Package: ScISI

Version: 1.25.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ScISI_1.25.0.tar.gz

StartedAt: 2011-07-07 05:42:05 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:44:44 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 159.3 seconds

RetCode: 0

Status:  OK

CheckDir: ScISI.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ScISI.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ScISI/DESCRIPTION' ... OK
* this is package 'ScISI' version '1.25.0'
* 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 installed package size ... 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 for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                       old_size new_size compress
  ScISI.rda                34Kb     13Kb    bzip2
  ScISIC.rda               18Kb      8Kb    bzip2
  ScISIverified.rda        11Kb      8Kb    bzip2
  gavin2mergeMG.rda        12Kb      7Kb    bzip2
  ho2mergeMGG.rda          15Kb      9Kb    bzip2
  krogan2mergeMGGH.rda     11Kb      7Kb    bzip2
  locScISI.rda             82Kb     27Kb    bzip2
* 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 '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
  'browseVignettes()'. 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 ...
*** tangling vignette sources ...
   'vignette.Rnw' 
** testing if installed package can be loaded

* DONE (ScISI)

name	user	system	elapsed
JaccardCoef	0.001	0.001	0.001
ScISI	0.305	0.009	0.315
ScISI2html	0.000	0.001	0.000
arp23	0.003	0.001	0.005
arp23G	0.003	0.001	0.003
arp23Orf	0.002	0.000	0.004
arp23Y2HG	0.002	0.001	0.004
cfia	0.002	0.001	0.004
cfiaOrf	0.002	0.001	0.003
createGODataFrame	0	0	0
createGOMatrix	0	0	0
createMipsMatrix	0	0	0
createYeastDataObj	0	0	0
dataS	0.003	0.001	0.004
eAt	0.003	0.001	0.004
eAt2	0.003	0.001	0.004
egEBI16112	0.003	0.000	0.004
expStats	0.002	0.001	0.003
findSubComp	0	0	0
gavin2mergeMG	0.029	0.003	0.031
getAPMSData	0.524	0.471	1.077
getGOInfo	0	0	0
getMipsInfo	0.000	0.000	0.001
ho2mergeMGG	0.044	0.002	0.047
krogan2mergeMGGH	0.022	0.001	0.023
locScISI	1.084	0.032	1.117
mapping2SysG	0.003	0.001	0.003
mappingsG	0.003	0.001	0.003
maximizeSimilarity	0	0	0
mergeBGMat	0	0	0
mips2go	0.015	0.002	0.015
nAtMap	0.002	0.001	0.003
nonGenes	0.003	0.001	0.003
nucComp	0.003	0.001	0.004
recCompSize	0.000	0.000	0.001
redundantM	0.003	0.001	0.004
runAlignment	0.001	0.001	0.001
runCompareComplex	0	0	0
subCompM	0.003	0.001	0.003
sumStats	0.000	0.001	0.000
unWantedComp	0	0	0
unwanted	0.002	0.001	0.004
xtraGO	0.003	0.001	0.003
yeastData-class	0	0	0