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BioC 3.2: CHECK report for ALDEx2 on perceval

This page was generated on 2015-10-27 17:36:41 -0400 (Tue, 27 Oct 2015).

Package 35/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ALDEx2 1.2.0
Greg Gloor
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ALDEx2
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ALDEx2
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ALDEx2_1.2.0.tar.gz
StartedAt: 2015-10-27 05:18:45 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:21:52 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 187.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ALDEx2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ALDEx2_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ALDEx2.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.0’
* 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 ... [14s/14s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/38s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
aldex.glm 13.700  0.040  13.742
aldex      3.697  0.212   8.148
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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-package0.0000.0000.001
aldex3.6970.2128.148
aldex.clr-class0.1150.0060.121
aldex.clr.function-methods0.1150.0010.116
aldex.corr0.0010.0000.001
aldex.effect4.6320.0064.639
aldex.glm13.700 0.04013.742
aldex.ttest3.2270.0343.263
getFeatureNames-method0.1050.0050.110
getFeatures-method0.1000.0030.103
getMonteCarloInstances-method0.1030.0040.107
getMonteCarloReplicate-method0.0960.0020.098
getReads-method0.1130.0030.116
getSampleIDs-method0.1340.0110.145
numConditions-method0.1100.0030.113
numFeatures-method0.1060.0020.109
numMCInstances-method0.1150.0030.117
plot.aldex0.0000.0000.001