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This page was generated on 2022-01-14 13:07:27 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 machv2


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? here 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 97/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.46.0  (landing page)
Samuel Zimmerman
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/attract
git_branch: RELEASE_3_14
git_last_commit: 8500b7d
git_last_commit_date: 2021-10-26 11:56:18 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: attract
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:attract.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings attract_1.46.0.tar.gz
StartedAt: 2022-01-13 10:14:00 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 10:21:59 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 478.6 seconds
RetCode: 0
Status:   OK  
CheckDir: attract.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:attract.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings attract_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/attract.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.46.0’
* 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 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
calcFuncSynexprs 119.899 18.895 141.142
findAttractors    75.096  2.561  79.454
findCorrPartners   9.885  0.208  11.839
findSynexprs       9.144  0.047  10.909
plotsynexprs       9.131  0.047  10.982
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/attract.Rcheck/00check.log’
for details.



Installation output

attract.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-package0.0000.0000.001
buildCorMatrix0.0000.0010.001
buildKeggIncidenceMatrix000
calcFuncSynexprs119.899 18.895141.142
calcInform0.0010.0010.000
calcModfstat0.0000.0010.001
calcRss0.0000.0010.001
exprs.dat0.1820.0050.188
filterDataSet0.4310.0260.457
findAttractors75.096 2.56179.454
findCorrPartners 9.885 0.20811.839
findOnepwaySynexprs0.0000.0010.000
findSynexprs 9.144 0.04710.909
flagPwayExists000
getCustomGenes0.0000.0000.001
getPwayGenes0.0000.0000.001
loring.eset0.2170.0050.223
plotsynexprs 9.131 0.04710.982
removeFlatGenes0.1900.0040.195
samp.info0.0020.0020.003
subset.loring.eset0.1190.0040.123