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Package 390/479HostnameOS / ArchBUILDCHECKBUILD BIN
Rgraphviz 1.31.1
Kasper Hansen
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rgraphviz
Last Changed Rev: 55242 / Revision: 56603
Last Changed Date: 2011-05-03 20:37:26 -0700 (Tue, 03 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64 N O T   S U P P O R T E D
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  ERROR  skipped  skipped 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ ERROR ] OK 

Summary

Package: Rgraphviz
Version: 1.31.1
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rgraphviz_1.31.1.tar.gz
StartedAt: 2011-07-07 05:21:52 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 05:22:49 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 56.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: Rgraphviz.Rcheck
Warnings: NA

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/Rgraphviz.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Rgraphviz/DESCRIPTION' ... OK
* this is package 'Rgraphviz' version '1.31.1'
* 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 installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ...sh: line 1: 17261 Trace/BPT trap          LANGUAGE=en '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'Rgraphviz-Ex.Rout' 2>&1 < Rgraphviz-Ex.R
 ERROR
Running examples in 'Rgraphviz-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: toFile
> ### Title: Render a graph in a file with given format
> ### Aliases: toFile
> ### Keywords: models
> 
> ### ** Examples
> 
> 
> library("graph")
> library("Rgraphviz")
> 
> g1_gz <- gzfile(system.file("GXL/graphExample-01.gxl.gz",package="graph"), open="rb")
> g1 <- fromGXL(g1_gz)
Warning in readLines(con) :
  seek on a gzfile connection returned an internal error
> ag <- agopen(g1, name="test")
> 
> toFile(ag, layoutType="dot", filename="g1_dot.svg", fileType="svg")
NULL
> toFile(ag, layoutType="neato", filename="g1_neato.ps", fileType="ps")
NULL
> toFile(ag, layoutType="twopi", filename="g1_twopi.svg", fileType="svg")
R(17261) malloc: *** error for object 0x980190: Non-aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
NULL
> toFile(ag, layoutType="circo", filename="g1_circo.png", fileType="png")
dyld: lazy symbol binding failed: Symbol not found: _png_set_longjmp_fn
  Referenced from: /usr/local/lib/graphviz/libgvplugin_pango.6.dylib
  Expected in: dynamic lookup

dyld: Symbol not found: _png_set_longjmp_fn
  Referenced from: /usr/local/lib/graphviz/libgvplugin_pango.6.dylib
  Expected in: dynamic lookup

Rgraphviz.Rcheck/00install.out:

* installing *source* package 'Rgraphviz' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for whether compiler has bool... yes
configure: No --with-graphviz option was specified. Trying to find Graphviz using other methods.
checking for pkg-config... /usr/bin/pkg-config
configure: Found Graphviz version '2.29.20110628.0445'.
configure: Graphviz major version is '2' and minor version is '29'.
configure: Using the following compilation and linking flags for Rgraphviz
configure:    PKG_CPPFLAGS=-I/usr/local/include/graphviz  
configure:    PKG_LIBS=-L/usr/local/lib -lgvc -lgraph -lcdt  
configure:    GVIZ_DEFS= -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29 
configure: Setting Graphviz Build version to '2.29.20110628.0445'.
configure: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c LL_funcs.c -o LL_funcs.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Rgraphviz.c -o Rgraphviz.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c RgraphvizInit.c -o RgraphvizInit.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c agopen.c -o agopen.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c agread.c -o agread.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c agwrite.c -o agwrite.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c bezier.c -o bezier.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c buildEdgeList.c -o buildEdgeList.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c buildNodeList.c -o buildNodeList.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c doLayout.c -o doLayout.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c graphvizVersion.c -o graphvizVersion.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=29  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c init.c -o init.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rgraphviz.so 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 -L/usr/local/lib -lgvc -lgraph -lcdt -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/Rgraphviz.Rcheck/Rgraphviz/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for "head" from package "utils" in package "Rgraphviz"
Creating a generic function for "tail" from package "utils" in package "Rgraphviz"
Creating a generic function for "lines" from package "graphics" in package "Rgraphviz"
Creating a generic function for "plot" from package "graphics" in package "Rgraphviz"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Rgraphviz.Rnw' 
   'newRgraphvizInterface.Rnw' 
** testing if installed package can be loaded

* DONE (Rgraphviz)

Rgraphviz.Rcheck/Rgraphviz-Ex.timings:

nameusersystemelapsed
AgEdge-class0.0710.0080.088
AgNode-class0.0190.0010.020
AgTextLabel-class0.0320.0010.032
BezierCurve-class0.0190.0010.020
GraphvizLayouts0.0100.0010.010
Ragraph-class0.0730.0070.080
agopen0.0340.0010.035
agopenSimple0.0640.0010.065
agwrite0.0150.0010.031
boundingBox-class0.0160.0010.017
buildNodeList0.0120.0000.013
clusterData-methods0.5990.0170.666
getDefaultAttrs0.0010.0000.001
graphLayout0.0160.0000.016
graphvizVersion0.0010.0010.002
layoutGraph0.3100.0030.313
makeNodeAttrs0.0120.0010.012
pEdge-class0.0140.0010.015
pNode-class0.0110.0010.011
pieGlyph0.0210.0010.022
plot-methods0.0010.0000.000
removedEdges0.0120.0010.013
renderGraph0.3090.0020.312
toDot-methods0.0240.0020.027