Package: GGtools

Version: 1.6.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check GGtools_1.6.0.tar.gz

RetCode: 0

Time: 644.8 seconds

Status: OK

CheckDir: GGtools.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/GGtools.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '1.6.0'
* checking package name space information ... OK
* 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 for sufficient/correct file permissions ... 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 ... NOTE
snps3PrimeTo: no visible binding for global variable 'geneLocs_hsa'
snps5PrimeTo: no visible binding for global variable 'geneLocs_hsa'
snpsNear: no visible binding for global variable 'geneLocs'
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating GGtools-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating GGtools-manual.tex ... OK
* checking GGtools-manual.tex ... OK

* Installing *source* package 'GGtools' ...
** libs
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c minfra.cc -o minfra.o
minfra.cc: In function `matrix operator/(matrix&, matrix&)':
minfra.cc:459: warning: unused variable `int a2c'
minfra.cc: In function `matrix delete_col(matrix, int)':
minfra.cc:545: warning: unused variable `int ncop'
minfra.cc:545: warning: unused variable `int nresel'
minfra.cc:545: warning: unused variable `int skip'
minfra.cc:546: warning: unused variable `double*resbase'
minfra.cc:546: warning: unused variable `double*Xbase'
minfra.cc: In function `int split(matrix&, matrix&, matrix*)':
minfra.cc:1210: warning: unused variable `int j'
minfra.cc: In function `matrix* split(matrix&, matrix&)':
minfra.cc:1245: warning: unused variable `int j'
g++ -shared -L/usr/local/lib -o GGtools.so minfra.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** preparing package 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: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: mgu74av2
** help
Note: unmatched right brace in 'snpMeta-class' on or after line 44
 >>> Building/Updating help pages for package 'GGtools'
     Formats: text html latex example 
  GGfitter-class                    text    html    latex   example
  HM2rac                            text    html    latex   example
  HMworkflow                        text    html    latex   example
  Strains2rac                       text    html    latex   example
  geneLocs                          text    html    latex   example
  genoStrings                       text    html    latex   example
  make_racExSet                     text    html    latex   example
  oGtypeExSet-class                 text    html    latex   example
  plot_EvG                          text    html    latex   example
  racExSet-class                    text    html    latex   example
  snpMeta-class                     text    html    latex   example
  snpScreen                         text    html    latex   example
  snps                              text    html    latex   example
** building package indices ...
Loading required package: methods
* DONE (GGtools)