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: 2011-03-17 17:35:05 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:41:41 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 396.2 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) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 installed package size ... NOTE
  installed size is 25.4Mb
  sub-directories of 1Mb or more:
    data     13.7Mb
    extdata  11.3Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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	0.027	0.002	0.029
AtongFnDomain	5.747	0.083	5.830
AtongPair	0.675	0.024	0.698
SDL	0.007	0.000	0.008
SGA	0.008	0.001	0.009
SGD.SL	0.136	0.003	0.140
TFmat	0.170	0.005	0.175
byComplex	0.933	0.044	0.977
comemberIn	1.041	0.065	1.118
compare	23.829	11.780	35.613
congruence	0.003	0.000	0.004
createSquareMatrix	0.262	0.036	0.298
domainDist	2.625	0.040	2.664
essglist	0.007	0.005	0.011
getFASTAname	6.991	0.058	7.049
getInteraction	0.004	0.000	0.004
getSharedDomains	0.144	0.007	0.182
getSharedInteraction	0.002	0.000	0.002
getTestedPairs	0.013	0.001	0.013
getUniquePairs	0.030	0.001	0.031
gi2005	0.060	0.003	0.062
gi2007	0.188	0.005	0.194
gi2Interactome	0.000	0.001	0.001
hyperG	0.005	0.000	0.006
iSummary	41.255	1.899	43.173
modelSLGI	33.052	9.785	42.839
normInteraction	12.602	4.547	17.150
plot	37.255	10.121	47.378
seqMatcherAlign	0.000	0.000	0.001
sharedBy	4.015	0.027	4.041
sharedInt	0.004	0.000	0.004
siResult-class	32.748	11.208	43.958
test2Interact	0.004	0.000	0.004
topInteraction	17.185	5.027	22.213
twoWayTable	10.218	0.110	10.328
withinComplex	1.189	0.068	1.257