Package: SLGI

Version: 1.10.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.10.0.tar.gz

StartedAt: 2011-04-07 09:08:18 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 09:15:21 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 423.0 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/SLGI.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.10.0’
* 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
  'openVignette()'. 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	0.016	0.004	0.018
AtongFnDomain	7.584	0.064	7.649
AtongPair	0.768	0.008	0.778
SDL	0.004	0.000	0.007
SGA	0.004	0.000	0.007
SGD.SL	0.088	0.000	0.091
TFmat	0.1	0.0	0.1
byComplex	0.628	0.008	0.636
comemberIn	0.86	0.00	0.86
compare	34.230	0.012	34.241
congruence	0.004	0.000	0.003
createSquareMatrix	0.165	0.012	0.176
domainDist	3.752	0.044	3.796
essglist	0.004	0.008	0.011
getFASTAname	5.940	0.048	5.987
getInteraction	0.004	0.000	0.004
getSharedDomains	0.128	0.004	0.179
getSharedInteraction	0.004	0.000	0.002
getTestedPairs	0.012	0.000	0.012
getUniquePairs	0.032	0.000	0.030
gi2005	0.036	0.000	0.037
gi2007	0.092	0.004	0.102
gi2Interactome	0.004	0.000	0.000
hyperG	0.004	0.000	0.005
iSummary	42.591	0.048	42.674
modelSLGI	35.922	0.004	35.926
normInteraction	14.501	0.016	14.537
plot	39.254	0.036	39.332
seqMatcherAlign	0.000	0.000	0.001
sharedBy	3.561	0.028	3.590
sharedInt	0.004	0.000	0.005
siResult-class	43.706	0.008	43.724
test2Interact	0.004	0.000	0.004
topInteraction	23.518	0.004	23.546
twoWayTable	14.237	0.100	14.373
withinComplex	1.388	0.012	1.407