BioC 3.5: CHECK report for SigCheck on toluca2

Package: SigCheck

Version: 2.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SigCheck_2.7.0.tar.gz

StartedAt: 2017-04-23 09:55:44 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 10:03:57 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 493.1 seconds

RetCode: 0

Status:  OK

CheckDir: SigCheck.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 SigCheck_2.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SigCheck.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SigCheck/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SigCheck’ version ‘2.7.0’
* 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 ‘SigCheck’ 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 ... NOTE
sigCheckKnown: no visible binding for global variable ‘knownSignatures’
Undefined global functions or variables:
  knownSignatures
* 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
Examples with CPU or elapsed time > 5s
                    user system elapsed
sigCheckAll      144.546 14.074 159.920
sigCheckKnown     62.120  6.602  69.229
sigCheck          19.139  1.364  20.661
sigCheckPermuted  18.664  1.481  20.226
sigCheckPlot      18.274  1.506  19.907
sigCheckRandom    13.231  0.966  14.262
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/SigCheck.Rcheck/00check.log’
for details.

* installing *source* package ‘SigCheck’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘MLInterfaces’
Creating a new generic function for ‘signature’ in package ‘SigCheck’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘MLInterfaces’
* DONE (SigCheck)

name	user	system	elapsed
SigCheckObject-class	0.005	0.001	0.005
classifyResults	0.109	0.006	0.115
knownSignatures	0.026	0.002	0.027
nkiResults	0.083	0.013	0.096
sigCheck	19.139	1.364	20.661
sigCheckAll	144.546	14.074	159.920
sigCheckKnown	62.120	6.602	69.229
sigCheckPermuted	18.664	1.481	20.226
sigCheckPlot	18.274	1.506	19.907
sigCheckRandom	13.231	0.966	14.262