Package: SLGI

Version: 1.13.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.13.0.tar.gz

StartedAt: 2011-05-09 14:18:01 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:25:41 -0700 (Mon, 09 May 2011)

EllapsedTime: 459.4 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/SLGI.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.13.0’
* 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:
    extdata  11.3Mb
    data     13.8Mb
* 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 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	0.024	0.000	0.025
AtongFnDomain	8.936	0.088	9.167
AtongPair	0.864	0.008	0.893
SDL	0.008	0.000	0.007
SGA	0.008	0.000	0.011
SGD.SL	0.088	0.012	0.104
TFmat	0.100	0.008	0.123
byComplex	0.692	0.068	0.767
comemberIn	0.912	0.060	1.026
compare	44.039	0.016	44.717
congruence	0.004	0.000	0.005
createSquareMatrix	0.436	0.036	0.495
domainDist	2.120	0.004	2.202
essglist	0.008	0.004	0.015
getFASTAname	8.329	0.060	8.551
getInteraction	0.004	0.000	0.004
getSharedDomains	0.148	0.008	0.169
getSharedInteraction	0.004	0.000	0.002
getTestedPairs	0.016	0.000	0.016
getUniquePairs	0.040	0.000	0.038
gi2005	0.044	0.004	0.045
gi2007	0.128	0.004	0.151
gi2Interactome	0.000	0.000	0.001
hyperG	0.004	0.004	0.007
iSummary	55.779	0.236	58.581
modelSLGI	47.115	0.092	47.852
normInteraction	19.442	0.000	19.446
plot	49.415	0.008	49.553
seqMatcherAlign	0.004	0.000	0.000
sharedBy	5.888	0.008	5.895
sharedInt	0.004	0.000	0.006
siResult-class	44.507	0.012	44.622
test2Interact	0.004	0.000	0.004
topInteraction	23.749	0.012	23.839
twoWayTable	15.393	0.112	15.516
withinComplex	1.380	0.016	1.396