Package: Rgraphviz

Version: 1.12.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check Rgraphviz_1.12.0.tar.gz

RetCode: 0

Time: 181.3 seconds

Status: WARNINGS

CheckDir: Rgraphviz.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/Rgraphviz.Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file 'Rgraphviz/DESCRIPTION' ... OK
* this is package 'Rgraphviz' version '1.12.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rgraphviz' 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 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 compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating Rgraphviz-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF:
  /loc/biocbuild/1.9d/Rpacks/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/inst/doc/layingOutPathways.Rnw
  /loc/biocbuild/1.9d/Rpacks/Rgraphviz.Rcheck/00_pkg_src/Rgraphviz/inst/doc/Rgraphviz.Rnw
Bus Error - core dumped
* creating Rgraphviz-manual.tex ... OK
* checking Rgraphviz-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/biocbuild/1.9d/Rpacks/Rgraphviz.Rcheck/00check.log
for details

* Installing *source* package 'Rgraphviz' ...
checking for pkg-config... /usr/local/bin/pkg-config
sh: gnome-config: not found
Package libgvc was not found in the pkg-config search path.
Perhaps you should add the directory containing `libgvc.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libgvc' found
configure: pkg-config was not able to find graphviz.  Verify graphviz is installed and that PKG_CONFIG_PATH is correct.
checking for dotneato-config... /usr/local/bin/dotneato-config
configure: Found graphviz 2.2.1
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include/graphviz -DGRAPHVIZGT_1_16 -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c Rgraphviz.c -o Rgraphviz.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:32,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:15,
                 from Rgraphviz.c:1:
/loc/biocbuild/1.9d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
Rgraphviz.c: In function 'getListElement':
Rgraphviz.c:54: warning: implicit declaration of function 'Rf_type2char'
Rgraphviz.c: In function 'Rgraphviz_doLayout':
Rgraphviz.c:437: warning: implicit declaration of function 'circo_layout'
Rgraphviz.c:441: warning: implicit declaration of function 'fdp_layout'
Rgraphviz.c: At top level:
common.h:46: warning: 'gvc' defined but not used
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include/graphviz -DGRAPHVIZGT_1_16 -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c RgraphvizInit.c -o RgraphvizInit.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:32,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:15,
                 from RgraphvizInit.c:1:
/loc/biocbuild/1.9d/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
common.h:46: warning: 'gvc' defined but not used
gcc -G -L/usr/local/lib -o Rgraphviz.so Rgraphviz.o RgraphvizInit.o -L/usr/local/lib/graphviz -ldotneato -lm  
** R
** inst
** save image
Loading required package: graph
Loading required package: geneplotter
Loading required package: annotate
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Creating a new generic function for "lines" in "Rgraphviz"
Creating a new generic function for "plot" in "Rgraphviz"
** help
 >>> Building/Updating help pages for package 'Rgraphviz'
     Formats: text html latex example 
  AgEdge-class                      text    html    latex   example
  AgNode-class                      text    html    latex   example
  AgTextLabel-class                 text    html    latex   example
  BezierCurve-class                 text    html    latex   example
  GraphvizAttributes                text    html    latex   example
  GraphvizLayouts                   text    html    latex   example
  Ragraph-class                     text    html    latex   example
  agopen                            text    html    latex   example
  agwrite                           text    html    latex   example
  boundingBox-class                 text    html    latex   example
  buildNodeList                     text    html    latex   example
  getDefaultAttrs                   text    html    latex   example
  graphvizVersion                   text    html    latex   example
  imageMap                          text    html    latex   example
  layoutGraph                       text    html    latex   example
  makeNodeAttrs                     text    html    latex   example
  pEdge-class                       text    html    latex   example
  pNode-class                       text    html    latex   example
  pieGlyph                          text    html    latex   example
  plot-methods                      text    html    latex   example
  removedEdges                      text    html    latex   example
  toDot-methods                     text    html    latex   example
  xyPoint-class                     text    html    latex   example
** building package indices ...
* DONE (Rgraphviz)