BioC 2.12: CHECK report for ScISI on petty

Package: ScISI

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ScISI_1.32.0.tar.gz

StartedAt: 2013-10-08 23:53:37 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:57:40 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 243.9 seconds

RetCode: 0

Status:  OK

CheckDir: ScISI.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ScISI.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ScISI/DESCRIPTION' ... OK
* this is package 'ScISI' version '1.32.0'
* 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 ... [24s/24s] 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 ... [15s/15s] 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
** testing if installed package can be loaded
* DONE (ScISI)

name	user	system	elapsed
JaccardCoef	0.274	0.003	0.278
ScISI	0.331	0.028	0.359
ScISI2html	0.010	0.007	0.018
arp23	0.010	0.003	0.012
arp23G	0.009	0.003	0.012
arp23Orf	0.008	0.003	0.011
arp23Y2HG	0.009	0.003	0.012
cfia	0.010	0.003	0.013
cfiaOrf	0.009	0.003	0.013
createGODataFrame	0.006	0.002	0.009
createGOMatrix	0.007	0.003	0.010
createMipsMatrix	0.007	0.002	0.011
createYeastDataObj	0.007	0.003	0.010
dataS	0.010	0.003	0.013
eAt	0.009	0.003	0.013
eAt2	0.009	0.004	0.014
egEBI16112	0.012	0.004	0.015
expStats	0.009	0.003	0.012
findSubComp	0.008	0.003	0.013
gavin2mergeMG	0.020	0.012	0.032
getAPMSData	0.366	0.431	0.814
getGOInfo	0.009	0.005	0.014
getMipsInfo	0.006	0.002	0.009
ho2mergeMGG	0.021	0.010	0.031
krogan2mergeMGGH	0.015	0.007	0.023
locScISI	0.983	0.069	1.054
mapping2SysG	0.005	0.005	0.010
mappingsG	0.009	0.014	0.024
maximizeSimilarity	0.007	0.006	0.015
mergeBGMat	0.007	0.008	0.017
mips2go	0.010	0.006	0.017
nAtMap	0.005	0.004	0.011
nonGenes	0.009	0.005	0.014
nucComp	0.005	0.005	0.011
recCompSize	0.004	0.006	0.010
redundantM	0.005	0.005	0.011
runAlignment	0.009	0.006	0.016
runCompareComplex	0.008	0.005	0.017
subCompM	0.009	0.007	0.017
sumStats	0.003	0.005	0.008
unWantedComp	0.004	0.006	0.009
unwanted	0.005	0.004	0.010
xtraGO	0.005	0.002	0.007
yeastData-class	0.007	0.006	0.013