* using log directory 'C:/R/biocbld/1.7/build-area/buildSandbox/checkOutput/splicegear.Rcheck'
* using R version 2.2.0, 2005-10-10 
* checking for file 'splicegear/DESCRIPTION' ... OK
* this is package 'splicegear' version '1.2.0'
* checking if this is a source package ... OK
* checking whether package 'splicegear' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'buildSpliceSites':
queryPALSdb
  Code: function(query, disp = c("data", "browser"), field =
                 c("keyword", "ug.id", "gb.id", "human.cytoband",
                 "mouse.cytoband", "cluster_count"), species =
                 c("human", "mouse"), e.value = "1e-1", ident.threshold
                 = c("90% 50b", "95% 50b", "90% 45b"))
  Docs: function(query, disp = c("data", "browser"), field =
                 c("keyword", "ug_id", "gb_id", "human.cytoband",
                 "mouse.cytoband", "cluster_count"), species =
                 c("human", "mouse"), e.value = "1e-1", ident.threshold
                 = c("90% 50b", "95% 50b", "90% 45b"))
getPALSdbURL
  Code: function(query, disp = c("data", "browser"), field =
                 c("keyword", "ug.id", "gb.id", "human.cytoband",
                 "mouse.cytoband", "cluster_count"), species =
                 c("human", "mouse"), e.value = "1e-1", ident.threshold
                 = c("90% 50b", "95% 50b", "90% 45b"))
  Docs: function(query, disp = c("data", "browser"), field =
                 c("keyword", "ug_id", "gb_id", "human.cytoband",
                 "mouse.cytoband", "cluster_count"), species =
                 c("human", "mouse"), e.value = "1e-1", ident.threshold
                 = c("90% 50b", "95% 50b", "90% 45b"))

* checking Rd \usage sections ... OK
* creating splicegear-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating splicegear-manual.tex ... OK
* checking splicegear-manual.tex ... OK