Package: SLGI

Version: 1.8.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.8.0.tar.gz

StartedAt: 2010-10-04 19:56:06 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 20:03:44 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 458.0 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/SLGI.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SLGI/DESCRIPTION' ... OK
* this is package 'SLGI' version '1.8.0'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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	0.020	0.000	0.021
AtongFnDomain	7.636	0.112	7.750
AtongPair	0.764	0.016	0.785
SDL	0.000	0.008	0.007
SGA	0.008	0.000	0.008
SGD.SL	0.096	0.000	0.097
TFmat	0.104	0.004	0.110
byComplex	0.708	0.032	0.742
comemberIn	0.824	0.032	0.856
compare	37.775	0.032	37.823
congruence	0.000	0.000	0.003
createSquareMatrix	0.456	0.028	0.486
domainDist	2.552	0.024	2.577
essglist	0.004	0.004	0.009
getFASTAname	5.876	0.016	5.891
getInteraction	0.004	0.000	0.003
getSharedDomains	0.144	0.000	0.175
getSharedInteraction	0.000	0.000	0.002
getTestedPairs	0.012	0.000	0.012
getUniquePairs	0.032	0.000	0.032
gi2005	0.040	0.000	0.041
gi2007	0.104	0.008	0.112
gi2Interactome	0.000	0.000	0.001
hyperG	0.008	0.000	0.005
iSummary	56.224	0.200	56.427
modelSLGI	38.814	0.080	39.059
normInteraction	16.229	0.016	16.244
plot	41.319	0.104	42.264
seqMatcherAlign	0.000	0.000	0.001
sharedBy	4.868	0.012	4.880
sharedInt	0.004	0.000	0.006
siResult-class	44.619	0.092	44.919
test2Interact	0.004	0.000	0.004
topInteraction	24.253	0.096	24.454
twoWayTable	15.277	0.144	15.430
withinComplex	1.337	0.004	1.339