Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:38 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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

Package 600/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DriverNet 1.42.0  (landing page)
Jiarui Ding
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/DriverNet
git_branch: RELEASE_3_18
git_last_commit: 80a010d
git_last_commit_date: 2023-10-24 09:52:06 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for DriverNet on kunpeng2


To the developers/maintainers of the DriverNet package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: DriverNet
Version: 1.42.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DriverNet_1.42.0.tar.gz
StartedAt: 2023-11-02 10:08:14 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 10:09:47 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 93.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DriverNet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DriverNet_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DriverNet.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DriverNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DriverNet’ version ‘1.42.0’
* 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 loading without being on the library search path ... 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       34.284  0.971  35.626
computeDrivers          20.209  0.040  20.293
computeRandomizedResult 14.573  0.008  14.614
* 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-3.18-bioc/meat/DriverNet.Rcheck/00check.log’
for details.



Installation output

DriverNet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL DriverNet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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-package34.284 0.97135.626
DriverNetResult-class0.0110.0000.013
actualEvents0.0320.0150.048
computeDrivers20.209 0.04020.293
computeRandomizedResult14.573 0.00814.614
drivers0.0240.0240.049
getPatientOutlierMatrix0.2120.0000.213
preprocessMatrices0.1760.0200.196
resultSummary0.2020.0000.203
sampleDriversList0.0110.0000.011
sampleGeneNames0.0210.0000.021
sampleInfluenceGraph0.1420.0030.146
samplePatientExpressionMatrix0.0600.0040.064
samplePatientMutationMatrix0.0060.0040.010
samplePatientOutlierMatrix0.0100.0000.011
sampleRandomDriversResult0.0010.0000.001
totalEvents0.0110.0000.011