Package: GGtools

Version: 1.5.3

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check GGtools_1.5.3.tar.gz

RetCode: 0

Time: 567.2 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 Under development (unstable) (2007-08-06 r42439)
* checking for file 'GGtools/DESCRIPTION' ... OK
* this is package 'GGtools' version '1.5.3'
* 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'
snps5PrimeTo: no visible binding for global variable 'geneLocs'
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: 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 
  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)