BioC 3.5: CHECK report for alpine on toluca2

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: 2017-04-23 00:13:40 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 00:19:32 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 352.1 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 r72187)
* 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     13.627  1.238  15.190
estimateAbundance 11.570  0.721  12.955
predictCoverage    6.676  0.738   7.541
* 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	3.560	0.171	3.748
estimateAbundance	11.570	0.721	12.955
extractAlpine	0.014	0.001	0.015
fitBiasModels	13.627	1.238	15.190
getFragmentWidths	2.073	0.091	2.315
getReadLength	1.240	0.063	1.334
mergeGenes	0.292	0.005	0.301
normalizeDESeq	0.002	0.001	0.002
plotFragLen	0.012	0.001	0.013
plotGC	0.033	0.001	0.034
plotGRL	0.188	0.004	0.194
plotOrder0	0.048	0.002	0.051
plotRelPos	0.015	0.002	0.016
predictCoverage	6.676	0.738	7.541
splitGenesAcrossChroms	0.644	0.005	0.653
splitLongGenes	0.447	0.017	0.468