BioC 2.9: CHECK report for ScISI on pitt

Package: ScISI

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ScISI_1.26.0.tar.gz

StartedAt: 2012-03-24 04:10:02 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 04:13:26 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 204.3 seconds

RetCode: 0

Status: OK

CheckDir: ScISI.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ScISI.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.26.0'
* 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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                       old_size new_size compress
  ScISI.rda                34Kb     13Kb    bzip2
  ScISIC.rda               18Kb      8Kb    bzip2
  ScISIverified.rda        11Kb      8Kb    bzip2
  gavin2mergeMG.rda        12Kb      7Kb    bzip2
  ho2mergeMGG.rda          15Kb      9Kb    bzip2
  krogan2mergeMGGH.rda     11Kb      7Kb    bzip2
  locScISI.rda             82Kb     27Kb    bzip2
* 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'vignette.Rnw' 
** testing if installed package can be loaded

* DONE (ScISI)

name	user	system	elapsed
JaccardCoef	0.000	0.001	0.001
ScISI	0.388	0.010	0.398
ScISI2html	0.001	0.000	0.000
arp23	0.003	0.001	0.004
arp23G	0.002	0.001	0.003
arp23Orf	0.001	0.001	0.003
arp23Y2HG	0.002	0.001	0.003
cfia	0.003	0.001	0.003
cfiaOrf	0.002	0.001	0.002
createGODataFrame	0	0	0
createGOMatrix	0.000	0.000	0.001
createMipsMatrix	0.001	0.000	0.000
createYeastDataObj	0.000	0.001	0.000
dataS	0.002	0.001	0.003
eAt	0.003	0.001	0.004
eAt2	0.002	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	0.027	0.002	0.030
getAPMSData	0.617	0.475	1.115
getGOInfo	0	0	0
getMipsInfo	0.000	0.000	0.001
ho2mergeMGG	0.044	0.003	0.047
krogan2mergeMGGH	0.021	0.001	0.023
locScISI	1.280	0.034	1.326
mapping2SysG	0.002	0.000	0.003
mappingsG	0.002	0.000	0.002
maximizeSimilarity	0.001	0.000	0.000
mergeBGMat	0.000	0.000	0.001
mips2go	0.014	0.001	0.016
nAtMap	0.002	0.001	0.003
nonGenes	0.001	0.001	0.003
nucComp	0.002	0.001	0.003
recCompSize	0.000	0.001	0.000
redundantM	0.002	0.001	0.003
runAlignment	0.000	0.000	0.001
runCompareComplex	0.000	0.001	0.000
subCompM	0.002	0.001	0.003
sumStats	0	0	0
unWantedComp	0.000	0.001	0.000
unwanted	0.002	0.001	0.003
xtraGO	0.002	0.001	0.003
yeastData-class	0.000	0.000	0.001

Summary

Command output