BioC 3.5: CHECK report for ALDEx2 on malbec2

Package: ALDEx2

Version: 1.8.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ALDEx2_1.8.0.tar.gz

StartedAt: 2017-10-17 21:06:27 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:09:13 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 165.1 seconds

RetCode: 0

Status:  OK

CheckDir: ALDEx2.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ALDEx2_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ALDEx2.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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 ‘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 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 1.748    0.2  40.753
* 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	0.000	0.000	0.001
aldex	1.748	0.200	40.753
aldex.clr-class	0.132	0.000	0.130
aldex.clr.function-methods	0.052	0.000	0.051
aldex.corr	0	0	0
aldex.effect	2.388	0.004	2.391
aldex.glm	1.988	0.000	1.990
aldex.set.mode	0.040	0.000	0.037
aldex.ttest	0.368	0.000	0.367
getFeatureNames-method	0.036	0.000	0.038
getFeatures-method	0.040	0.000	0.037
getMonteCarloInstances-method	0.04	0.00	0.04
getMonteCarloReplicate-method	0.036	0.004	0.043
getReads-method	0.036	0.000	0.037
getSampleIDs-method	0.036	0.000	0.036
numConditions-method	0.040	0.000	0.037
numFeatures-method	0.036	0.000	0.036
numMCInstances-method	0.040	0.000	0.039
plot.aldex	0	0	0