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NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier
Package 43/238HostnameOSArchBUILDCHECKBUILD BIN

Category

2.3.13

S. Falcon
Last Changed Date: 2007-06-09 10:46:21 -0700
Last Changed Rev: 25296
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK [ OK ]
churchill Solaris 2.9 sparc  OK  OK 
lemming Windows Server 2003 (32-bit) x64  OK  OK skipped
Package: Category
Version: 2.3.13
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check Category_2.3.13.tar.gz
RetCode: 0
Time: 332.7 seconds
Status: OK
CheckDir: Category.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/Category.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-06-03 r41797)
* checking for file 'Category/DESCRIPTION' ... OK
* this is package 'Category' version '2.3.13'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Category' 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
gseaperm : <anonymous>: no visible global function definition for
  'Matrix'
gseaperm: no visible binding for global variable 'x'
htmlReportFromDf: no visible global function definition for 'xtable'
makeEBcontr: no visible global function definition for 'ebPatterns'
* 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
* creating Category-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating Category-manual.tex ... OK
* checking Category-manual.tex ... OK

Category.Rcheck/00install.out:

* Installing *source* package 'Category' ...
** R
** inst
** preparing package for lazy loading
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: graph
Loading required package: KEGG
Loading required package: GO
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
** help
 >>> Building/Updating help pages for package 'Category'
     Formats: text html latex example 
  ChrMapHyperGParams-class          text    html    latex   example
  ChrMapHyperGResult-class          text    html    latex   example
  DatPkg-class                      text    html    latex   example
  GOHyperGParams-class              text    html    latex
  HyperGParams-class                text    html    latex
  HyperGResult-accessors            text    html    latex
  HyperGResult-class                text    html    latex
  HyperGResultBase-class            text    html    latex
  KEGGHyperGParams-class            text    html    latex
  MAPAmat                           text    html    latex   example
  applyByCategory                   text    html    latex   example
  cateGOryMatrix                    text    html    latex   example
  categoryToEntrezBuilder           text    html    latex
  cb_contingency                    text    html    latex
  cb_parse_band_hsa                 text    html    latex   example
  chrBandInciMat                    text    html    latex   example
  findAMstats                       text    html    latex   example
  geneGoHyperGeoTest                text    html    latex
  geneKeggHyperGeoTest              text    html    latex
  getPathNames                      text    html    latex   example
  gseaperm                          text    html    latex
  hyperGTest                        text    html    latex
  makeChrBandGraph                  text    html    latex   example
  makeEBcontr                       text    html    latex   example
  makeValidParams                   text    html    latex
  probes2MAP                        text    html    latex   example
  probes2Path                       text    html    latex   example
  ttperm                            text    html    latex   example
  universeBuilder                   text    html    latex
** building package indices ...
* DONE (Category)