Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-12 11:04:40 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4167
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 attract on nebbiolo2


To the developers/maintainers of the attract package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/attract.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 96/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.49.0  (landing page)
Samuel Zimmerman
Snapshot Date: 2022-08-11 14:00:04 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/attract
git_branch: master
git_last_commit: 01ae39e
git_last_commit_date: 2022-04-26 11:05:09 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: attract
Version: 1.49.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings attract_1.49.0.tar.gz
StartedAt: 2022-08-11 18:57:29 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 19:02:01 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 272.3 seconds
RetCode: 0
Status:   OK  
CheckDir: attract.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings attract_1.49.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/attract.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘attract/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘attract’ version ‘1.49.0’
* 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 ‘attract’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels):
  partial argument match of 'lab' to 'labels'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'n' to 'number'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'adjust' to 'adjust.method'
* 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
calcFuncSynexprs 64.852  2.528  69.683
findAttractors   38.123  1.136  41.567
findCorrPartners  4.664  0.104   6.725
findSynexprs      4.149  0.212   5.763
plotsynexprs      4.009  0.236   5.438
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/attract.Rcheck/00check.log’
for details.



Installation output

attract.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL attract
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘attract’ ...
** 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 (attract)

Tests output


Example timings

attract.Rcheck/attract-Ex.timings

nameusersystemelapsed
AttractorModuleSet-class000
SynExpressionSet-class0.0010.0000.001
attract-package000
buildCorMatrix000
buildKeggIncidenceMatrix000
calcFuncSynexprs64.852 2.52869.683
calcInform000
calcModfstat000
calcRss0.0010.0000.000
exprs.dat0.1230.0080.131
filterDataSet0.2280.0040.232
findAttractors38.123 1.13641.567
findCorrPartners4.6640.1046.725
findOnepwaySynexprs000
findSynexprs4.1490.2125.763
flagPwayExists000
getCustomGenes000
getPwayGenes000
loring.eset0.1240.0120.136
plotsynexprs4.0090.2365.438
removeFlatGenes0.1640.0240.187
samp.info0.0010.0000.001
subset.loring.eset0.0730.0000.074