[BioC] Problem installing graph package
Robert Gentleman
rgentlem at jimmy.harvard.edu
Wed Oct 27 20:44:41 CEST 2004
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 |
+---------------------------------------------------------------------------+
More information about the Bioconductor
mailing list