BioC 2.14: CHECK report for LPE on petty

Package: LPE

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch LPE_1.38.0.tar.gz

StartedAt: 2014-10-07 22:44:03 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:44:52 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 49.4 seconds

RetCode: 0

Status:  OK

CheckDir: LPE.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 --no-multiarch LPE_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/LPE.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LPE/DESCRIPTION’ ... OK
* this is package ‘LPE’ version ‘1.38.0’
* 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 ‘LPE’ can be installed ... [2s/2s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/19s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
resamp.adj 5.737  0.036   5.792
* 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

* installing *source* package ‘LPE’ ...
** 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 (LPE)

name	user	system	elapsed
am.trans	0.003	0.001	0.004
baseOlig.error	0.970	0.039	1.010
baseOlig.error.step1	0.427	0.012	0.439
baseOlig.error.step2	0.779	0.015	0.795
fdr.adjust	4.501	0.038	4.565
fixbounds.predict.smooth.spline	0.878	0.038	0.988
iqr	0.002	0.000	0.002
lowess.normalize	0.091	0.009	0.106
lpe	1.769	0.033	1.835
mt.rawp2adjp	1.401	0.014	1.420
n.genes.adaptive.int	0.495	0.012	0.509
permute	0.002	0.001	0.003
preprocess	0.192	0.009	0.202
quan.norm	0.002	0.000	0.002
quartile.normalize	0.086	0.009	0.096
resamp.adj	5.737	0.036	5.792