BioC experimental data: CHECK report for curatedMetagenomicData on malbec1

Package: curatedMetagenomicData

Version: 1.7.5

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings curatedMetagenomicData_1.7.5.tar.gz

StartedAt: 2017-08-15 10:38:05 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 10:40:37 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 152.0 seconds

RetCode: 0

Status:  OK

CheckDir: curatedMetagenomicData.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings curatedMetagenomicData_1.7.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/curatedMetagenomicData.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.5’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ExpressionSet2phyloseq 4.864  0.272   5.212
* 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

* installing *source* package ‘curatedMetagenomicData’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in read.dcf(con) :
  URL 'https://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
* DONE (curatedMetagenomicData)

name	user	system	elapsed
AsnicarF_2017	1.016	0.056	1.458
BritoIL_2016	0.360	0.000	0.498
Castro-NallarE_2015	0.296	0.000	0.530
ChngKR_2016	0.148	0.004	0.231
ExpressionSet2MRexperiment	1.764	0.032	1.950
ExpressionSet2phyloseq	4.864	0.272	5.212
FengQ_2015	0.260	0.004	0.464
HMP_2012	0.140	0.000	0.197
Heitz-BuschartA_2016	0.140	0.004	0.198
KarlssonFH_2013	0.136	0.000	0.199
LeChatelierE_2013	0.152	0.004	0.212
LiuW_2016	0.148	0.004	0.203
LomanNJ_2013	0.144	0.000	0.203
NielsenHB_2014	0.160	0.000	0.216
Obregon-TitoAJ_2015	0.132	0.000	0.210
OhJ_2014	0.176	0.004	0.238
QinJ_2012	0.188	0.004	0.243
QinN_2014	0.156	0.004	0.215
RampelliS_2015	0.156	0.000	0.210
RaymondF_2016	0.144	0.004	0.210
SchirmerM_2016	0.172	0.000	0.239
TettAJ_2016	0.144	0.004	0.204
VatanenT_2016	0.228	0.008	0.289
VincentC_2016	0.160	0.000	0.229
VogtmannE_2016	0.256	0.016	0.323
XieH_2016	0.172	0.004	0.235
YuJ_2015	0.160	0.000	0.217
ZellerG_2014	0.240	0.044	0.342
cmdValidVersions	0.004	0.000	0.003
curatedMetagenomicData	3.040	0.204	3.355
getMetaphlanTree	2.012	0.412	2.426
mergeData	0.808	0.020	1.114