Rgraphviz 1.30.1
Kasper Hansen
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/Rgraphviz | | Last Changed Rev: 55243 / Revision: 59457 | | Last Changed Date: 2011-05-03 20:39:09 -0700 (Tue, 03 May 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/Rgraphviz.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.30.1'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... NOTE
'qpdf' made some significant size reductions:
compacted 'Rgraphviz.pdf' from 823Kb to 386Kb
compacted 'newRgraphvizInterface.pdf' from 475Kb to 261Kb
consider running tools::compactPDF() on these files
* checking examples ...sh: line 1: 58155 Trace/BPT trap LANGUAGE=en '/Library/Frameworks/R.framework/Versions/2.13/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(58155) malloc: *** error for object 0x97fc90: 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
* 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 '2.29.20110629.0445'.
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 '2.29.20110629.0445'.
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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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-2.8-bioc/meat/Rgraphviz.Rcheck/Rgraphviz/libs/i386
** R
** inst
** preparing package for lazy loading
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"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (Rgraphviz)