Package: ScISI

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ScISI_1.24.0.tar.gz

StartedAt: 2011-10-20 17:18:18 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:20:27 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 128.6 seconds

RetCode: 0

Status:  OK

CheckDir: ScISI.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/ScISI.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.24.0'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... OK
* 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
** 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	0.304	0.010	0.315
ScISI2html	0.001	0.000	0.001
arp23	0.003	0.001	0.004
arp23G	0.002	0.000	0.003
arp23Orf	0.002	0.001	0.003
arp23Y2HG	0.002	0.001	0.002
cfia	0.002	0.001	0.003
cfiaOrf	0.002	0.001	0.003
createGODataFrame	0	0	0
createGOMatrix	0	0	0
createMipsMatrix	0	0	0
createYeastDataObj	0.000	0.000	0.001
dataS	0.002	0.000	0.003
eAt	0.003	0.000	0.003
eAt2	0.003	0.001	0.003
egEBI16112	0.002	0.001	0.003
expStats	0.002	0.001	0.003
findSubComp	0.001	0.000	0.000
gavin2mergeMG	0.028	0.002	0.030
getAPMSData	0.502	0.456	0.975
getGOInfo	0	0	0
getMipsInfo	0.000	0.001	0.000
ho2mergeMGG	0.044	0.003	0.048
krogan2mergeMGGH	0.022	0.002	0.023
locScISI	1.065	0.032	1.098
mapping2SysG	0.002	0.001	0.004
mappingsG	0.003	0.001	0.004
maximizeSimilarity	0	0	0
mergeBGMat	0	0	0
mips2go	0.015	0.002	0.016
nAtMap	0.003	0.001	0.004
nonGenes	0.002	0.001	0.003
nucComp	0.003	0.001	0.004
recCompSize	0	0	0
redundantM	0.002	0.001	0.003
runAlignment	0.000	0.001	0.000
runCompareComplex	0	0	0
subCompM	0.002	0.001	0.004
sumStats	0	0	0
unWantedComp	0	0	0
unwanted	0.002	0.001	0.003
xtraGO	0.002	0.001	0.002
yeastData-class	0	0	0