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BioC 3.0: CHECK report for attract on oaxaca

This page was generated on 2015-04-10 10:04:12 -0700 (Fri, 10 Apr 2015).

Package 63/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
attract 1.18.0
Jessica Mar
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/attract
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: attract
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch attract_1.18.0.tar.gz
StartedAt: 2015-04-09 21:31:58 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:36:50 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 292.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: attract.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch attract_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/attract.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.18.0’
* 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 ... [24s/24s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘AnnotationDbi::makeGOGraph’ when loading ‘attract’
See ‘/Users/biocbuild/bbs-3.0-bioc/meat/attract.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘AnnotationDbi’ ‘KEGG.db’ ‘limma’ ‘cluster’ ‘GOstats’ ‘graphics’ ‘methods’ ‘stats’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘GOstats’ ‘KEGG.db’ ‘cluster’ ‘limma’
  Please remove these calls from your code.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/51s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
findCorrPartners 13.106  0.150  13.287
findAttractors   12.493  0.157  12.871
findSynexprs     11.424  0.094  11.564
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/attract.Rcheck/00check.log’
for details.

attract.Rcheck/00install.out:

* installing *source* package ‘attract’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘AnnotationDbi::makeGOGraph’ when loading ‘attract’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘AnnotationDbi::makeGOGraph’ when loading ‘attract’
* DONE (attract)

attract.Rcheck/attract-Ex.timings:

nameusersystemelapsed
AttractorModuleSet-class0.0010.0000.000
SynExpressionSet-class0.0020.0000.003
attract-package0.0010.0000.001
buildCorMatrix0.0010.0000.000
buildKeggIncidenceMatrix0.0010.0000.001
calcFuncSynexprs0.0010.0000.001
calcInform0.0000.0000.001
calcModfstat0.0010.0010.001
calcRss0.0010.0000.001
exprs.dat0.2040.0150.228
findAttractors12.493 0.15712.871
findCorrPartners13.106 0.15013.287
findOnepwaySynexprs0.0010.0000.001
findSynexprs11.424 0.09411.564
flagPwayExists0.0010.0000.000
loring.eset0.2130.0190.233
plotsynexprs0.0010.0000.001
removeFlatGenes0.5000.0280.529
samp.info0.0030.0000.003
subset.loring.eset0.1030.0120.117