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Package 222/260HostnameOS / ArchBUILDCHECKBUILD BIN
ScISI 1.12.0
Tony Chiang
Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/ScISI
Last Changed Rev: 31430 / Revision: 34573
Last Changed Date: 2008-04-29 16:50:18 -0700 (Tue, 29 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK [ OK ]
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: ScISI
Version: 1.12.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check ScISI_1.12.0.tar.gz
StartedAt: 2008-10-16 05:57:26 -0700 (Thu, 16 Oct 2008)
EndedAt: 2008-10-16 06:03:09 -0700 (Thu, 16 Oct 2008)
EllapsedTime: 343.1 seconds
RetCode: 0
Status: OK
CheckDir: ScISI.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/ScISI.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'ScISI/DESCRIPTION' ... OK
* this is package 'ScISI' version '1.12.0'
* 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 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 name space can be loaded with stated dependencies ... 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 ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating ScISI-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating ScISI-manual.tex ... OK
* checking ScISI-manual.tex using pdflatex ... OK

ScISI.Rcheck/00install.out:

* Installing *source* package 'ScISI' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: apComplex
Loading required package: graph
Loading required package: RBGL
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: YEAST

******* Deprecation warning *******:

The package 'YEAST' is deprecated and will not be supported in the future. 

Instead we strongly reccomend that you should start using the 'org.Sc.sgd.db' package. 

We hope you will enjoy these new packages.  If you still have questions, you can search 
(http://dir.gmane.org/gmane.science.biology.informatics.conductor) or ask the mailing list 
(http://bioconductor.org/docs/mailList.html).  


Loading required package: GO

******* Deprecation warning *******:

The package 'GO' is deprecated and will not be supported in the future. 

Instead we strongly reccomend that you should start using the 'GO.db' package. 

We hope you will enjoy these new packages.  If you still have questions, you can search 
(http://dir.gmane.org/gmane.science.biology.informatics.conductor) or ask the mailing list 
(http://bioconductor.org/docs/mailList.html).  


Loading required package: GOstats
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

Loading required package: DBI
Loading required package: RSQLite

Attaching package: 'GO.db'


	The following object(s) are masked from package:GO :

	 GO,
	 GOBPANCESTOR,
	 GOBPCHILDREN,
	 GOBPOFFSPRING,
	 GOBPPARENTS,
	 GOCCANCESTOR,
	 GOCCCHILDREN,
	 GOCCOFFSPRING,
	 GOCCPARENTS,
	 GOMAPCOUNTS,
	 GOMFANCESTOR,
	 GOMFCHILDREN,
	 GOMFOFFSPRING,
	 GOMFPARENTS,
	 GOOBSOLETE,
	 GOSYNONYM,
	 GOTERM 

Loading required package: annotate
Loading required package: xtable

Attaching package: 'annotate'


	The following object(s) are masked from package:Rgraphviz :

	 toFile 

Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: Rintact
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:xtable :

	 label,
	 label<- 


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

	 head,
	 tail 


	The following object(s) are masked from package:Rgraphviz :

	 head,
	 tail 


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

	 head,
	 tail 

** help
Note: removing empty section \details
Note: removing empty section \references
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \note
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \examples
 >>> Building/Updating help pages for package 'ScISI'
     Formats: text html latex example 
  Desc-methods                      text    html    latex
  ID-methods                        text    html    latex
  JaccardCoef                       text    html    latex   example
  ScISI                             text    html    latex   example
  ScISI2html                        text    html    latex   example
  arp23                             text    html    latex   example
  arp23G                            text    html    latex   example
  arp23Orf                          text    html    latex   example
  arp23Y2HG                         text    html    latex   example
  calcGraphStats                    text    html    latex
  cfia                              text    html    latex   example
  cfiaOrf                           text    html    latex   example
  checkComplex                      text    html    latex
  checkSGN                          text    html    latex
  compBijection                     text    html    latex
  compareComplex                    text    html    latex
  createGODataFrame                 text    html    latex   example
  createGOMatrix                    text    html    latex   example
  createMipsDataFrame               text    html    latex
  createMipsMatrix                  text    html    latex   example
  createYeastDataObj                text    html    latex   example
  dataS                             text    html    latex   example
  eAt                               text    html    latex   example
  eAt2                              text    html    latex   example
  edgeProp                          text    html    latex
  egEBI16112                        text    html    latex   example
  expStats                          text    html    latex   example
  findSubComp                       text    html    latex   example
  gavin2mergeMG                     text    html    latex   example
  getAPMSData                       text    html    latex   example
  getGOInfo                         text    html    latex   example
  getLocOrfs                        text    html    latex
  getMipsInfo                       text    html    latex   example
  getURL-methods                    text    html    latex
  graphSumStats                     text    html    latex
  ho2mergeMGG                       text    html    latex   example
  krogan2mergeMGGH                  text    html    latex   example
  locScISI                          text    html    latex   example
  mapping2SysG                      text    html    latex   example
  mappingsG                         text    html    latex   example
  maximizeSimilarity                text    html    latex   example
  meanDeg                           text    html    latex
  mergeBGMat                        text    html    latex   example
  mips2go                           text    html    latex   example
  nAt                               text    html    latex
  nAtMap                            text    html    latex   example
  nonGenes                          text    html    latex   example
  nucComp                           text    html    latex   example
  recCompSize                       text    html    latex   example
  redundantM                        text    html    latex   example
  rmByEvi                           text    html    latex
  runAlignment                      text    html    latex   example
  runCompareComplex                 text    html    latex   example
  subCompM                          text    html    latex   example
  sumStats                          text    html    latex   example
  unWantedComp                      text    html    latex   example
  unwanted                          text    html    latex   example
  xtraGO                            text    html    latex   example
  xtraGONodes                       text    html    latex
  yeastData-class                   text    html    latex   example
** building package indices ...
* DONE (ScISI)