BioC 3.2: CHECK report for SummarizedExperiment on perceval

Package: SummarizedExperiment

Version: 0.3.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SummarizedExperiment_0.3.3.tar.gz

StartedAt: 2015-08-24 05:37:42 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 05:40:48 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 186.2 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_0.3.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SummarizedExperiment.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SummarizedExperiment/DESCRIPTION’ ... OK
* this is package ‘SummarizedExperiment’ version ‘0.3.3’
* 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/12s] 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 ... [26s/26s] OK
Examples with CPU or elapsed time > 5s
                                            user system elapsed
makeSummarizedExperimentFromExpressionSet 17.208  0.499  17.898
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘SummarizedExperiment_unit_tests.R’ [35s/35s]
 [36s/36s] 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	0.063	0.005	0.068
RangedSummarizedExperiment-class	0.423	0.007	0.431
SummarizedExperiment0-class	0.071	0.003	0.075
coverage-methods	0.104	0.002	0.106
findOverlaps-methods	0.174	0.002	0.176
inter-range-methods	0.214	0.002	0.215
intra-range-methods	0.136	0.002	0.138
makeSummarizedExperimentFromExpressionSet	17.208	0.499	17.898
nearest-methods	1.068	0.003	1.072