Package: SLGI

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.11.0.tar.gz

StartedAt: 2011-02-24 21:27:56 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:40:08 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 731.8 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/SLGI.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.11.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘SLGI’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 ... OK
* 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 ... NOTE
'library' or 'require' call not declared from: YEAST
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: RpsiXML
Loading required package: annotate
Loading required package: graph
Loading required package: RBGL
Loading required package: XML

Attaching package: 'XML'

The following object(s) are masked from 'package:graph':

    addNode

Loading required package: hypergraph

Attaching package: 'hypergraph'

The following object(s) are masked from 'package:AnnotationDbi':

    head, tail

The following object(s) are masked from 'package:utils':

    head, tail

Loading required package: apComplex
Creating a new generic function for "plot" in "SLGI"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (SLGI)

name	user	system	elapsed
Atong	0.038	0.003	0.042
AtongFnDomain	8.920	0.146	9.128
AtongPair	0.964	0.025	0.999
SDL	0.010	0.001	0.011
SGA	0.012	0.001	0.012
SGD.SL	0.174	0.006	0.181
TFmat	0.234	0.011	0.246
byComplex	1.261	0.103	1.401
comemberIn	1.394	0.121	1.537
compare	40.383	32.822	74.124
congruence	0.005	0.001	0.005
createSquareMatrix	0.391	0.078	0.473
domainDist	3.865	0.063	3.947
essglist	0.025	0.007	0.032
getFASTAname	8.297	0.075	8.409
getInteraction	0.006	0.000	0.006
getSharedDomains	0.214	0.014	0.266
getSharedInteraction	0.003	0.000	0.003
getTestedPairs	0.019	0.001	0.021
getUniquePairs	0.049	0.002	0.052
gi2005	0.093	0.007	0.101
gi2007	0.291	0.015	0.307
gi2Interactome	0.002	0.001	0.003
hyperG	0.007	0.000	0.008
iSummary	54.158	19.651	74.985
modelSLGI	49.458	34.180	85.187
normInteraction	19.906	18.305	39.043
plot	51.906	33.493	86.720
seqMatcherAlign	0.001	0.000	0.001
sharedBy	5.453	0.067	5.570
sharedInt	0.006	0.000	0.007
siResult-class	49.764	31.783	83.022
test2Interact	0.007	0.000	0.006
topInteraction	27.654	18.725	47.410
twoWayTable	14.319	0.233	14.899
withinComplex	1.622	0.113	1.810