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BioC 3.0: CHECK report for ALDEx2 on zin1

This page was generated on 2015-04-10 09:42:37 -0700 (Fri, 10 Apr 2015).

Package 32/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.0.0
Greg Gloor
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ALDEx2
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ALDEx2
Version: 1.0.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ALDEx2_1.0.0.tar.gz
StartedAt: 2015-04-09 21:27:18 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:29:12 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 113.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ALDEx2_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/ALDEx2.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.0.0’
* 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 ... [9s/9s] 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 ... NOTE
'library' or 'require' calls in package code:
  ‘BiocParallel’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aldex.clr.function: no visible global function definition for
  ‘bplapply’
aldex.clr.function: no visible global function definition for
  ‘mclapply’
aldex.clr.function: no visible global function definition for
  ‘detectCores’
aldex.effect: no visible global function definition for ‘mclapply’
aldex.effect: no visible global function definition for ‘detectCores’
aldex.glm: no visible global function definition for ‘mclapply’
aldex.glm: no visible global function definition for ‘detectCores’
* 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 ... [26s/26s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
aldex.glm 11.765   0.02  11.814
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/ALDEx2.Rcheck/00check.log’
for details.

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
aldex3.3360.2523.560
aldex.clr-class0.0880.0000.087
aldex.clr.function-methods0.0880.0000.090
aldex.corr000
aldex.effect3.2080.0283.252
aldex.glm11.765 0.02011.814
aldex.ttest2.2040.0002.208
getFeatureNames-method0.0720.0000.069
getFeatures-method0.0720.0000.072
getMonteCarloInstances-method0.0720.0000.070
getMonteCarloReplicate-method0.0720.0000.071
getReads-method0.0680.0000.068
getSampleIDs-method0.0680.0000.069
numConditions-method0.0720.0040.077
numFeatures-method0.0680.0000.068
numMCInstances-method0.0680.0000.069
plot.aldex000