 2.091 | |
| BritoIL_2016 | 0.176 | 0.012 | 0.982 | |
| Castro-NallarE_2015 | 0.204 | 0.000 | 0.877 | |
| Castro_NallarE_2015 | 0.192 | 0.012 | 0.845 | |
| ChngKR_2016 | 0.204 | 0.004 | 0.396 | |
| ExpressionSet2MRexperiment | 1.240 | 0.008 | 1.538 | |
| ExpressionSet2phyloseq | 3.212 | 0.040 | 3.795 | |
| FengQ_2015 | 0.192 | 0.008 | 0.377 | |
| HMP_2012 | 0.180 | 0.004 | 0.315 | |
| HanniganGD_2017 | 0.536 | 0.008 | 1.902 | |
| Heitz-BuschartA_2016 | 0.156 | 0.004 | 0.372 | |
| Heitz_BuschartA_2016 | 0.156 | 0.008 | 0.409 | |
| KarlssonFH_2013 | 0.192 | 0.008 | 0.622 | |
| LeChatelierE_2013 | 0.184 | 0.004 | 0.469 | |
| LiJ_2014 | 0.272 | 0.000 | 0.900 | |
| LiJ_2017 | 0.272 | 0.004 | 0.384 | |
| LiuW_2016 | 0.232 | 0.008 | 0.430 | |
| LomanNJ_2013 | 0.144 | 0.004 | 0.256 | |
| LouisS_2016 | 0.152 | 0.004 | 0.399 | |
| NielsenHB_2014 | 0.212 | 0.004 | 0.437 | |
| Obregon-TitoAJ_2015 | 0.160 | 0.004 | 0.290 | |
| Obregon_TitoAJ_2015 | 0.176 | 0.000 | 0.388 | |
| OhJ_2014 | 0.176 | 0.008 | 0.361 | |
| QinJ_2012 | 0.192 | 0.004 | 0.320 | |
| QinN_2014 | 0.192 | 0.000 | 0.335 | |
| RampelliS_2015 | 0.160 | 0.008 | 0.517 | |
| RaymondF_2016 | 0.160 | 0.008 | 0.527 | |
| SchirmerM_2016 | 0.196 | 0.004 | 0.459 | |
| SmitsSA_2017 | 0.156 | 0.000 | 0.285 | |
| TettAJ_2016 | 0.168 | 0.004 | 0.347 | |
| VatanenT_2016 | 0.284 | 0.008 | 0.625 | |
| VincentC_2016 | 0.172 | 0.012 | 0.533 | |
| VogtmannE_2016 | 0.180 | 0.008 | 0.405 | |
| XieH_2016 | 0.196 | 0.000 | 0.372 | |
| YuJ_2015 | 0.188 | 0.004 | 0.311 | |
| ZellerG_2014 | 0.28 | 0.00 | 0.51 | |
| cmdValidVersions | 0.008 | 0.000 | 0.005 | |
| curatedMetagenomicData | 0.584 | 0.016 | 6.000 | |
| getMetaphlanTree | 0.368 | 0.000 | 0.366 | |
| mergeData | 0.972 | 0.008 | 1.400 | |