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Package 102/251HostnameOS / ArchBUILDCHECKBUILD BIN
GSEABase 1.1.14
Biocore Team c/o BioC user list
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSEABase
Last Changed Rev: 29050 / Revision: 29143
Last Changed Date: 2007-12-05 13:57:42 -0800 (Wed, 05 Dec 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK [ WARNINGS ]
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  WARNINGS  OK 
Package: GSEABase
Version: 1.1.14
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check GSEABase_1.1.14.tar.gz
StartedAt: 2007-12-11 03:50:30 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:52:22 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 112.2 seconds
RetCode: 0
Status: WARNINGS
CheckDir: GSEABase.Rcheck
Warnings: 1

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/GSEABase.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '1.1.14'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GSEABase' 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  subsets
Undocumented S4 methods:
  generic 'Logic' and siglist 'CollectionType,CollectionType'
  generic 'Logic' and siglist 'CollectionIdType,CollectionIdType'
  generic 'Logic' and siglist 'character,GeneSet'
  generic 'Logic' and siglist 'character,GeneSetCollection'
  generic 'Logic' and siglist 'GeneSet,GeneSetCollection'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating GSEABase-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './GSEABase.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './GSEABase.tex' ...
* creating GSEABase-manual.tex ... OK
* checking GSEABase-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/home/biocbuild/bbs-2.2-bioc/meat/GSEABase.Rcheck/00check.log
for details

GSEABase.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/GSEABase.Rcheck
* Installing *source* package 'GSEABase' ...
** 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: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: annotate
Loading required package: xtable
** help
Note: removing empty section \details
 >>> Building/Updating help pages for package 'GSEABase'
     Formats: text html latex example 
  CollectionType-class              text    html    latex   example
  CollectionType-constructors       text    html    latex   example
  GSEABase-package                  text    html    latex   example
  GeneColorSet-class                text    html    latex   example
  GeneColorSet-methods              text    html    latex
  GeneIdentifierType-class          text    html    latex   example
  GeneIdentifierType-constructors   text    html    latex   example
  GeneSet-class                     text    html    latex   example
  GeneSet-methods                   text    html    latex   example
  GeneSetCollection-class           text    html    latex   example
  GeneSetCollection-methods         text    html    latex   example
  OBOCollection-class               text    html    latex   example
  details-methods                   text    html    latex
  getOBOCollection                  text    html    latex   example
  getObjects                        text    html    latex   example
  goSlim-methods                    text    html    latex   example
  incidence-methods                 text    html    latex   example
  mapIdentifiers-methods            text    html    latex
** building package indices ...
* DONE (GSEABase)