Package: ScISI

Version: 1.20.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings ScISI_1.20.0.tar.gz

StartedAt: 2010-10-04 19:48:13 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 19:49:38 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 85.7 seconds

RetCode: 0

Status:  OK

CheckDir: ScISI.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/ScISI.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* 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: compareComplex.Rd:45-47: Dropping empty section \examples
prepare_Rd: compBijection.Rd:68-69: 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	0.236	0.000	0.237
ScISI2html	0	0	0
arp23	0.000	0.000	0.003
arp23G	0.000	0.000	0.003
arp23Orf	0.004	0.000	0.002
arp23Y2HG	0.004	0.000	0.002
cfia	0.004	0.000	0.003
cfiaOrf	0.000	0.000	0.002
createGODataFrame	0	0	0
createGOMatrix	0	0	0
createMipsMatrix	0	0	0
createYeastDataObj	0	0	0
dataS	0.000	0.000	0.002
eAt	0.004	0.000	0.002
eAt2	0.000	0.004	0.002
egEBI16112	0.000	0.004	0.002
expStats	0.000	0.000	0.002
findSubComp	0	0	0
gavin2mergeMG	0.012	0.000	0.014
getAPMSData	0.340	0.216	0.589
getGOInfo	0	0	0
getMipsInfo	0	0	0
ho2mergeMGG	0.024	0.000	0.021
krogan2mergeMGGH	0.012	0.000	0.010
locScISI	0.812	0.008	0.820
mapping2SysG	0.000	0.004	0.003
mappingsG	0.004	0.000	0.002
maximizeSimilarity	0.000	0.000	0.001
mergeBGMat	0.000	0.000	0.001
mips2go	0.004	0.004	0.008
nAtMap	0.004	0.000	0.002
nonGenes	0.004	0.000	0.001
nucComp	0.000	0.000	0.002
recCompSize	0.004	0.000	0.000
redundantM	0.000	0.000	0.002
runAlignment	0	0	0
runCompareComplex	0	0	0
subCompM	0.000	0.000	0.002
sumStats	0	0	0
unWantedComp	0	0	0
unwanted	0.004	0.000	0.002
xtraGO	0.000	0.000	0.002
yeastData-class	0	0	0