BioC 3.3: CHECK report for DriverNet on morelia

Package: DriverNet

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DriverNet_1.11.0.tar.gz

StartedAt: 2016-04-21 01:48:45 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 01:50:09 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 83.1 seconds

RetCode: 0

Status:  OK

CheckDir: DriverNet.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 DriverNet_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/DriverNet.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DriverNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DriverNet’ version ‘1.11.0’
* 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 ‘DriverNet’ can be installed ... [1s/1s] 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
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.computeDriversHelper: no visible global function definition for ‘new’
getPatientOutlierMatrix: no visible binding for global variable ‘sd’
getPatientOutlierMatrix: no visible global function definition for
  ‘dnorm’
resultSummary: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dnorm new sd write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... [57s/61s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DriverNet-package       26.275  1.077  28.388
computeDrivers          17.128  1.135  18.858
computeRandomizedResult  9.394  0.054  11.954
* 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-3.3-bioc/meat/DriverNet.Rcheck/00check.log’
for details.

* installing *source* package ‘DriverNet’ ...
** 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 (DriverNet)

name	user	system	elapsed
DriverNet-package	26.275	1.077	28.388
DriverNetResult-class	0.021	0.002	0.023
actualEvents	0.114	0.036	0.151
computeDrivers	17.128	1.135	18.858
computeRandomizedResult	9.394	0.054	11.954
drivers	0.112	0.037	0.169
getPatientOutlierMatrix	0.225	0.018	0.279
preprocessMatrices	0.197	0.005	0.229
resultSummary	0.234	0.007	0.271
sampleDriversList	0.023	0.002	0.027
sampleGeneNames	0.031	0.007	0.043
sampleInfluenceGraph	0.163	0.005	0.193
samplePatientExpressionMatrix	0.098	0.010	0.125
samplePatientMutationMatrix	0.012	0.002	0.015
samplePatientOutlierMatrix	0.021	0.006	0.030
sampleRandomDriversResult	0.003	0.003	0.005
totalEvents	0.022	0.002	0.029