BioC 3.4: CHECK report for SummarizedExperiment on zin1

Package: SummarizedExperiment

Version: 1.3.82

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SummarizedExperiment_1.3.82.tar.gz

StartedAt: 2016-09-20 13:06:57 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:08:53 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 115.9 seconds

RetCode: 0

Status:  OK

CheckDir: SummarizedExperiment.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SummarizedExperiment_1.3.82.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SummarizedExperiment.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SummarizedExperiment/DESCRIPTION’ ... OK
* this is package ‘SummarizedExperiment’ version ‘1.3.82’
* 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 ... 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
makeSummarizedExperimentFromExpressionSet 4.86  0.104   5.048
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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 ‘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	0.096	0.000	0.095
RangedSummarizedExperiment-class	0.200	0.008	0.208
SummarizedExperiment-class	0.056	0.000	0.057
coverage-methods	0.064	0.000	0.062
findOverlaps-methods	0.120	0.000	0.118
inter-range-methods	0.112	0.000	0.112
intra-range-methods	0.096	0.000	0.097
makeSummarizedExperimentFromDataFrame	0.04	0.00	0.04
makeSummarizedExperimentFromExpressionSet	4.860	0.104	5.048
nearest-methods	0.544	0.028	0.571
readKallisto	1.172	0.008	1.178