Package: GGtools

Version: 1.2.0

Command: D:\biocbld\1.9d\R\bin\R.exe CMD check GGtools_1.2.0.tar.gz

RetCode: 1

Time: 1122.1 seconds

Status: ERROR

CheckDir: GGtools.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory 'D:/biocbld/1.9d/Rpacks/GGtools.Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '1.2.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GGtools' 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 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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)
Warning: NAs introduced by coercion
Error in matrix(NA, nr = nline, nc = nind) : 
	matrix: invalid 'nrow' value (too large or NA)
Execution halted

installing R.css in D:/biocbld/1.9d/Rpacks/GGtools.Rcheck


---------- Making package GGtools ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making minfra.d from minfra.cc
g++   -Id:/biocbld/1.9d/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 --include-dir d:/biocbld/1.9d/R/include  -i GGtools_res.rc -o GGtools_res.o
g++  -shared -s  -o GGtools.dll GGtools.def minfra.o GGtools_res.o  -Ld:/biocbld/1.9d/R/bin   -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package GGtools for lazy data loading
  installing man source files
  installing indices
  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
  geneLocs                          text    html    latex   example chm
  genoStrings                       text    html    latex   example chm
  make_racExSet                     text    html    latex   example chm
  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 d:\biocbld\1.9d\Rpacks\GGtools.Rcheck\00_pkg_src\GGtools\chm\GGtools.chm


Compile time: 0 minutes, 0 seconds
11	Topics
82	Local links
0	Internet links
1	Graphic


Created d:\biocbld\1.9d\Rpacks\GGtools.Rcheck\00_pkg_src\GGtools\chm\GGtools.chm, 32,256 bytes
Compression decreased file by 25,032 bytes.
  adding MD5 sums

* DONE (GGtools)