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CHECK report for attract on malbec2

This page was generated on 2020-10-17 11:54:23 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE attract PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 98/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.40.0
Samuel Zimmerman
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/attract
Branch: RELEASE_3_11
Last Commit: 9cb8ad2
Last Changed Date: 2020-04-27 14:22:21 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: attract
Version: 1.40.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings attract_1.40.0.tar.gz
StartedAt: 2020-10-16 22:59:57 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:05:32 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 335.6 seconds
RetCode: 0
Status:  OK 
CheckDir: attract.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings attract_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/attract.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.40.0’
* 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 91.117  1.432  95.090
findAttractors   52.758  0.756  55.115
findCorrPartners  8.991  0.088   9.913
plotsynexprs      6.769  0.000   7.610
findSynexprs      6.507  0.008   7.387
* 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-3.11-bioc/meat/attract.Rcheck/00check.log’
for details.



Installation output

attract.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL attract
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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
buildKeggIncidenceMatrix0.0010.0000.000
calcFuncSynexprs91.117 1.43295.090
calcInform0.0000.0000.001
calcModfstat000
calcRss000
exprs.dat0.1140.0040.118
filterDataSet0.2110.0160.228
findAttractors52.758 0.75655.115
findCorrPartners8.9910.0889.913
findOnepwaySynexprs000
findSynexprs6.5070.0087.387
flagPwayExists0.0000.0000.001
getCustomGenes0.0000.0000.001
getPwayGenes0.0000.0000.001
loring.eset0.1750.0040.179
plotsynexprs6.7690.0007.610
removeFlatGenes0.1350.0000.135
samp.info0.0010.0000.001
subset.loring.eset0.0660.0000.066