Package: SLGI

Version: 1.11.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings SLGI_1.11.0.tar.gz

StartedAt: 2011-02-24 21:57:06 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 22:04:34 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 447.9 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/SLGI.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
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	0.03	0.00	0.03
AtongFnDomain	7.41	0.06	7.47
AtongPair	0.81	0.00	0.81
SDL	0	0	0
SGA	0.02	0.00	0.01
SGD.SL	0.11	0.00	0.11
TFmat	0.12	0.02	0.14
byComplex	0.82	0.01	0.84
comemberIn	0.84	0.02	0.96
compare	33.61	0.01	33.65
congruence	0	0	0
createSquareMatrix	0.37	0.02	0.39
domainDist	2.57	0.00	2.57
essglist	0.01	0.00	0.01
getFASTAname	6.27	0.03	6.30
getInteraction	0.01	0.00	0.02
getSharedDomains	0.11	0.00	0.17
getSharedInteraction	0	0	0
getTestedPairs	0.02	0.00	0.01
getUniquePairs	0.03	0.00	0.03
gi2005	0.05	0.02	0.07
gi2007	0.14	0.00	0.14
gi2Interactome	0	0	0
hyperG	0	0	0
iSummary	49.50	5.00	54.51
modelSLGI	38.94	1.68	40.75
normInteraction	15.29	1.97	17.28
plot	41.19	1.78	42.99
seqMatcherAlign	0	0	0
sharedBy	4.92	0.04	4.95
sharedInt	0.02	0.00	0.02
siResult-class	41.25	3.36	44.70
test2Interact	0.01	0.00	0.02
topInteraction	18.67	2.82	21.56
twoWayTable	13.66	0.03	13.69
withinComplex	1.75	0.02	1.76