BioC 3.4: CHECK report for ALDEx2 on morelia

Package: ALDEx2

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ALDEx2_1.5.1.tar.gz

StartedAt: 2016-09-20 03:01:16 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:03:21 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 124.8 seconds

RetCode: 0

Status:  OK

CheckDir: ALDEx2.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 ALDEx2_1.5.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ALDEx2.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ALDEx2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ALDEx2’ version ‘1.5.1’
* 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 ‘ALDEx2’ 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 sizes of PDF files under ‘inst/doc’ ... 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
aldex 1.093  0.106   11.45
* 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 ‘ALDEx2’ ...
** 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 (ALDEx2)

name	user	system	elapsed
ALDEx2m-package	0	0	0
aldex	1.093	0.106	11.450
aldex.clr-class	0.047	0.001	0.099
aldex.clr.function-methods	0.063	0.003	0.066
aldex.corr	0.001	0.001	0.001
aldex.effect	1.590	0.014	1.605
aldex.glm	2.634	0.011	2.648
aldex.set.mode	0.037	0.002	0.039
aldex.ttest	0.405	0.002	0.407
getFeatureNames-method	0.053	0.002	0.056
getFeatures-method	0.038	0.002	0.039
getMonteCarloInstances-method	0.040	0.001	0.041
getMonteCarloReplicate-method	0.041	0.001	0.042
getReads-method	0.044	0.001	0.045
getSampleIDs-method	0.038	0.001	0.039
numConditions-method	0.051	0.001	0.053
numFeatures-method	0.041	0.001	0.042
numMCInstances-method	0.041	0.001	0.043
plot.aldex	0	0	0