BioC 3.2: CHECK report for SummarizedExperiment on oaxaca

Package: SummarizedExperiment

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SummarizedExperiment_1.0.2.tar.gz

StartedAt: 2016-04-23 04:49:44 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:52:01 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 136.8 seconds

RetCode: 0

Status:  OK

CheckDir: SummarizedExperiment.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 SummarizedExperiment_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SummarizedExperiment.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SummarizedExperiment/DESCRIPTION’ ... OK
* this is package ‘SummarizedExperiment’ version ‘1.0.2’
* 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 ‘SummarizedExperiment’ can be installed ... [11s/11s] 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 ... [16s/17s] OK
Examples with CPU or elapsed time > 5s
                                           user system elapsed
makeSummarizedExperimentFromExpressionSet 7.477  0.242   8.609
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘SummarizedExperiment_unit_tests.R’ [18s/18s]
 [18s/18s] 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 ‘SummarizedExperiment’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SummarizedExperiment)

name	user	system	elapsed
Assays-class	0.062	0.002	0.063
RangedSummarizedExperiment-class	0.339	0.004	0.344
SummarizedExperiment0-class	0.056	0.002	0.058
coverage-methods	0.084	0.000	0.084
findOverlaps-methods	0.142	0.001	0.143
inter-range-methods	0.181	0.001	0.182
intra-range-methods	0.133	0.001	0.134
makeSummarizedExperimentFromExpressionSet	7.477	0.242	8.609
nearest-methods	0.780	0.002	0.782
readKallisto	1.156	0.024	1.261