Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for attract on merida1

This page was generated on 2020-08-10 12:32:02 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:attract.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings attract_1.41.0.tar.gz
StartedAt: 2020-08-09 23:14:49 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 23:22:01 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 431.8 seconds
RetCode: 0
Status:  OK 
CheckDir: attract.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:attract.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings attract_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/attract.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.41.0’
* 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 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 114.085 11.274 127.109
findAttractors    69.105  2.167  72.390
findCorrPartners   8.913  0.165  10.236
findSynexprs       8.560  0.051   9.433
plotsynexprs       7.784  0.105   8.711
* 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-3.12-bioc/meat/attract.Rcheck/00check.log’
for details.



Installation output

attract.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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-class0.0000.0000.001
SynExpressionSet-class0.0010.0010.001
attract-package0.0000.0000.001
buildCorMatrix0.0000.0000.001
buildKeggIncidenceMatrix0.0010.0000.001
calcFuncSynexprs114.085 11.274127.109
calcInform000
calcModfstat0.0010.0010.001
calcRss0.0000.0010.001
exprs.dat0.2130.0120.227
filterDataSet0.3600.0180.378
findAttractors69.105 2.16772.390
findCorrPartners 8.913 0.16510.236
findOnepwaySynexprs0.0000.0000.001
findSynexprs8.5600.0519.433
flagPwayExists0.0000.0000.001
getCustomGenes0.0010.0010.001
getPwayGenes0.0000.0010.000
loring.eset0.2000.0050.205
plotsynexprs7.7840.1058.711
removeFlatGenes0.1940.0130.207
samp.info0.0020.0020.003
subset.loring.eset0.1010.0030.104