Package: ScISI

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings ScISI_1.20.0.tar.gz

StartedAt: 2010-10-04 18:40:56 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:42:55 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 118.8 seconds

RetCode: 0

Status:  OK

CheckDir: ScISI.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/ScISI.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ScISI/DESCRIPTION' ... OK
* this is package 'ScISI' version '1.20.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ScISI' can be installed ... OK
* 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 ... NOTE
checkComplex: no visible binding for global variable ‘ScISI’
getAPMSData: no visible binding for global variable ‘yNameTAP’
getAPMSData: no visible binding for global variable ‘MBMEcHMSPCI’
getAPMSData: no visible binding for global variable ‘MBMEcKrogan’
getGOInfo: no visible binding for global variable ‘xtraGO’
getGOInfo: no visible binding for global variable ‘unwanted’
getMipsInfo: no visible binding for global variable ‘nonGenes’
* checking Rd files ... NOTE
prepare_Rd: arp23Orf.Rd:14-15: Dropping empty section \details
prepare_Rd: calcGraphStats.Rd:63: Dropping empty section \references
prepare_Rd: calcGraphStats.Rd:66-70: Dropping empty section \examples
prepare_Rd: checkComplex.Rd:47-48: Dropping empty section \examples
prepare_Rd: checkSGN.Rd:24-25: Dropping empty section \note
prepare_Rd: checkSGN.Rd:26-28: Dropping empty section \examples
prepare_Rd: compBijection.Rd:68-69: Dropping empty section \examples
prepare_Rd: compareComplex.Rd:45-47: Dropping empty section \examples
prepare_Rd: createMipsDataFrame.Rd:35-37: Dropping empty section \examples
prepare_Rd: edgeProp.Rd:25-27: Dropping empty section \details
prepare_Rd: edgeProp.Rd:37-39: Dropping empty section \examples
prepare_Rd: getLocOrfs.Rd:60-61: Dropping empty section \examples
prepare_Rd: graphSumStats.Rd:20-22: Dropping empty section \details
prepare_Rd: graphSumStats.Rd:47-49: Dropping empty section \examples
prepare_Rd: meanDeg.Rd:21-23: Dropping empty section \details
prepare_Rd: meanDeg.Rd:28-29: Dropping empty section \examples
prepare_Rd: rmByEvi.Rd:40-42: Dropping empty section \examples
prepare_Rd: runCompareComplex.Rd:23-25: Dropping empty section \details
prepare_Rd: subCompM.Rd:16-18: Dropping empty section \details
prepare_Rd: sumStats.Rd:24-26: Dropping empty section \details
prepare_Rd: xtraGONodes.Rd:25-27: Dropping empty section \examples
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package ‘ScISI’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
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

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ScISI)

name	user	system	elapsed
JaccardCoef	0	0	0
ScISI	0.290	0.009	0.299
ScISI2html	0.001	0.000	0.000
arp23	0.003	0.001	0.004
arp23G	0.003	0.001	0.004
arp23Orf	0.003	0.001	0.003
arp23Y2HG	0.003	0.001	0.004
cfia	0.003	0.001	0.003
cfiaOrf	0.002	0.001	0.003
createGODataFrame	0.000	0.001	0.001
createGOMatrix	0	0	0
createMipsMatrix	0.000	0.000	0.001
createYeastDataObj	0.001	0.000	0.001
dataS	0.003	0.001	0.003
eAt	0.003	0.001	0.004
eAt2	0.003	0.001	0.002
egEBI16112	0.002	0.001	0.003
expStats	0.002	0.001	0.003
findSubComp	0.000	0.000	0.001
gavin2mergeMG	0.027	0.002	0.029
getAPMSData	0.714	0.473	1.202
getGOInfo	0.001	0.000	0.001
getMipsInfo	0.001	0.000	0.001
ho2mergeMGG	0.043	0.003	0.046
krogan2mergeMGGH	0.021	0.002	0.023
locScISI	1.040	0.035	1.087
mapping2SysG	0.003	0.000	0.003
mappingsG	0.003	0.000	0.003
maximizeSimilarity	0.000	0.000	0.001
mergeBGMat	0.001	0.000	0.000
mips2go	0.014	0.001	0.015
nAtMap	0.002	0.001	0.003
nonGenes	0.002	0.001	0.007
nucComp	0.002	0.001	0.004
recCompSize	0.000	0.001	0.000
redundantM	0.002	0.001	0.003
runAlignment	0.000	0.000	0.001
runCompareComplex	0.000	0.001	0.000
subCompM	0.002	0.001	0.003
sumStats	0.000	0.000	0.001
unWantedComp	0.000	0.001	0.001
unwanted	0.002	0.000	0.003
xtraGO	0.002	0.000	0.002
yeastData-class	0.001	0.000	0.001