Package: attract

Version: 1.34.1

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_1.34.1.tar.gz

StartedAt: 2019-04-15 22:26:54 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:33:30 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 395.8 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_1.34.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/attract.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.34.1’
* 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 118.546  7.130 129.552
findAttractors    67.590  2.335  72.702
findCorrPartners   9.782  0.399  11.976
findSynexprs       8.709  0.116  10.896
plotsynexprs       8.203  0.053  10.312
* 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-3.8-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	0	0
SynExpressionSet-class	0.001	0.000	0.001
attract-package	0.000	0.001	0.001
buildCorMatrix	0.001	0.000	0.000
buildKeggIncidenceMatrix	0	0	0
calcFuncSynexprs	118.546	7.130	129.552
calcInform	0	0	0
calcModfstat	0	0	0
calcRss	0	0	0
exprs.dat	0.188	0.015	0.205
filterDataSet	0.358	0.043	0.402
findAttractors	67.590	2.335	72.702
findCorrPartners	9.782	0.399	11.976
findOnepwaySynexprs	0.000	0.000	0.001
findSynexprs	8.709	0.116	10.896
flagPwayExists	0	0	0
getCustomGenes	0.000	0.001	0.000
getPwayGenes	0.000	0.000	0.001
loring.eset	0.184	0.016	0.200
plotsynexprs	8.203	0.053	10.312
removeFlatGenes	0.161	0.018	0.182
samp.info	0.002	0.002	0.003
subset.loring.eset	0.107	0.010	0.118