BioC 3.5: CHECK report for MultiAssayExperiment on oaxaca

Package: MultiAssayExperiment

Version: 1.1.21

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.1.21.tar.gz

StartedAt: 2017-03-04 06:14:00 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 06:17:06 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 186.0 seconds

RetCode: 0

Status:  OK

CheckDir: MultiAssayExperiment.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.1.21.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MultiAssayExperiment.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiAssayExperiment/DESCRIPTION’ ... OK
* this is package ‘MultiAssayExperiment’ version ‘1.1.21’
* 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 ‘MultiAssayExperiment’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
RangedRaggedAssay-class 7.268  0.035    7.31
* 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 ‘MultiAssayExperiment’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MultiAssayExperiment)

name	user	system	elapsed
API	0.001	0.000	0.001
ExperimentList-class	0.022	0.000	0.022
ExperimentList	0.292	0.003	0.295
MultiAssayExperiment-class	3.364	0.054	3.536
MultiAssayExperiment	0.777	0.011	0.789
PrepMultiAssay	0.786	0.008	0.796
RangedRaggedAssay-class	7.268	0.035	7.310
RangedRaggedAssay	0.167	0.005	0.173
assay-RangedRaggedAssay-missing-method	0.218	0.004	0.222
clusterOn	0.562	0.006	0.569
experiments-set	0.403	0.005	0.422
experiments	0.400	0.006	0.407
getHits	1.174	0.013	1.295
hasAssay	0.004	0.000	0.005
mapToList	0.065	0.001	0.066
rearrange	0.338	0.005	0.342
sampleMap-set	0.476	0.006	0.482
sampleMap	0.038	0.001	0.038
subsetByAssay	0.860	0.010	0.871
subsetByColumn	0.802	0.008	0.810
subsetByRow	0.834	0.009	0.845
upsetSamples	2.786	0.014	2.802