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: 2011-05-09 17:07:09 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 17:19:06 -0700 (Mon, 09 May 2011)

EllapsedTime: 717.0 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) (2011-04-24 r55634)
* 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 new generic function for "plot" in "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	0.041
AtongFnDomain	8.962	0.142	9.188
AtongPair	0.979	0.025	1.019
SDL	0.010	0.001	0.011
SGA	0.012	0.003	0.015
SGD.SL	0.185	0.015	0.200
TFmat	0.236	0.011	0.251
byComplex	1.313	0.104	1.431
comemberIn	1.381	0.119	1.531
compare	38.932	31.630	72.114
congruence	0.005	0.000	0.005
createSquareMatrix	0.490	0.079	0.601
domainDist	4.235	0.062	4.373
essglist	0.025	0.007	0.032
getFASTAname	9.660	0.148	9.968
getInteraction	0.006	0.000	0.006
getSharedDomains	0.209	0.011	0.273
getSharedInteraction	0.003	0.001	0.003
getTestedPairs	0.018	0.001	0.019
getUniquePairs	0.042	0.002	0.044
gi2005	0.092	0.005	0.102
gi2007	0.294	0.013	0.309
gi2Interactome	0.002	0.001	0.002
hyperG	0.007	0.000	0.007
iSummary	55.841	19.170	76.052
modelSLGI	49.118	32.852	89.339
normInteraction	21.061	18.867	42.766
plot	52.657	31.896	87.098
seqMatcherAlign	0.000	0.001	0.001
sharedBy	6.048	0.064	6.152
sharedInt	0.007	0.000	0.008
siResult-class	50.350	31.921	85.357
test2Interact	0.006	0.001	0.007
topInteraction	27.163	18.854	47.784
twoWayTable	14.363	0.263	14.715
withinComplex	1.697	0.130	1.837