BioC 2.9: CHECK report for ScISI on moscato1

Package: ScISI

Version: 1.25.0

Command: mkdir ScISI.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ScISI.buildbin-libdir ScISI_1.25.0.tar.gz >ScISI-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=ScISI.buildbin-libdir --install="check:ScISI-install.out" --force-multiarch --no-vignettes --timings ScISI_1.25.0.tar.gz && mv ScISI.buildbin-libdir/* ScISI.Rcheck/ && rmdir ScISI.buildbin-libdir

StartedAt: 2011-07-07 06:15:17 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 06:17:39 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 141.9 seconds

RetCode: 0

Status: OK

CheckDir: ScISI.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/ScISI.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ScISI/DESCRIPTION' ... OK
* this is package 'ScISI' version '1.25.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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
* loading checks for arch 'i386'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 tools::resaveRdaFiles() or 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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


install for i386

* installing *source* package 'ScISI' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: DBI

Loading required package: annotate
Loading required package: graph
Loading required package: RBGL
Loading required package: XML

Attaching package: 'XML'

The following object(s) are masked from 'package:graph':

    addNode

Loading required package: hypergraph

Attaching package: 'hypergraph'

The following object(s) are masked from 'package:AnnotationDbi':

    head, tail

The following object(s) are masked from 'package:utils':

    head, tail


** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'vignette.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'ScISI' ...
** testing if installed package can be loaded
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
* MD5 sums
packaged installation of 'ScISI' as ScISI_1.25.0.zip

* DONE (ScISI)

name	user	system	elapsed
JaccardCoef	0	0	0
ScISI	0.30	0.00	0.29
ScISI2html	0	0	0
arp23	0	0	0
arp23G	0	0	0
arp23Orf	0	0	0
arp23Y2HG	0	0	0
cfia	0.00	0.02	0.01
cfiaOrf	0	0	0
createGODataFrame	0	0	0
createGOMatrix	0	0	0
createMipsMatrix	0	0	0
createYeastDataObj	0	0	0
dataS	0.00	0.01	0.02
eAt	0	0	0
eAt2	0.00	0.02	0.02
egEBI16112	0	0	0
expStats	0	0	0
findSubComp	0	0	0
gavin2mergeMG	0.03	0.00	0.03
getAPMSData	0.49	0.11	0.59
getGOInfo	0	0	0
getMipsInfo	0	0	0
ho2mergeMGG	0.03	0.00	0.03
krogan2mergeMGGH	0.01	0.00	0.02
locScISI	0.70	0.03	0.73
mapping2SysG	0.00	0.02	0.02
mappingsG	0	0	0
maximizeSimilarity	0	0	0
mergeBGMat	0	0	0
mips2go	0.02	0.00	0.01
nAtMap	0	0	0
nonGenes	0	0	0
nucComp	0.00	0.01	0.02
recCompSize	0	0	0
redundantM	0	0	0
runAlignment	0	0	0
runCompareComplex	0	0	0
subCompM	0	0	0
sumStats	0	0	0
unWantedComp	0	0	0
unwanted	0	0	0
xtraGO	0	0	0
yeastData-class	0	0	0

Summary

Command output