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This page was generated on 2024-06-28 17:43 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 1034/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iNETgrate 1.2.0  (landing page)
Habil Zare
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/iNETgrate
git_branch: RELEASE_3_19
git_last_commit: cfa5063
git_last_commit_date: 2024-04-30 11:50:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for iNETgrate on merida1

To the developers/maintainers of the iNETgrate package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iNETgrate.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.

raw results


Summary

Package: iNETgrate
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iNETgrate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iNETgrate_1.2.0.tar.gz
StartedAt: 2024-06-27 06:14:59 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 06:44:29 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 1769.0 seconds
RetCode: 0
Status:   OK  
CheckDir: iNETgrate.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iNETgrate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iNETgrate_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/iNETgrate.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iNETgrate’ version ‘1.2.0’
* 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 ‘iNETgrate’ 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 code 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
iNETgrate         212.603  5.147 262.257
toyComputEloci    117.553  3.849 140.036
toyEigengenes      84.123  0.613  96.762
computEigengenes   82.010  0.713 100.711
analyzeSurvival    59.961  1.122  77.041
makeNetwork        51.630  0.321  58.497
computEigenloci    35.305  1.626  44.438
cleanAllData       19.256  1.139  25.251
accelFailAnalysis   7.353  0.748   9.841
distanceToTss       7.242  0.241   8.949
sampleData          2.041  3.142   5.738
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

iNETgrate.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iNETgrate
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘iNETgrate’ ...
** using staged installation
** R
** data
** inst
** 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 (iNETgrate)

Tests output


Example timings

iNETgrate.Rcheck/iNETgrate-Ex.timings

nameusersystemelapsed
accelFailAnalysis7.3530.7489.841
analyzeSurvival59.961 1.12277.041
bestInetgrator0.4220.2351.130
cleanAllData19.256 1.13925.251
computEigengenes 82.010 0.713100.711
computEigenloci35.305 1.62644.438
computeInetgrator0.4360.1190.659
computeUnion2.5840.0643.167
coxAnalysis2.4350.0352.956
createLocusGene0.2880.0140.357
distanceToTss7.2420.2418.949
downloaData0.0000.0000.001
electGenes3.8270.1144.649
filterLowCor1.3380.0421.638
findAliveCutoff0.2600.0170.322
findCore2.4480.0373.010
findTcgaDuplicates0.3930.0170.491
iNETgrate-package0.4200.1130.637
iNETgrate212.603 5.147262.257
inferEigengenes0.4220.1170.611
makeNetwork51.630 0.32158.497
plotKM0.4110.0450.481
plotLociNum0.4440.0320.498
plotLociTss0.0370.0050.045
prepareSurvival0.2970.0170.337
preprocessDnam1.7170.0821.878
sample2pat0.3660.0170.405
sampleData2.0413.1425.738
toyCleanedAml0.2350.0140.279
toyComputEloci117.553 3.849140.036
toyEigengenes84.123 0.61396.762
toyRawAml0.2890.0140.349