Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:55 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for DriverNet on machv2


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? 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 542/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DriverNet 1.34.0  (landing page)
Jiarui Ding
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/DriverNet
git_branch: RELEASE_3_14
git_last_commit: a6f3e1e
git_last_commit_date: 2021-10-26 12:05:39 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DriverNet_1.34.0.tar.gz
StartedAt: 2022-04-12 12:48:15 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 12:49:59 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 103.1 seconds
RetCode: 0
Status:   OK  
CheckDir: DriverNet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DriverNet_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/DriverNet.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.34.0’
* 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       31.491  0.779  32.301
computeDrivers          19.088  0.588  19.691
computeRandomizedResult 12.261  0.051  12.326
* 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-3.14-bioc/meat/DriverNet.Rcheck/00check.log’
for details.



Installation output

DriverNet.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DriverNet
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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-package31.491 0.77932.301
DriverNetResult-class0.0170.0020.020
actualEvents0.0820.1150.197
computeDrivers19.088 0.58819.691
computeRandomizedResult12.261 0.05112.326
drivers0.0760.1050.181
getPatientOutlierMatrix0.2280.0070.235
preprocessMatrices0.2490.0060.255
resultSummary0.2900.0170.308
sampleDriversList0.0120.0020.014
sampleGeneNames0.0310.0010.033
sampleInfluenceGraph0.2180.0030.221
samplePatientExpressionMatrix0.1120.0030.115
samplePatientMutationMatrix0.0150.0020.017
samplePatientOutlierMatrix0.0160.0020.018
sampleRandomDriversResult0.0020.0010.003
totalEvents0.0180.0020.021