CHECK report for SAGElyzer on churchill

* checking for working latex ... OK * using log directory '/loc/biocbuild/2.0d/Rpacks/SAGElyzer.Rcheck' * using R version 2.5.0 Under development (unstable) (2006-12-05 r40126) * checking for file 'SAGElyzer/DESCRIPTION' ... OK * this is package 'SAGElyzer' version '1.13.0' * checking package dependencies ... WARNING 'library' or 'require' calls not declared from: RODBC Rdbi RdbiPgSQL Biobase See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. * checking if this is a source package ... OK * checking whether package 'SAGElyzer' 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 syntax errors ... OK * checking R files for non-ASCII characters ... 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 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: SAGEFromGEO findNG4Tag getBinding getDBArgs getLibCounts getSAGEKNN getSLyzerArgs getTag getUnixDBArgs getWinDBArgs linkTag2UG mapLib2File mapSAGE2UG modSLyzerArgs procSAGE remapTagNUG runSLyzer setKNNArgs setSLyzerArgs showDBError writeSAGEKNN writeSLyzerArgs All user-level objects in a package 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 SAGElyzer-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating SAGElyzer-manual.tex ... OK * checking SAGElyzer-manual.tex ... OK WARNING: There were 2 warnings, see /loc/biocbuild/2.0d/Rpacks/SAGElyzer.Rcheck/00check.log for details

* Installing *source* package 'SAGElyzer' ... ** R ** data ** exec ** inst ** preparing package for lazy loading Loading required package: AnnBuilder Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: XML Loading required package: annotate Loading required package: tkWidgets Loading required package: widgetTools Loading Tcl/Tk interface ... done Loading required package: DynDoc Loading required package: genefilter Loading required package: survival Loading required package: splines ** help >>> Building/Updating help pages for package 'SAGElyzer' Formats: text html latex example SAGELyzer text html latex example SAGEMapper text html latex example SAGEToolTips text html latex example SAGEWidget text html latex example con4Win text html latex example getGEOSAGE text html latex example getNormFactor text html latex example getTargetRow text html latex example mergeSAGE text html latex example mergeSAGEWidget text html latex example querySAGE text html latex example ** building package indices ... * DONE (SAGElyzer)

Package 177/208	OS	Arch	BUILD	CHECK	BUILD BIN
SAGElyzer 1.13.0 Jianhua Zhang	Linux (SUSE 9.2)	x86_64	OK	WARNINGS
	Linux (SUSE 10.1)	x86_64	OK	WARNINGS
	Linux (SUSE 9.2)	i686	OK	WARNINGS
	Solaris 2.9	sparc	OK	[ WARNINGS ]
	Windows Server 2003	x86_64	OK	ERROR	OK
	Windows Server 2003	NA	OK	ERROR	OK
	Mac OS X (10.4.6)	i686	OK	ERROR

SAGElyzer

1.13.0

Command output