BioC 3.2: CHECK report for attract on linux1.bioconductor.org

Package: attract

Version: 1.22.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings attract_1.22.0.tar.gz

StartedAt: 2015-10-27 01:10:14 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:12:47 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 152.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: attract.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings attract_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/attract.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.22.0’
* 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 ... [13s/13s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘AnnotationDbi::makeGOGraph’ when loading ‘attract’
See ‘/home/biocbuild/bbs-3.2-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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
findAttractors   8.290  0.071   8.367
findCorrPartners 8.170  0.032   8.204
findSynexprs     5.714  0.008   5.723
* 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 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/attract.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
AttractorModuleSet-class	0	0	0
SynExpressionSet-class	0.001	0.000	0.001
attract-package	0.001	0.000	0.001
buildCorMatrix	0.001	0.000	0.001
buildKeggIncidenceMatrix	0.001	0.000	0.001
calcFuncSynexprs	0.001	0.000	0.001
calcInform	0.001	0.000	0.001
calcModfstat	0.001	0.000	0.001
calcRss	0.001	0.000	0.001
exprs.dat	0.203	0.004	0.207
findAttractors	8.290	0.071	8.367
findCorrPartners	8.170	0.032	8.204
findOnepwaySynexprs	0	0	0
findSynexprs	5.714	0.008	5.723
flagPwayExists	0	0	0
loring.eset	0.119	0.000	0.119
plotsynexprs	0	0	0
removeFlatGenes	0.15	0.00	0.15
samp.info	0.001	0.000	0.002
subset.loring.eset	0.059	0.008	0.068