Package: biomaRt

Version: 1.12.0

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check biomaRt_1.12.0.tar.gz

RetCode: 0

Time: 220.2 seconds

Status: WARNINGS

CheckDir: biomaRt.Rcheck

Warnings: 3

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/biomaRt.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'biomaRt/DESCRIPTION' ... OK
* this is package 'biomaRt' version '1.12.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'biomaRt' can be installed ... OK
* 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 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 ... WARNING
Loading required package: methods
Loading required package: RCurl
Error in paste(normalizePath(file.path(libname, pkgname, "libs")), file.path(Sys.getenv("R_HOME"),  : 
  could not find function "normalizePath"
Error : .onLoad failed in 'loadNamespace' for 'XML'
Error: package/namespace load failed for 'biomaRt'
Execution halted

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking whether the name space can be loaded with stated dependencies ... WARNING
Error in paste(normalizePath(file.path(libname, pkgname, "libs")), file.path(Sys.getenv("R_HOME"),  : 
  could not find function "normalizePath"
Error: .onLoad failed in 'loadNamespace' for 'XML'
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 for unstated dependencies in R code ... WARNING
Error: package/namespace load failed for 'biomaRt'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)), 
       call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating biomaRt-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating biomaRt-manual.tex ... OK
* checking biomaRt-manual.tex ... OK

WARNING: There were 3 warnings, see
  E:/biocbld/bbs-2.1-bioc/meat/biomaRt.Rcheck/00check.log
for details

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/biomaRt.Rcheck


---------- Making package biomaRt ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  preparing package biomaRt for lazy loading
Loading required package: RCurl
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'biomaRt'
     Formats: text html latex example chm 
  Mart-class                        text    html    latex           chm
  attributeSummary                  text    html    latex   example chm
  exportFASTA                       text    html    latex   example chm
  filterOptions                     text    html    latex   example chm
  filterSummary                     text    html    latex   example chm
  filterType                        text    html    latex   example chm
  getAffyArrays                     text    html    latex   example chm
  getBM                             text    html    latex   example chm
  getFeature                        text    html    latex   example chm
  getGO                             text    html    latex   example chm
  getGene                           text    html    latex   example chm
  getHomolog                        text    html    latex   example chm
  getLDS                            text    html    latex   example chm
  getSNP                            text    html    latex   example chm
  getSequence                       text    html    latex   example chm
  listAttributes                    text    html    latex   example chm
  listDatasets                      text    html    latex   example chm
  listFilters                       text    html    latex   example chm
  listMarts                         text    html    latex   example chm
  martDisconnect                    text    html    latex   example chm
  parseAttributes                   text    html    latex           chm
  parseFilters                      text    html    latex           chm
  useDataset                        text    html    latex   example chm
  useMart                           text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\biomaRt.Rcheck\00_pkg_src\biomaRt\chm\biomaRt.chm


Compile time: 0 minutes, 0 seconds
25	Topics
49	Local links
9	Internet links
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\biomaRt.Rcheck\00_pkg_src\biomaRt\chm\biomaRt.chm, 35,964 bytes
Compression decreased file by 31,207 bytes.
  adding MD5 sums

* DONE (biomaRt)