BioC 3.5: CHECK report for alpine on oaxaca

Package: alpine

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings alpine_1.1.3.tar.gz

StartedAt: 2017-03-03 22:57:17 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:02:50 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 332.6 seconds

RetCode: 0

Status:  OK

CheckDir: alpine.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 alpine_1.1.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/alpine.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 ‘alpine/DESCRIPTION’ ... OK
* this is package ‘alpine’ version ‘1.1.3’
* 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 ‘alpine’ 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
fitBiasModels     14.189  1.188  16.502
estimateAbundance 11.293  0.643  26.605
predictCoverage    6.656  0.742   7.511
* 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 ‘alpine’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (alpine)

name	user	system	elapsed
buildFragtypes	3.643	0.190	4.811
estimateAbundance	11.293	0.643	26.605
extractAlpine	0.015	0.001	0.015
fitBiasModels	14.189	1.188	16.502
getFragmentWidths	1.865	0.083	2.755
getReadLength	1.168	0.067	1.362
mergeGenes	0.258	0.006	0.263
normalizeDESeq	0.003	0.000	0.002
plotFragLen	0.013	0.002	0.014
plotGC	0.039	0.002	0.042
plotGRL	0.217	0.007	0.224
plotOrder0	0.056	0.004	0.060
plotRelPos	0.015	0.001	0.016
predictCoverage	6.656	0.742	7.511
splitGenesAcrossChroms	0.374	0.004	0.378
splitLongGenes	0.425	0.022	0.447