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This page was generated on 2021-10-15 15:05:39 -0400 (Fri, 15 Oct 2021).

CHECK results for DriverNet on nebbiolo1

To the developers/maintainers of the DriverNet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DriverNet.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 533/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DriverNet 1.32.0  (landing page)
Jiarui Ding
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/DriverNet
git_branch: RELEASE_3_13
git_last_commit: 91602de
git_last_commit_date: 2021-05-19 11:54:51 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DriverNet
Version: 1.32.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DriverNet_1.32.0.tar.gz
StartedAt: 2021-10-14 09:39:26 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:40:41 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 74.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DriverNet.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DriverNet_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/DriverNet.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.32.0’
* 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 (user + system) or elapsed time > 5s
                          user system elapsed
DriverNet-package       27.031  0.056  27.088
computeDrivers          16.159  0.024  16.183
computeRandomizedResult 12.019  0.008  12.028
* 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-3.13-bioc/meat/DriverNet.Rcheck/00check.log’
for details.



Installation output

DriverNet.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DriverNet
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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)

Tests output


Example timings

DriverNet.Rcheck/DriverNet-Ex.timings

nameusersystemelapsed
DriverNet-package27.031 0.05627.088
DriverNetResult-class0.0090.0000.009
actualEvents0.0240.0800.103
computeDrivers16.159 0.02416.183
computeRandomizedResult12.019 0.00812.028
drivers0.0390.0680.107
getPatientOutlierMatrix0.1160.0080.124
preprocessMatrices0.1460.0000.145
resultSummary0.1600.0040.164
sampleDriversList0.0050.0030.009
sampleGeneNames0.020.000.02
sampleInfluenceGraph0.1250.0000.124
samplePatientExpressionMatrix0.0700.0040.074
samplePatientMutationMatrix0.0080.0000.009
samplePatientOutlierMatrix0.0060.0040.010
sampleRandomDriversResult0.0020.0000.001
totalEvents0.0090.0000.009