Package: SLGI

Version: 1.13.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch SLGI_1.13.0.tar.gz

StartedAt: 2011-07-07 06:21:43 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 06:28:55 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 432.1 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/SLGI.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* 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 '1.13.0'
* 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 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

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 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
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.

* DONE (SLGI)

name	user	system	elapsed
Atong	0.04	0.00	0.03
AtongFnDomain	7.31	0.05	7.36
AtongPair	0.78	0.00	0.78
SDL	0	0	0
SGA	0.01	0.00	0.02
SGD.SL	0.11	0.00	0.11
TFmat	0.13	0.01	0.14
byComplex	0.87	0.00	0.87
comemberIn	0.86	0.00	0.86
compare	35.03	0.02	35.07
congruence	0	0	0
createSquareMatrix	0.33	0.01	0.34
domainDist	2.58	0.03	2.61
essglist	0.02	0.00	0.02
getFASTAname	6.54	0.10	6.65
getInteraction	0	0	0
getSharedDomains	0.16	0.01	0.22
getSharedInteraction	0	0	0
getTestedPairs	0.03	0.00	0.03
getUniquePairs	0.03	0.00	0.03
gi2005	0.05	0.00	0.05
gi2007	0.14	0.00	0.14
gi2Interactome	0	0	0
hyperG	0.02	0.00	0.02
iSummary	43.42	1.75	45.17
modelSLGI	38.59	3.85	42.47
normInteraction	16.59	3.01	19.62
plot	43.61	2.89	46.52
seqMatcherAlign	0	0	0
sharedBy	5.71	0.02	5.72
sharedInt	0	0	0
siResult-class	42.59	5.12	47.81
test2Interact	0	0	0
topInteraction	22.92	3.77	26.78
twoWayTable	16.36	0.06	16.42
withinComplex	1.94	0.03	1.97