BioC 2.12: CHECK report for ScISI on pelham

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: 2013-03-20 10:11:46 -0700 (Wed, 20 Mar 2013)

EndedAt: 2013-03-20 10:15:25 -0700 (Wed, 20 Mar 2013)

EllapsedTime: 219.2 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 3.0.0 alpha (2013-03-16 r62280)
* 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 '1.31.0'
* 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 ... [21s/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 installed files from 'inst/doc' ... OK
* checking examples ... [14s/14s] 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	0.011	0.002	0.012
ScISI	0.337	0.027	0.368
ScISI2html	0.011	0.009	0.020
arp23	0.010	0.003	0.014
arp23G	0.008	0.004	0.012
arp23Orf	0.011	0.004	0.014
arp23Y2HG	0.009	0.003	0.012
cfia	0.009	0.003	0.013
cfiaOrf	0.009	0.004	0.013
createGODataFrame	0.007	0.003	0.010
createGOMatrix	0.007	0.003	0.010
createMipsMatrix	0.011	0.004	0.015
createYeastDataObj	0.007	0.003	0.010
dataS	0.010	0.004	0.014
eAt	0.013	0.003	0.017
eAt2	0.009	0.003	0.012
egEBI16112	0.009	0.004	0.013
expStats	0.013	0.004	0.018
findSubComp	0.007	0.003	0.012
gavin2mergeMG	0.020	0.008	0.029
getAPMSData	0.641	0.497	1.177
getGOInfo	0.016	0.001	0.017
getMipsInfo	0.012	0.001	0.013
ho2mergeMGG	0.028	0.008	0.037
krogan2mergeMGGH	0.014	0.010	0.024
locScISI	0.955	0.067	1.030
mapping2SysG	0.005	0.006	0.011
mappingsG	0.010	0.017	0.026
maximizeSimilarity	0.008	0.009	0.018
mergeBGMat	0.007	0.008	0.015
mips2go	0.009	0.006	0.015
nAtMap	0.005	0.005	0.010
nonGenes	0.010	0.006	0.015
nucComp	0.009	0.008	0.018
recCompSize	0.003	0.007	0.010
redundantM	0.004	0.004	0.009
runAlignment	0.003	0.005	0.009
runCompareComplex	0.008	0.005	0.014
subCompM	0.010	0.006	0.016
sumStats	0.009	0.008	0.017
unWantedComp	0.009	0.009	0.019
unwanted	0.005	0.006	0.011
xtraGO	0.004	0.005	0.010
yeastData-class	0.008	0.007	0.015

Summary

Command output