Package: attract

Version: 1.32.0

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_1.32.0.tar.gz

StartedAt: 2018-10-16 19:57:19 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:03:26 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 367.5 seconds

RetCode: 0

Status:  OK

CheckDir: attract.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/attract.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.32.0’
* 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 or elapsed time > 5s
                    user system elapsed
calcFuncSynexprs 109.550  6.394 119.476
findAttractors    64.676  2.217  69.690
findCorrPartners   9.307  0.362  11.857
findSynexprs       7.836  0.073   9.045
plotsynexprs       7.574  0.058   9.597
* 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-3.7-bioc/meat/attract.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL attract
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘attract’ ...
** 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
* DONE (attract)

name	user	system	elapsed
AttractorModuleSet-class	0.001	0.000	0.001
SynExpressionSet-class	0.001	0.000	0.002
attract-package	0.002	0.000	0.002
buildCorMatrix	0.001	0.000	0.002
buildKeggIncidenceMatrix	0.001	0.001	0.002
calcFuncSynexprs	109.550	6.394	119.476
calcInform	0.001	0.000	0.002
calcModfstat	0.001	0.000	0.002
calcRss	0.002	0.001	0.002
exprs.dat	0.180	0.015	0.195
filterDataSet	0.319	0.031	0.353
findAttractors	64.676	2.217	69.690
findCorrPartners	9.307	0.362	11.857
findOnepwaySynexprs	0.002	0.000	0.002
findSynexprs	7.836	0.073	9.045
flagPwayExists	0.002	0.000	0.002
getCustomGenes	0.002	0.000	0.003
getPwayGenes	0.002	0.000	0.002
loring.eset	0.195	0.016	0.212
plotsynexprs	7.574	0.058	9.597
removeFlatGenes	0.124	0.014	0.137
samp.info	0.004	0.002	0.005
subset.loring.eset	0.087	0.007	0.095