Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1027/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iNETgrate 1.4.0  (landing page)
Habil Zare
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/iNETgrate
git_branch: RELEASE_3_20
git_last_commit: 83bb9a4
git_last_commit_date: 2024-10-29 11:21:42 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for iNETgrate on teran2

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: 1.4.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:iNETgrate.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings iNETgrate_1.4.0.tar.gz
StartedAt: 2024-11-20 04:38:48 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 04:53:36 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 888.0 seconds
RetCode: 0
Status:   OK  
CheckDir: iNETgrate.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:iNETgrate.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings iNETgrate_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/iNETgrate.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iNETgrate’ version ‘1.4.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
iNETgrate         106.151  0.501 106.660
toyEigengenes      67.192  0.060  66.701
computEigengenes   63.124  0.028  63.181
analyzeSurvival    53.013  0.076  52.987
makeNetwork        45.161  0.284  45.463
toyComputEloci     38.832  1.061  39.900
cleanAllData       12.185  0.784  13.022
computEigenloci    11.620  0.543  12.164
accelFailAnalysis   6.404  0.066   6.434
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

iNETgrate.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL iNETgrate
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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
accelFailAnalysis6.4040.0666.434
analyzeSurvival53.013 0.07652.987
bestInetgrator0.1610.0350.401
cleanAllData12.185 0.78413.022
computEigengenes63.124 0.02863.181
computEigenloci11.620 0.54312.164
computeInetgrator0.1710.0230.195
computeUnion1.8900.0031.894
coxAnalysis1.8050.0031.809
createLocusGene0.1390.0030.141
distanceToTss1.9800.0292.010
downloaData000
electGenes2.3080.0012.297
filterLowCor0.4780.0010.479
findAliveCutoff0.1410.0020.143
findCore1.8200.0031.823
findTcgaDuplicates0.1850.0050.190
iNETgrate-package0.1610.0300.190
iNETgrate106.151 0.501106.660
inferEigengenes0.1710.0180.190
makeNetwork45.161 0.28445.463
plotKM0.3140.0030.317
plotLociNum0.2400.0010.242
plotLociTss0.0370.0000.037
prepareSurvival0.1490.0020.151
preprocessDnam0.5360.0080.544
sample2pat0.1650.0020.168
sampleData0.5330.2570.792
toyCleanedAml0.1230.0040.127
toyComputEloci38.832 1.06139.900
toyEigengenes67.192 0.06066.701
toyRawAml0.1470.0040.152