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BioC 3.5: CHECK report for attract on oaxaca

This page was generated on 2017-03-04 16:39:29 -0500 (Sat, 04 Mar 2017).

Package 74/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.27.0
Samuel Zimmerman
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/attract
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

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

Command output

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


* 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.


attract.Rcheck/00install.out:

* 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)

attract.Rcheck/attract-Ex.timings:

nameusersystemelapsed
AttractorModuleSet-class0.0010.0000.001
SynExpressionSet-class0.0020.0000.002
attract-package0.0010.0000.001
buildCorMatrix0.0000.0000.001
buildKeggIncidenceMatrix000
calcFuncSynexprs79.665 2.69485.668
calcInform0.0000.0000.001
calcModfstat0.0010.0000.001
calcRss0.0000.0010.000
exprs.dat0.1610.0120.173
filterDataSet0.3530.0340.386
findAttractors72.065 2.49476.321
findCorrPartners10.755 0.23513.396
findOnepwaySynexprs0.0010.0000.001
findSynexprs 8.418 0.08310.562
flagPwayExists0.0000.0000.001
getCustomGenes0.0010.0000.000
getPwayGenes0.0010.0010.001
loring.eset0.1890.0150.204
plotsynexprs 9.424 0.11712.750
removeFlatGenes0.1820.0360.218
samp.info0.0030.0010.003
subset.loring.eset0.0910.0050.096