BioC 2.12: CHECK report for ScISI on petty

Package: ScISI

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ScISI_1.31.0.tar.gz

StartedAt: 2013-03-25 04:40:55 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:44:03 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 188.5 seconds

RetCode: 0

Status: OK

CheckDir: ScISI.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ScISI.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.31.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'ScISI' can be installed ... [18s/18s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
getGOInfo : <anonymous>: warning in
  mget(names(parsed[[z]])[these[[z]]], env = org.Sc.sgdGO2ORF,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
getGOInfo: warning in mget(names(cMembers), env = GOCCCHILDREN,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
getGOInfo: warning in mget(names(comp)[alsoThese], env =
  org.Sc.sgdGO2ORF, ifnotfound = NA): partial argument match of 'env'
  to 'envir'
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 installed files from 'inst/doc' ... OK
* checking examples ... [11s/11s] 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ScISI.Rcheck/00check.log'
for details.

* installing *source* package 'ScISI' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'vignette.Rnw' 
** testing if installed package can be loaded
* DONE (ScISI)

name	user	system	elapsed
JaccardCoef	0.010	0.008	0.016
ScISI	0.204	0.019	0.223
ScISI2html	0.010	0.009	0.020
arp23	0.147	0.006	0.154
arp23G	0.008	0.006	0.014
arp23Orf	0.008	0.007	0.014
arp23Y2HG	0.009	0.007	0.015
cfia	0.008	0.006	0.015
cfiaOrf	0.008	0.007	0.014
createGODataFrame	0.006	0.006	0.012
createGOMatrix	0.006	0.006	0.013
createMipsMatrix	0.006	0.006	0.012
createYeastDataObj	0.007	0.006	0.013
dataS	0.008	0.007	0.015
eAt	0.008	0.007	0.016
eAt2	0.008	0.007	0.015
egEBI16112	0.008	0.007	0.014
expStats	0.008	0.007	0.014
findSubComp	0.009	0.007	0.017
gavin2mergeMG	0.019	0.008	0.029
getAPMSData	0.602	0.509	1.134
getGOInfo	0.014	0.010	0.025
getMipsInfo	0.009	0.007	0.016
ho2mergeMGG	0.031	0.011	0.043
krogan2mergeMGGH	0.016	0.008	0.025
locScISI	0.565	0.054	0.621
mapping2SysG	0.005	0.004	0.009
mappingsG	0.004	0.005	0.009
maximizeSimilarity	0.004	0.006	0.009
mergeBGMat	0.003	0.005	0.008
mips2go	0.008	0.005	0.013
nAtMap	0.004	0.005	0.009
nonGenes	0.004	0.004	0.009
nucComp	0.005	0.005	0.010
recCompSize	0.003	0.005	0.008
redundantM	0.004	0.004	0.008
runAlignment	0.003	0.004	0.008
runCompareComplex	0.002	0.005	0.007
subCompM	0.004	0.005	0.009
sumStats	0.006	0.007	0.014
unWantedComp	0.006	0.008	0.013
unwanted	0.006	0.006	0.013
xtraGO	0.007	0.007	0.014
yeastData-class	0.005	0.007	0.012

Summary

Command output