CHECK report for GEOquery on lemming

* checking for working latex ... OK * using log directory 'D:/biocbld/1.9d/Rpacks/GEOquery.Rcheck' * using R version 2.4.0 alpha (2006-09-10 r39242) * checking for file 'GEOquery/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GEOquery' version '1.7.3' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'GEOquery' can be installed ... WARNING Found the following significant warnings: missing link(s): dataTable-class * checking package directory ... OK * checking for portable file names ... 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 ... WARNING Error in eval(expr, envir, enclos) : could not find function "setClass" Error: unable to load R code in package 'GEOquery' 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 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 ... WARNING Missing link(s) in documentation object 'GEOData-class.Rd': dataTable-class * checking for missing documentation entries ... WARNING Undocumented code objects: Accession Columns dataTable GPLList GSMList Meta Table 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 GEOquery-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating GEOquery-manual.tex ... OK * checking GEOquery-manual.tex ... OK WARNING: There were 4 warnings, see D:/biocbld/1.9d/Rpacks/GEOquery.Rcheck/00check.log for details

installing R.css in D:/biocbld/1.9d/Rpacks/GEOquery.Rcheck ---------- Making package GEOquery ------------ adding build stamp to DESCRIPTION installing NAMESPACE file and metadata installing R files installing inst files installing man source files installing indices installing help >>> Building/Updating help pages for package 'GEOquery' Formats: text html latex example chm GDS-class text html latex chm GDS2MA text html latex example chm GEOData-class text html latex chm missing link(s): dataTable-class GEODataTable-class text html latex chm GPL-class text html latex chm GSE-class text html latex chm GSM-class text html latex chm getGEO text html latex example chm getGEOfile text html latex example chm parseGEO text html latex chm Microsoft HTML Help Compiler 4.74.8702 Compiling d:\biocbld\1.9d\Rpacks\GEOquery.Rcheck\00_pkg_src\GEOquery\chm\GEOquery.chm Compile time: 0 minutes, 0 seconds 11 Topics 49 Local links 1 Internet link 1 Graphic Created d:\biocbld\1.9d\Rpacks\GEOquery.Rcheck\00_pkg_src\GEOquery\chm\GEOquery.chm, 28,171 bytes Compression decreased file by 7,933 bytes. adding MD5 sums * DONE (GEOquery)

Package 73/205	OS	Arch	BUILD	CHECK	BUILD BIN
GEOquery 1.7.3 Sean Davis	Linux (SUSE 9.2)	x86_64	OK	WARNINGS
	Linux (SUSE 9.2)	i686	OK	WARNINGS
	Solaris 2.9	sparc	OK	WARNINGS
	Linux (SUSE 10.0)	x86_64	OK	WARNINGS
	Windows Server 2003	x86_64	OK	[ WARNINGS ]	OK
	Windows XP	i686	OK	WARNINGS	skipped
	Mac OS X (10.4.6)	i686	OK	WARNINGS

GEOquery

1.7.3

Command output