[BioC] Problem installing graph package

[Matt McCall]

Using R v2.0.0 on MacOS X in the R console.
I was able to install most of bioconductor. I wanted to use the GOstats  
package (amoung a few others), and it didn't install properly. So I  
went back to try to find the problem, and it seems that the graph  
package isn't installing. Any suggestions?
Matt

 > getBioC("prog", develOK=T)
Running getBioC version 1.2.66....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R

Please direct any concerns or questions to  
bioconductor at stat.math.ethz.ch.

Please select an installation directory:
1:/Users/mmccall/Library/R/library
2:/Library/Frameworks/R.framework/Resources/library
Selection: 1
[1] "Attempting to download graph from  
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing graph"
* Installing *source* package 'graph' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
  -I/usr/local/include   -fno-common  -g -O2 -c graph.c -o graph.o
graph.c: In function `intersectStrings':
graph.c:39: warning: assignment makes pointer from integer without a  
cast
graph.c:56: warning: assignment makes pointer from integer without a  
cast
graph.c: In function `graphIntersection':
graph.c:118: warning: assignment makes pointer from integer without a  
cast
graph.c: In function `checkEdgeList':
graph.c:157: warning: assignment makes pointer from integer without a  
cast
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
graph.so graph.o  -lcc_dynamic -framework R
ld: warning multiple definitions of symbol _xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
_xerbla_
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
/usr/lib/libz.1.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
/usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
/usr/lib/libz.1.dylib(deflate.o) definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of  
_deflateReset
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of  
_deflateSetDictionary
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of  
_deflateInit2_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of  
_deflateParams
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
ld: warning multiple definitions of symbol _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of  
_deflateInit_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
ld: warning multiple definitions of symbol _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
/usr/lib/libz.1.dylib(zutil.o) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
/usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
ld: warning multiple definitions of symbol _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
ld: warning multiple definitions of symbol _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of  
_inflateSyncPoint
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
/usr/lib/libz.1.dylib(inflate.o) definition of _inflate
ld: warning multiple definitions of symbol _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of  
_inflateSetDictionary
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of  
_inflateInit2_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of  
_inflateReset
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of  
_inflateInit_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
ld: warning multiple definitions of symbol _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
/usr/lib/libz.1.dylib(adler32.o) definition of _adler32
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
ld: warning multiple definitions of symbol _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
/usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
/usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
/usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
/usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
ld: warning multiple definitions of symbol _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
ld: warning multiple definitions of symbol _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
ld: warning multiple definitions of symbol _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
ld: warning multiple definitions of symbol _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
/usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
ld: warning multiple definitions of symbol _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
/usr/lib/libz.1.dylib(gzio.o) definition of _gzread
ld: warning multiple definitions of symbol _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
/usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
ld: warning multiple definitions of symbol _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
/usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
ld: warning multiple definitions of symbol _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
/usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
ld: warning multiple definitions of symbol _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
/usr/lib/libz.1.dylib(gzio.o) definition of _gztell
ld: warning multiple definitions of symbol _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
/usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
** R
** data
** inst
** save image
[1] TRUE
[1] TRUE
[1] TRUE
Loading required package: cluster
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
	 Vignettes contain introductory material.  To view,
	 simply type: openVignette()
	 For details on reading vignettes, see
	 the openVignette help page.
[1] "propertyHolder"
[1] "property"
[1] "property"
[1] "property<-"
[1] "property<-"
[1] "asGraphProperty"
[1] "asGraphProperty"
[1] "asGraphProperty"
[1] "asGraphProperty"
[1] "asGraphProperty"
[1] "graph"
[1] "edgemode"
[1] "edgemode"
[1] "edgemode<-"
[1] "edgemode<-"
[1] "graphNEL"
[1] "initialize"
[1] "nodes"
[1] "nodes"
[1] "nodes<-"
[1] "nodes<-"
[1] "edges"
[1] "edges"
[1] "edges"
[1] "degree"
[1] "degree"
[1] "degree"
[1] "edgeWeights"
[1] "edgeWeights"
[1] "adj"
[1] "adj"
[1] "acc"
[1] "acc"
[1] "DFS"
[1] "DFS"
[1] "edgeL"
[1] "edgeL"
[1] "subGraph"
[1] "subGraph"
[1] "intersection2"
[1] "intersection2"
[1] "intersection"
[1] "intersection"
[1] "join"
[1] "join"
[1] "union"
[1] "union"
[1] "complement"
[1] "complement"
[1] "connComp"
[1] "connComp"
[1] "isConnected"
[1] "isConnected"
[1] "numNodes"
[1] "numNodes"
[1] "numNodes"
[1] "addNode"
[1] "addNode"
[1] "addNode"
[1] "removeNode"
[1] "removeNode"
[1] "clearNode"
[1] "clearNode"
[1] "removeEdge"
[1] "removeEdge"
[1] "addEdge"
[1] "addEdge"
[1] "combineNodes"
[1] "combineNodes"
[1] "inEdges"
[1] "inEdges"
[1] "inEdges"
[1] "inEdges"
[1] "show"
[1] "edgeNames"
[1] "edgeNames"
[1] "clusteringCoefficient"
[1] "clusteringCoefficient"
Error in assign("nullgraphID", getuuid()) :
	couldn't find function "getuuid"
Execution halted
cat: ** Removing '/Users/mmccall/Library/R/library/graph'
** Restoring previous '/Users/mmccall/Library/R/library/graph'
stdout: Broken pipe
ERROR: execution of package source for 'graph' failed
[1] "Attempting to download hexbin from  
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing hexbin"
* Installing *source* package 'hexbin' ...
** libs
g77   -fno-common  -g -O2 -c hbin.f -o hbin.o
** Removing '/Users/mmccall/Library/R/library/hexbin'
make: g77: Command not found
make: *** [hbin.o] Error 127
ERROR: compilation failed for package 'hexbin'
** Restoring previous '/Users/mmccall/Library/R/library/hexbin'
[1] "Attempting to download Ruuid from  
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing Ruuid"
* Installing *source* package 'Ruuid' ...
creating cache ./config.cache
checking for glib-config... no
checking how to run the C preprocessor... cc -E
checking for /usr/include/unistd.h... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
-I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include    
-fno-common  -g -O2 -c Rinit.c -o Rinit.o
In file included from Ruuid.h:5,
                  from Rinit.c:1:
uuidP.h:24:18: glib.h: No such file or directory
In file included from Ruuid.h:5,
                  from Rinit.c:1:
uuidP.h:36: error: parse error before "guint32"
uuidP.h:36: warning: no semicolon at end of struct or union
uuidP.h:37: warning: data definition has no type or storage class
uuidP.h:38: error: parse error before "time_hi_and_version"
uuidP.h:38: warning: data definition has no type or storage class
uuidP.h:39: error: parse error before "clock_seq"
uuidP.h:39: warning: data definition has no type or storage class
uuidP.h:40: error: parse error before "node"
uuidP.h:40: warning: data definition has no type or storage class
uuidP.h:41: error: parse error before '}' token
** Removing '/Users/mmccall/Library/R/library/Ruuid'
** Restoring previous '/Users/mmccall/Library/R/library/Ruuid'
make: *** [Rinit.o] Error 1
ERROR: compilation failed for package 'Ruuid'
 From URL:  http://www.bioconductor.org/repository/devel/package/Source
	graph version 1.4.22
	hexbin version 1.1-2
	Ruuid version 1.4.5

Packages Rgraphviz and rhdf5 require special libraries to be installed.
Please see the URL http://www.bioconductor.org/faq.html#Other Notes for
more details on installing these packages if they fail
to install properly

Warning messages:
1: Installation of package graph had non-zero exit status in:  
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
2: Installation of package hexbin had non-zero exit status in:  
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
3: Installation of package Ruuid had non-zero exit status in:  
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
 >