Package: GGtools

Version: 1.4.0

Command: E:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check GGtools_1.4.0.tar.gz

RetCode: 1

Time: 74.9 seconds

Status: ERROR

CheckDir: GGtools.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.0-bioc/meat/GGtools.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '1.4.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GGtools' can be installed ... WARNING
Found the following significant warnings:
       missing link(s):  ExpressionSet-class eSet-class VersionedBiobase-class Versioned-class
See 'E:/biocbld/bbs-2.0-bioc/meat/GGtools.Rcheck/00install.out' for details.
* 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 ... 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:
  addAnno getSNPindices tx_rsnum
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
* checking data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating GGtools-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'GGtools-Ex.R' failed.
The error most likely occurred in:

> ### * HM2rac
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: HM2rac
> ### Title: compute rare allele count from a hapmap file
> ### Aliases: HM2rac thinHM2rac thinHM2meta df2snpMeta getRare countRare
> ### Keywords: models
> 
> ### ** Examples
> 
> fi = system.file("fileDemos/geno20demo.txt.gz", package="GGtools")
> racstr =  thinHM2rac(fi)
Error in strsplit(stats, " +")[[1]] : subscript out of bounds
Execution halted

installing R.css in E:/biocbld/bbs-2.0-bioc/meat/GGtools.Rcheck


---------- Making package GGtools ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making minfra.d from minfra.cc
g++   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O2   -c minfra.cc -o minfra.o
minfra.cc: In function `matrix operator/(matrix&, matrix&)':
minfra.cc:459: warning: unused variable 'a2c'
minfra.cc: In function `matrix delete_col(matrix, int)':
minfra.cc:545: warning: unused variable 'ncop'
minfra.cc:545: warning: unused variable 'nresel'
minfra.cc:545: warning: unused variable 'skip'
minfra.cc:546: warning: unused variable 'resbase'
minfra.cc:546: warning: unused variable 'Xbase'
minfra.cc: In function `int split(matrix&, matrix&, matrix*)':
minfra.cc:1210: warning: unused variable 'j'
minfra.cc: In function `matrix* split(matrix&, matrix&)':
minfra.cc:1245: warning: unused variable 'j'
windres -I e:/biocbld/bbs-2.0-bioc/R/include  -i GGtools_res.rc -o GGtools_res.o
g++  -shared -s  -o GGtools.dll GGtools.def minfra.o GGtools_res.o  -Le:/biocbld/bbs-2.0-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
Loading required package: methods
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'GGtools'
     Formats: text html latex example chm 
  HM2rac                            text    html    latex   example chm
  HMworkflow                        text    html    latex   example chm
  Strains2rac                       text    html    latex   example chm
  geneLocs                          text    html    latex   example chm
  genoStrings                       text    html    latex   example chm
  make_racExSet                     text    html    latex   example chm
  oGtypeExSet-class                 text    html    latex   example chm
     missing link(s):  ExpressionSet-class eSet-class VersionedBiobase-class Versioned-class
  plot_EvG                          text    html    latex   example chm
  racExSet-class                    text    html    latex   example chm
  snpMeta-class                     text    html    latex   example chm
  snpScreen                         text    html    latex   example chm
  snps                              text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.0-bioc\meat\GGtools.Rcheck\00_pkg_src\GGtools\chm\GGtools.chm


Compile time: 0 minutes, 0 seconds
13	Topics
107	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.0-bioc\meat\GGtools.Rcheck\00_pkg_src\GGtools\chm\GGtools.chm, 37,422 bytes
Compression decreased file by 38,324 bytes.
  preparing package GGtools 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: hgfocus
Loading required package: geneplotter
Loading required package: annotate
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: mgu74av2
Creating a new generic function for "nrow" in "GGtools"
  adding MD5 sums

* DONE (GGtools)