[BioC] Problem installing graph package

Byron Ellis bellis at hsph.harvard.edu
Thu Oct 28 09:05:27 CEST 2004 

Subscribing to the Mac SIG mailing list might also be a good idea, it  
can be really useful when g77 goes weird on you.

Oh, and the repository version of Ruuid doesn't require glib on OS X  
(sort of a heavy requirement for something like 5 typedefs), you might  
try building that version instead.

On Oct 27, 2004, at 11:44 AM, Robert Gentleman wrote:

> Hi,
>  First your real problem is that you do not have Ruuid installed (and
>  that is what graph reports as the problem). So that would be your
>  first port of call. There are some details of how to do this, and
>  what libraries you need in the mailing list archives.
>
>  so do install.packages2("Ruuid")
>  and then see what libraries you do not have installed on your system,
>  then get them and install them.
>
>  Second, you do not have g77, so you won't be able to install any
>  fortran code (and that is what is in hexbin). Again, this is because
>  you lack the right tools in OS X, so you need to find them and
>  install them. Stefano Iacus keeps a nice web page that describes what
>  you need to have installed etc. for building R packages. The OS X
>  FAQ, is another place to look for details (and probably the first
>  place to look),
>
>  Best
>   Robert
>
> On Wed, Oct 27, 2004 at 02:28:50PM -0400, Matt McCall wrote:
>> 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)
>>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> --  
> +---------------------------------------------------------------------- 
> -----+
> | Robert Gentleman                 phone : (617) 632-5250               
>      |
> | Associate Professor              fax:   (617)  632-2444               
>      |
> | Department of Biostatistics      office: M1B20                        
>      |
> | Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu    
>      |
> +---------------------------------------------------------------------- 
> -----+
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
---
Byron Ellis (ellis at stat.harvard.edu)
"Oook" -- The Librarian

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