BioC 3.1: CHECK report for ALDEx2 on petty

Package: ALDEx2

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ALDEx2_1.0.0.tar.gz

StartedAt: 2015-10-08 21:24:15 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 21:26:55 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 160.6 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ALDEx2.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.0.0’
* 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 ... [11s/11s] 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 ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
aldex.glm 15.658  0.049  15.716
* 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-3.1-bioc/meat/ALDEx2.Rcheck/00check.log’
for details.

* installing *source* package ‘ALDEx2’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (ALDEx2)

name	user	system	elapsed
ALDEx2m-package	0.001	0.000	0.001
aldex	4.395	0.115	4.515
aldex.clr-class	0.115	0.007	0.122
aldex.clr.function-methods	0.098	0.002	0.100
aldex.corr	0.001	0.000	0.001
aldex.effect	4.590	0.011	4.600
aldex.glm	15.658	0.049	15.716
aldex.ttest	3.557	0.013	3.572
getFeatureNames-method	0.122	0.002	0.124
getFeatures-method	0.102	0.002	0.103
getMonteCarloInstances-method	0.094	0.001	0.094
getMonteCarloReplicate-method	0.120	0.002	0.121
getReads-method	0.102	0.001	0.104
getSampleIDs-method	0.130	0.002	0.131
numConditions-method	0.122	0.002	0.124
numFeatures-method	0.115	0.002	0.117
numMCInstances-method	0.111	0.001	0.114
plot.aldex	0	0	0