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Package 449/514HostnameOS / ArchBUILDCHECKBUILD BIN
ScISI 1.26.0
Tony Chiang
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/ScISI
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ScISI
Version: 1.26.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ScISI_1.26.0.tar.gz
StartedAt: 2012-03-24 02:40:33 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 02:43:13 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 160.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ScISI.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ScISI.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.26.0’
* 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 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

ScISI.Rcheck/00install.out:

* 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)

ScISI.Rcheck/ScISI-Ex.timings:

nameusersystemelapsed
JaccardCoef000
ScISI0.3880.0040.393
ScISI2html0.0000.0000.001
arp230.0080.0000.003
arp23G0.0000.0000.002
arp23Orf0.0000.0040.002
arp23Y2HG0.0040.0000.003
cfia0.0040.0000.002
cfiaOrf0.0040.0000.002
createGODataFrame0.0000.0000.001
createGOMatrix0.0000.0000.001
createMipsMatrix0.0000.0000.001
createYeastDataObj000
dataS0.0000.0000.003
eAt0.0040.0000.003
eAt20.0040.0000.002
egEBI161120.0040.0000.002
expStats0.0000.0000.003
findSubComp000
gavin2mergeMG0.0160.0000.014
getAPMSData0.5440.1880.740
getGOInfo0.0000.0000.001
getMipsInfo0.0040.0000.000
ho2mergeMGG0.020.000.02
krogan2mergeMGGH0.0080.0040.012
locScISI1.1400.0081.152
mapping2SysG0.0040.0000.003
mappingsG0.0040.0000.003
maximizeSimilarity000
mergeBGMat000
mips2go0.0080.0000.008
nAtMap0.0040.0000.003
nonGenes0.0040.0000.003
nucComp0.0040.0000.003
recCompSize000
redundantM0.0000.0000.002
runAlignment000
runCompareComplex000
subCompM0.0040.0000.002
sumStats0.0000.0000.001
unWantedComp000
unwanted0.0000.0000.002
xtraGO0.0040.0000.003
yeastData-class000