BioC 3.6: CHECK report for SigCheck on malbec1

Package: SigCheck

Version: 2.9.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SigCheck_2.9.0.tar.gz

StartedAt: 2017-08-16 02:24:58 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:30:23 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 324.4 seconds

RetCode: 0

Status:  OK

CheckDir: SigCheck.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SigCheck_2.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SigCheck.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘2.9.0’
* 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 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      96.548  1.012  97.611
sigCheckKnown    46.608  0.256  46.890
sigCheckPermuted 12.736  0.080  12.821
sigCheck         12.392  0.216  12.626
sigCheckPlot     11.824  0.132  11.970
sigCheckRandom    8.480  0.072   8.563
* 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
  ‘/home/biocbuild/bbs-3.6-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	0.004	0.000	0.003
classifyResults	0.072	0.000	0.075
knownSignatures	0.024	0.000	0.023
nkiResults	0.056	0.000	0.055
sigCheck	12.392	0.216	12.626
sigCheckAll	96.548	1.012	97.611
sigCheckKnown	46.608	0.256	46.890
sigCheckPermuted	12.736	0.080	12.821
sigCheckPlot	11.824	0.132	11.970
sigCheckRandom	8.480	0.072	8.563