Package: SLGI

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.13.0.tar.gz

StartedAt: 2011-06-22 05:26:18 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 05:38:06 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 708.2 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/SLGI.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.13.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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 generic function for "plot" from package "graphics" in package “SLGI”
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘SLGI.Rnw’ 
** testing if installed package can be loaded

* DONE (SLGI)

name	user	system	elapsed
Atong	0.038	0.003	0.040
AtongFnDomain	8.536	0.136	8.800
AtongPair	0.972	0.020	1.003
SDL	0.009	0.002	0.011
SGA	0.011	0.002	0.013
SGD.SL	0.178	0.010	0.188
TFmat	0.239	0.010	0.248
byComplex	1.345	0.098	1.481
comemberIn	1.364	0.115	1.500
compare	38.718	31.328	71.810
congruence	0.005	0.000	0.005
createSquareMatrix	0.374	0.073	0.450
domainDist	4.006	0.065	4.133
essglist	0.025	0.007	0.032
getFASTAname	9.773	0.143	10.118
getInteraction	0.005	0.001	0.006
getSharedDomains	0.189	0.011	0.249
getSharedInteraction	0.004	0.000	0.004
getTestedPairs	0.022	0.001	0.024
getUniquePairs	0.053	0.001	0.055
gi2005	0.093	0.006	0.101
gi2007	0.291	0.014	0.306
gi2Interactome	0.001	0.000	0.001
hyperG	0.007	0.000	0.008
iSummary	55.004	19.025	77.190
modelSLGI	49.925	32.847	87.137
normInteraction	20.445	18.415	41.389
plot	52.899	31.917	87.107
seqMatcherAlign	0.000	0.000	0.001
sharedBy	6.529	0.058	6.725
sharedInt	0.007	0.001	0.007
siResult-class	46.781	31.858	82.202
test2Interact	0.006	0.001	0.007
topInteraction	25.225	18.672	45.208
twoWayTable	14.365	0.285	14.749
withinComplex	1.706	0.130	1.855