Package: DriverNet

Version: 1.24.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DriverNet_1.24.0.tar.gz

StartedAt: 2019-10-16 01:19:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:21:28 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 89.9 seconds

RetCode: 0

Status:  OK

CheckDir: DriverNet.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DriverNet_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DriverNet.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.24.0’
* 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 ... 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DriverNet-package       32.059  0.067  32.181
computeDrivers          19.574  0.060  19.666
computeRandomizedResult 12.573  0.036  12.617
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/DriverNet.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DriverNet
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DriverNet’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DriverNet)

name	user	system	elapsed
DriverNet-package	32.059	0.067	32.181
DriverNetResult-class	0.031	0.016	0.046
actualEvents	0.079	0.036	0.116
computeDrivers	19.574	0.060	19.666
computeRandomizedResult	12.573	0.036	12.617
drivers	0.098	0.024	0.122
getPatientOutlierMatrix	0.210	0.000	0.211
preprocessMatrices	0.211	0.008	0.218
resultSummary	0.247	0.028	0.275
sampleDriversList	0.032	0.016	0.048
sampleGeneNames	0.029	0.004	0.034
sampleInfluenceGraph	0.180	0.004	0.184
samplePatientExpressionMatrix	0.098	0.004	0.101
samplePatientMutationMatrix	0.015	0.000	0.016
samplePatientOutlierMatrix	0.019	0.000	0.019
sampleRandomDriversResult	0.003	0.000	0.003
totalEvents	0.028	0.020	0.048