BioC 3.5: CHECK report for attract on oaxaca

Package: attract

Version: 1.27.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings attract_1.27.0.tar.gz

StartedAt: 2017-03-03 23:16:46 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:22:39 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 353.7 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 --no-vignettes --timings attract_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/attract.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.27.0’
* 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 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 79.665  2.694  85.668
findAttractors   72.065  2.494  76.321
findCorrPartners 10.755  0.235  13.396
plotsynexprs      9.424  0.117  12.750
findSynexprs      8.418  0.083  10.562
* 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-3.5-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	0.001	0.000	0.001
SynExpressionSet-class	0.002	0.000	0.002
attract-package	0.001	0.000	0.001
buildCorMatrix	0.000	0.000	0.001
buildKeggIncidenceMatrix	0	0	0
calcFuncSynexprs	79.665	2.694	85.668
calcInform	0.000	0.000	0.001
calcModfstat	0.001	0.000	0.001
calcRss	0.000	0.001	0.000
exprs.dat	0.161	0.012	0.173
filterDataSet	0.353	0.034	0.386
findAttractors	72.065	2.494	76.321
findCorrPartners	10.755	0.235	13.396
findOnepwaySynexprs	0.001	0.000	0.001
findSynexprs	8.418	0.083	10.562
flagPwayExists	0.000	0.000	0.001
getCustomGenes	0.001	0.000	0.000
getPwayGenes	0.001	0.001	0.001
loring.eset	0.189	0.015	0.204
plotsynexprs	9.424	0.117	12.750
removeFlatGenes	0.182	0.036	0.218
samp.info	0.003	0.001	0.003
subset.loring.eset	0.091	0.005	0.096