Package: ScISI

Version: 1.8.0

Command: /home/biocbuild/bbs-2.0-bioc/R/bin/R CMD check ScISI_1.8.0.tar.gz

RetCode: 0

Time: 222.6 seconds

Status: WARNINGS

CheckDir: ScISI.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.0-bioc/meat/ScISI.Rcheck'
* using R version 2.5.1 (2007-06-27)
* checking for file 'ScISI/DESCRIPTION' ... OK
* this is package 'ScISI' version '1.8.0'
* 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 ... WARNING
Loading required package: methods
Loading required package: utils
Error in getGeneric(f, TRUE, envir, package) : 
	no generic function found for "summary"
Execution halted

A namespace must be able to be loaded with just the base namespace loaded:
otherwise if the namespace gets loaded by a saved object, the session will
be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... OK
* 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 ... OK

WARNING: There was 1 warning, see
  /home/biocbuild/bbs-2.0-bioc/meat/ScISI.Rcheck/00check.log
for details

* 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: GO
Loading required package: GOstats
Loading required package: annotate
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: Category
Loading required package: KEGG
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice
Loading required package: Rgraphviz
Loading required package: geneplotter
KernSmooth 2.22 installed
Copyright M. P. Wand 1997

Attaching package: 'Rgraphviz'


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

	 toFile 

Loading required package: YEAST
Loading required package: xtable
** help
 >>> 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   example
  cfia                              text    html    latex   example
  cfiaOrf                           text    html    latex   example
  checkComplex                      text    html    latex   example
  checkSGN                          text    html    latex   example
  compBijection                     text    html    latex   example
  compareComplex                    text    html    latex   example
  createGODataFrame                 text    html    latex   example
  createGOMatrix                    text    html    latex   example
  createMipsDataFrame               text    html    latex   example
  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   example
  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   example
  getMipsInfo                       text    html    latex   example
  getURL-methods                    text    html    latex
  graphSumStats                     text    html    latex   example
  ho2mergeMGG                       text    html    latex   example
  krogan2mergeMGGH                  text    html    latex   example
  list2Matrix                       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   example
  mergeBGMat                        text    html    latex   example
  mips2go                           text    html    latex   example
  nAt                               text    html    latex
  nAtMap                            text    html    latex   example
  nucComp                           text    html    latex   example
  recCompSize                       text    html    latex   example
  redundantM                        text    html    latex   example
  rmByEvi                           text    html    latex   example
  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
  xtraGO                            text    html    latex   example
  xtraGONodes                       text    html    latex   example
  yeastData-class                   text    html    latex   example
** building package indices ...
* DONE (ScISI)