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CHECK report for attract on malbec1

This page was generated on 2020-08-10 11:34:34 -0400 (Mon, 10 Aug 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 95/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.41.0
Samuel Zimmerman
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/attract
Branch: master
Last Commit: 5d1da58
Last Changed Date: 2020-04-27 14:22:21 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: attract
Version: 1.41.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings attract_1.41.0.tar.gz
StartedAt: 2020-08-09 23:19:46 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 23:25:48 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 362.3 seconds
RetCode: 0
Status:  OK 
CheckDir: attract.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings attract_1.41.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/attract.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.41.0’
* 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 98.484  1.876 101.999
findAttractors   64.868  0.796  67.149
findCorrPartners  7.252  0.044   8.461
plotsynexprs      6.524  0.012   7.368
findSynexprs      5.776  0.008   6.605
* 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-3.12-bioc/meat/attract.Rcheck/00check.log’
for details.



Installation output

attract.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL attract
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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-class0.0040.0000.001
attract-package000
buildCorMatrix000
buildKeggIncidenceMatrix0.0000.0000.001
calcFuncSynexprs 98.484 1.876101.999
calcInform0.0040.0000.001
calcModfstat0.0000.0000.001
calcRss0.0000.0000.001
exprs.dat0.1840.0080.190
filterDataSet0.340.000.34
findAttractors64.868 0.79667.149
findCorrPartners7.2520.0448.461
findOnepwaySynexprs000
findSynexprs5.7760.0086.605
flagPwayExists0.0000.0000.001
getCustomGenes000
getPwayGenes000
loring.eset0.1400.0120.152
plotsynexprs6.5240.0127.368
removeFlatGenes0.1560.0000.157
samp.info0.0040.0000.001
subset.loring.eset0.0960.0000.098