BioC 3.4: CHECK report for attract on zin1

Package: attract

Version: 1.25.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings attract_1.25.1.tar.gz

StartedAt: 2016-09-20 03:21:21 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:25:51 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 270.3 seconds

RetCode: 0

Status:  OK

CheckDir: attract.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings attract_1.25.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/attract.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.25.1’
* 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 loading without being on the library search path ... 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'
calcFuncSynexprs : calc.func.onesyngroup: no visible global function
  definition for ‘new’
findAttractors: no visible global function definition for ‘new’
findCorrPartners: no visible global function definition for ‘new’
findOnepwaySynexprs: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
calcFuncSynexprs 64.636  0.428  67.357
findAttractors   52.088  0.496  56.531
findCorrPartners  7.000  0.024   8.442
findSynexprs      6.356  0.016   7.834
plotsynexprs      6.100  0.000   7.750
* 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-3.4-bioc/meat/attract.Rcheck/00check.log’
for details.

* installing *source* package ‘attract’ ...
** R
** data
** inst
** preparing 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	0.000	0.000	0.001
attract-package	0.000	0.000	0.001
buildCorMatrix	0	0	0
buildKeggIncidenceMatrix	0.000	0.000	0.001
calcFuncSynexprs	64.636	0.428	67.357
calcInform	0	0	0
calcModfstat	0.004	0.000	0.001
calcRss	0	0	0
exprs.dat	0.136	0.000	0.134
filterDataSet	0.308	0.000	0.387
findAttractors	52.088	0.496	56.531
findCorrPartners	7.000	0.024	8.442
findOnepwaySynexprs	0.000	0.000	0.001
findSynexprs	6.356	0.016	7.834
flagPwayExists	0	0	0
getCustomGenes	0	0	0
getPwayGenes	0.000	0.000	0.001
loring.eset	0.156	0.000	0.156
plotsynexprs	6.10	0.00	7.75
removeFlatGenes	0.164	0.000	0.162
samp.info	0.004	0.000	0.001
subset.loring.eset	0.068	0.004	0.085