Package: SLGI

Version: 1.11.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.11.0.tar.gz

StartedAt: 2011-02-24 22:49:47 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 22:56:56 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 428.2 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/SLGI.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.11.0’
* 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	0.020	0.000	0.019
AtongFnDomain	7.732	0.068	7.801
AtongPair	0.756	0.008	0.765
SDL	0.004	0.000	0.007
SGA	0.004	0.000	0.007
SGD.SL	0.092	0.000	0.093
TFmat	0.096	0.004	0.101
byComplex	0.66	0.00	0.66
comemberIn	0.916	0.008	0.925
compare	36.855	0.016	36.879
congruence	0.000	0.000	0.003
createSquareMatrix	0.356	0.008	0.366
domainDist	2.304	0.032	2.336
essglist	0.004	0.008	0.011
getFASTAname	5.988	0.028	6.016
getInteraction	0.000	0.004	0.003
getSharedDomains	0.116	0.000	0.134
getSharedInteraction	0.004	0.000	0.002
getTestedPairs	0.012	0.000	0.012
getUniquePairs	0.024	0.004	0.029
gi2005	0.036	0.000	0.039
gi2007	0.100	0.004	0.104
gi2Interactome	0.000	0.000	0.001
hyperG	0.008	0.000	0.005
iSummary	46.735	0.088	46.982
modelSLGI	39.467	0.008	39.485
normInteraction	17.441	0.004	17.444
plot	42.874	0.012	42.892
seqMatcherAlign	0	0	0
sharedBy	4.841	0.028	4.868
sharedInt	0.004	0.000	0.005
siResult-class	40.366	0.012	40.395
test2Interact	0.004	0.000	0.004
topInteraction	21.262	0.012	21.287
twoWayTable	14.136	0.096	14.243
withinComplex	1.289	0.008	1.299