Package: ScISI

Version: 1.24.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings ScISI_1.24.0.tar.gz

StartedAt: 2011-10-20 14:27:42 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:29:09 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 87.1 seconds

RetCode: 0

Status:  OK

CheckDir: ScISI.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/ScISI.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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	0.212	0.008	0.218
ScISI2html	0.000	0.000	0.001
arp23	0.000	0.004	0.003
arp23G	0.000	0.004	0.002
arp23Orf	0.000	0.004	0.002
arp23Y2HG	0.000	0.000	0.002
cfia	0.000	0.000	0.002
cfiaOrf	0.004	0.000	0.002
createGODataFrame	0	0	0
createGOMatrix	0	0	0
createMipsMatrix	0	0	0
createYeastDataObj	0.000	0.000	0.001
dataS	0.000	0.000	0.003
eAt	0.004	0.000	0.003
eAt2	0.004	0.000	0.002
egEBI16112	0.000	0.000	0.002
expStats	0.000	0.000	0.002
findSubComp	0	0	0
gavin2mergeMG	0.012	0.000	0.013
getAPMSData	0.308	0.232	0.552
getGOInfo	0	0	0
getMipsInfo	0	0	0
ho2mergeMGG	0.024	0.000	0.023
krogan2mergeMGGH	0.012	0.000	0.011
locScISI	0.788	0.004	0.792
mapping2SysG	0.000	0.004	0.003
mappingsG	0.004	0.000	0.003
maximizeSimilarity	0	0	0
mergeBGMat	0	0	0
mips2go	0.004	0.004	0.009
nAtMap	0.004	0.000	0.003
nonGenes	0.000	0.004	0.002
nucComp	0.004	0.000	0.003
recCompSize	0.000	0.000	0.001
redundantM	0.004	0.000	0.002
runAlignment	0.004	0.000	0.000
runCompareComplex	0	0	0
subCompM	0.000	0.000	0.004
sumStats	0	0	0
unWantedComp	0	0	0
unwanted	0.000	0.004	0.004
xtraGO	0.000	0.004	0.002
yeastData-class	0	0	0