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CHECK report for DriverNet on machv2

This page was generated on 2020-10-17 11:58:24 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DriverNet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 505/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DriverNet 1.28.0
Jiarui Ding
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DriverNet
Branch: RELEASE_3_11
Last Commit: 58844c5
Last Changed Date: 2020-04-27 14:32:16 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DriverNet
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DriverNet_1.28.0.tar.gz
StartedAt: 2020-10-17 00:41:44 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:43:29 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 105.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DriverNet.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DriverNet_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DriverNet.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.28.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
DriverNet-package       31.655  0.947  32.659
computeDrivers          19.103  0.604  19.731
computeRandomizedResult 12.814  0.040  12.876
* 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-3.11-bioc/meat/DriverNet.Rcheck/00check.log’
for details.



Installation output

DriverNet.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DriverNet
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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)

Tests output


Example timings

DriverNet.Rcheck/DriverNet-Ex.timings

nameusersystemelapsed
DriverNet-package31.655 0.94732.659
DriverNetResult-class0.0200.0030.024
actualEvents0.1370.1300.266
computeDrivers19.103 0.60419.731
computeRandomizedResult12.814 0.04012.876
drivers0.1310.1140.245
getPatientOutlierMatrix0.2370.0070.244
preprocessMatrices0.2420.0080.251
resultSummary0.3000.0190.319
sampleDriversList0.0200.0030.025
sampleGeneNames0.0350.0020.037
sampleInfluenceGraph0.2170.0050.225
samplePatientExpressionMatrix0.1110.0030.114
samplePatientMutationMatrix0.0140.0020.016
samplePatientOutlierMatrix0.0190.0030.021
sampleRandomDriversResult0.0020.0030.004
totalEvents0.0220.0030.025