Package: attract

Version: 1.32.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings attract_1.32.0.tar.gz

StartedAt: 2018-10-15 22:34:04 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 22:38:21 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 256.4 seconds

RetCode: 0

Status:  OK

CheckDir: attract.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings attract_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/attract.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.32.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
calcFuncSynexprs 74.560  1.416  77.756
findAttractors   45.264  0.656  47.996
findCorrPartners  5.660  0.036   7.272
findSynexprs      5.156  0.004   7.062
plotsynexprs      4.832  0.000   6.905
* 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-3.7-bioc/meat/attract.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL attract
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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	0.004	0.000	0.001
SynExpressionSet-class	0.004	0.000	0.001
attract-package	0	0	0
buildCorMatrix	0.004	0.000	0.001
buildKeggIncidenceMatrix	0	0	0
calcFuncSynexprs	74.560	1.416	77.756
calcInform	0.004	0.000	0.001
calcModfstat	0.000	0.000	0.001
calcRss	0	0	0
exprs.dat	0.116	0.004	0.120
filterDataSet	0.196	0.012	0.207
findAttractors	45.264	0.656	47.996
findCorrPartners	5.660	0.036	7.272
findOnepwaySynexprs	0.004	0.000	0.001
findSynexprs	5.156	0.004	7.062
flagPwayExists	0.000	0.000	0.001
getCustomGenes	0.000	0.000	0.001
getPwayGenes	0	0	0
loring.eset	0.120	0.004	0.125
plotsynexprs	4.832	0.000	6.905
removeFlatGenes	0.164	0.008	0.176
samp.info	0.000	0.000	0.001
subset.loring.eset	0.080	0.000	0.078