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This page was generated on 2023-01-02 09:00:27 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the DriverNet package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 561/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DriverNet 1.39.0  (landing page)
Jiarui Ding
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/DriverNet
git_branch: master
git_last_commit: 63fb167
git_last_commit_date: 2022-11-01 11:07:39 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: DriverNet
Version: 1.39.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DriverNet.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DriverNet_1.39.0.tar.gz
StartedAt: 2022-12-28 23:25:43 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 23:26:51 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 67.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DriverNet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DriverNet.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DriverNet_1.39.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DriverNet.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DriverNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DriverNet' version '1.39.0'
* 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 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       18.10   0.80   18.90
computeDrivers          10.45   0.21   10.66
computeRandomizedResult  7.91   0.06    7.97
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DriverNet.Rcheck/00check.log'
for details.



Installation output

DriverNet.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL DriverNet
###
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* installing to library 'F:/biocbuild/bbs-3.17-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-package18.1 0.818.9
DriverNetResult-class0.040.030.07
actualEvents0.050.090.14
computeDrivers10.45 0.2110.66
computeRandomizedResult7.910.067.97
drivers0.060.110.17
getPatientOutlierMatrix0.110.000.11
preprocessMatrices0.110.050.15
resultSummary0.160.070.24
sampleDriversList0.000.070.06
sampleGeneNames0.010.000.02
sampleInfluenceGraph0.090.010.11
samplePatientExpressionMatrix0.070.000.06
samplePatientMutationMatrix0.010.000.01
samplePatientOutlierMatrix0.000.020.02
sampleRandomDriversResult0.000.010.02
totalEvents0.020.070.07