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Package 204/260HostnameOS / ArchBUILDCHECKBUILD BIN
Rgraphviz 1.18.1
Li Long
Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/Rgraphviz
Last Changed Rev: 32020 / Revision: 34573
Last Changed Date: 2008-05-29 16:04:59 -0700 (Thu, 29 May 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ ERROR ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: Rgraphviz
Version: 1.18.1
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check Rgraphviz_1.18.1.tar.gz
StartedAt: 2008-10-16 07:14:04 -0700 (Thu, 16 Oct 2008)
EndedAt: 2008-10-16 07:15:08 -0700 (Thu, 16 Oct 2008)
EllapsedTime: 63.9 seconds
RetCode: 1
Status: ERROR
CheckDir: Rgraphviz.Rcheck
Warnings: NA

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/Rgraphviz.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'Rgraphviz/DESCRIPTION' ... OK
* this is package 'Rgraphviz' version '1.18.1'
* checking package name space information ... OK
* 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 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating Rgraphviz-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'Rgraphviz-Ex.R' failed.
The error most likely occurred in:

> ### * agwrite
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: agwrite
> ### Title: A function to write a Ragraph object to a file
> ### Aliases: agwrite agread
> ### Keywords: graphs
> 
> ### ** Examples
> 
> V <- letters[1:10]
> M <- 1:4
> g1 <- randomGraph(V, M, .2)
> z <- agopen(g1,"foo",layout=FALSE)
> 

Rgraphviz.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.2-bioc/meat/Rgraphviz.Rcheck


---------- Making package Rgraphviz ------------
GRAPHVIZ_INSTALL_DIR=C:\/Graphviz2.16
GRAPHVIZ_INSTALL_MAJOR=2
GRAPHVIZ_INSTALL_MINOR=16
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making LL_funcs.d from LL_funcs.c
making Rgraphviz.d from Rgraphviz.c
making RgraphvizInit.d from RgraphvizInit.c
making agopen.d from agopen.c
making agread.d from agread.c
making agwrite.d from agwrite.c
making bezier.d from bezier.c
making buildEdgeList.d from buildEdgeList.c
making buildNodeList.d from buildNodeList.c
making doLayout.d from doLayout.c
making graphvizVersion.d from graphvizVersion.c
making init.d from init.c
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c LL_funcs.c -o LL_funcs.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from LL_funcs.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from LL_funcs.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c Rgraphviz.c -o Rgraphviz.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from Rgraphviz.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from Rgraphviz.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
Rgraphviz.c:18: warning: C99 inline functions are not supported; using GNU89
Rgraphviz.c:18: warning: to disable this warning use -fgnu89-inline or the gnu_inline function attribute
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c RgraphvizInit.c -o RgraphvizInit.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from RgraphvizInit.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from RgraphvizInit.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c agopen.c -o agopen.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from agopen.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from agopen.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c agread.c -o agread.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from agread.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from agread.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c agwrite.c -o agwrite.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from agwrite.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from agwrite.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c bezier.c -o bezier.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from bezier.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from bezier.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c buildEdgeList.c -o buildEdgeList.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from buildEdgeList.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from buildEdgeList.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c buildNodeList.c -o buildNodeList.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from buildNodeList.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from buildNodeList.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c doLayout.c -o doLayout.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from doLayout.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from doLayout.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c graphvizVersion.c -o graphvizVersion.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from graphvizVersion.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from graphvizVersion.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
gcc  -std=gnu99 -IC:/Graphviz2.16/include -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=16 -DWin32 -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c init.c -o init.o
In file included from C:/Graphviz2.16/include/gvc.h:20,
                 from common.h:31,
                 from init.c:1:
C:/Graphviz2.16/include/types.h:27:1: warning: "TRUE" redefined
In file included from common.h:5,
                 from init.c:1:
e:/biocbld/bbs-2.2-bioc/R/include/Rdefines.h:150:1: warning: this is the location of the previous definition
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include  -i Rgraphviz_res.rc -o Rgraphviz_res.o
gcc  -std=gnu99  -shared -s  -o Rgraphviz.dll Rgraphviz.def LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o Rgraphviz_res.o  -Le:/biocbld/bbs-2.2-bioc/R/bin -LC:/Graphviz2.16/bin -lgvc -lgraph -lcdt   -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  preparing package Rgraphviz for lazy loading
Loading required package: graph
Loading required package: grid
Creating a new generic function for "head" in "Rgraphviz"
Creating a new generic function for "tail" in "Rgraphviz"
Creating a new generic function for "lines" in "Rgraphviz"
Creating a new generic function for "plot" in "Rgraphviz"
  installing man source files
  installing indices
  installing help
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
Note: removing empty section \seealso
 >>> Building/Updating help pages for package 'Rgraphviz'
     Formats: text html latex example chm 
  AgEdge-class                      text    html    latex   example chm
  AgNode-class                      text    html    latex   example chm
  AgTextLabel-class                 text    html    latex   example chm
  BezierCurve-class                 text    html    latex   example chm
  GraphvizAttributes                text    html    latex           chm
  GraphvizLayouts                   text    html    latex   example chm
  Ragraph-class                     text    html    latex   example chm
  agopen                            text    html    latex   example chm
  agopenSimple                      text    html    latex   example chm
  agwrite                           text    html    latex   example chm
  boundingBox-class                 text    html    latex   example chm
  buildNodeList                     text    html    latex   example chm
  clusterData-methods               text    html    latex   example chm
  getDefaultAttrs                   text    html    latex   example chm
  graphData-methods                 text    html    latex           chm
  graphDataDefaults-methods         text    html    latex           chm
  graphLayout                       text    html    latex   example chm
  graphvizVersion                   text    html    latex   example chm
  layoutGraph                       text    html    latex   example chm
  makeNodeAttrs                     text    html    latex   example chm
  pEdge-class                       text    html    latex   example chm
  pNode-class                       text    html    latex   example chm
  pieGlyph                          text    html    latex   example chm
  plot-methods                      text    html    latex   example chm
  removedEdges                      text    html    latex   example chm
  renderGraph                       text    html    latex   example chm
  toDot-methods                     text    html    latex   example chm
  toFile                            text    html    latex   example chm
  xyPoint-class                     text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.2-bioc\meat\Rgraphviz.Rcheck\00_pkg_src\Rgraphviz\chm\Rgraphviz.chm


Compile time: 0 minutes, 1 second
30	Topics
281	Local links
5	Internet links
1	Graphic


Created e:\biocbld\bbs-2.2-bioc\meat\Rgraphviz.Rcheck\00_pkg_src\Rgraphviz\chm\Rgraphviz.chm, 79,502 bytes
Compression decreased file by 118,816 bytes.
  adding MD5 sums

* DONE (Rgraphviz)