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BioC 3.6: CHECK report for ALDEx2 on veracruz1

This page was generated on 2017-08-16 13:46:00 -0400 (Wed, 16 Aug 2017).

Package 34/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.9.1
Greg Gloor
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ALDEx2
Last Changed Rev: 129912 / Revision: 131943
Last Changed Date: 2017-05-26 09:55:36 -0400 (Fri, 26 May 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ALDEx2
Version: 1.9.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ALDEx2_1.9.1.tar.gz
StartedAt: 2017-08-15 23:48:21 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:51:26 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 185.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ALDEx2_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ALDEx2.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.9.1’
* 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
* 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

ALDEx2.Rcheck/00install.out:

* 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)

ALDEx2.Rcheck/ALDEx2-Ex.timings:

nameusersystemelapsed
ALDEx2m-package000
aldex1.1410.1091.303
aldex.clr-class0.1500.0030.154
aldex.clr.function-methods0.0640.0040.072
aldex.corr0.0010.0000.001
aldex.effect2.4990.0392.595
aldex.glm2.2980.0182.381
aldex.set.mode0.0580.0020.062
aldex.ttest0.2220.0010.228
getFeatureNames-method0.0520.0010.053
getFeatures-method0.0480.0030.050
getMonteCarloInstances-method0.0540.0020.055
getMonteCarloReplicate-method0.0500.0010.052
getReads-method0.0530.0010.057
getSampleIDs-method0.0550.0020.057
numConditions-method0.0620.0020.072
numFeatures-method0.0550.0010.057
numMCInstances-method0.0580.0020.061
plot.aldex0.0010.0000.001